Description

This custom track displays regions of interest for the " "%s track.

"); printf("" "Display regions of interest (%d)", MULTI_REGION_BED_WIN_FULL, tdb->track, cgiEncode(regionFile), tdb->track, hStringFromTv(vis), CT_CUSTOM_DOC_TEXT_VAR, cgiEncode(customHtml), CT_CUSTOM_TEXT_VAR, cgiEncode(dyStringCannibalize(&dsCustomText)), regionCount); printf(" in multi-region view (custom regions mode)"); printf(" "); printf("(Help)\n"); printf("

, print a nice download link */ { char *parts[2]; int partCount = chopByWhiteRespectDoubleQuotes(downloadUrl, parts, 2); if (partCount!=2) { puts("Internal Error: The downloadUrl trackDb statement needs exactly two arguments, the file type and the URL."); return; } char* fileType = parts[0]; stripString(fileType, "\""); // Remove double quotes, weird that chopByWhiteRespectDoubleQuotes doesn't do this char* url = parts[1]; char *newUrl = replaceInUrl(url, "", NULL, database, "", 0, 0, track, FALSE, NULL); printf("
Download: %s", newUrl, fileType); } static void makeFileDownloads(struct trackDb *tdb, char *db) /* given either downloadUrl or downloadUrl.1/.2/... in trackDb, print links to these files. * File can be anywhere on the internet, useful e.g. for GTF files for gene tracks */ { char *downloadUrl = trackDbSetting(tdb, "downloadUrl"); struct slName* tdbNames = trackDbSettingsWildMatch(tdb, "downloadUrl.*"); if (downloadUrl) printDownloadUrl(downloadUrl, db, tdb->track); while (tdbNames != NULL) { struct slName *tdbName = slPopHead(&tdbNames); printDownloadUrl(trackDbSetting(tdb, tdbName->name), db, tdb->track); slNameFree(&tdbName); } } void extraUiLinks(char *db, struct trackDb *tdb, struct cart *cart) // Show metadata, and downloads, schema links where appropriate { makeMultiRegionLink(db, tdb, cart); struct slPair *pairs = trackDbMetaPairs(tdb); if (pairs != NULL) printf("Metadata:
%s\n", pairsAsHtmlTable( pairs, tdb, FALSE, FALSE)); else if (!tdbIsComposite(tdb) && !trackHubDatabase(db) && (metadataForTable(db, tdb, NULL) != NULL)) printf("Metadata:
%s\n", metadataAsHtmlTable(db, tdb, FALSE, FALSE)); boolean schemaLink = trackDataAccessible(db, tdb); boolean downloadLink = (trackDbSetting(tdb, "wgEncode") != NULL && !tdbIsSuperTrack(tdb)); int links = 0; if (schemaLink) links++; if (downloadLink) links++; if (links > 0) cgiDown(0.7); if (links > 1) printf("

View table: "); if (schemaLink && differentString("longTabix", tdb->type) && !isCustomComposite(tdb) && !tdbIsSuper(tdb)) // FIXME: hgTables.showSchmaLongTabix is a currently a dummy routine, so let's not got here // until it's implemented { makeSchemaLink(db,tdb,(links > 1 ? "Data format":"Data schema/format description and download")); if (downloadLink) printf(", "); } makeFileDownloads(tdb, db); if (downloadLink) { // special case exception (hg18:NHGRI BiPs are in 7 different dbs but only hg18 has downloads): char *targetDb = trackDbSetting(tdb, "compareGenomeLinks"); if (targetDb != NULL) { targetDb = cloneFirstWordByDelimiter(targetDb,'='); if (!startsWith("hg",targetDb)) freez(&targetDb); } if (targetDb == NULL) targetDb = cloneString(db); makeNamedDownloadsLink(targetDb, tdb, (links > 1 ? "downloads":"Downloads")); freez(&targetDb); } if (links > 1) printf("

"); } char *hUserCookie() /* Return our cookie name. */ { return cfgOptionDefault("central.cookie", "hguid"); } char *hDownloadsServer() /* get the downloads server from hg.conf or the default */ { return cfgOptionDefault("downloads.server", "hgdownload.soe.ucsc.edu"); } void setUdcTimeout(struct cart *cart) /* set the udc cache timeout */ { int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); } void setUdcCacheDir() /* set the path to the udc cache dir */ { if (cfgOptionBooleanDefault("udc.useLocalDiskCache", TRUE)) { char *cacheDir = getenv("UDC_CACHEDIR"); if (isEmpty(cacheDir)) cacheDir = cfgOptionDefault("udc.cacheDir", udcDefaultDir()); udcSetDefaultDir(cacheDir); } else udcDisableCache(); } void setUdcOptions(struct cart *cart) /* do udc setup: set timeout and resolver and anything else that requires cart or hg.conf */ { setUdcTimeout(cart); char *prots = cfgOption("resolvProts"); char *prefix = cfgOption("resolvPrefix"); char *cmd = cfgOption("resolvCmd"); if ((prots && cmd) || (prefix && cmd)) udcSetResolver(prots, prefix, cmd); } char *wrapWhiteFont(char *s) /* Write white font around s */ { static char buf[256]; safef(buf, sizeof(buf), "%s", s); return buf; } char *hDocumentRoot() /* get the path to the DocumentRoot, or the default */ { return cfgOptionDefault("browser.documentRoot", DOCUMENT_ROOT); } char *hHelpFile(char *fileRoot) /* Given a help file root name (e.g. "hgPcrResult" or "cutters"), * prepend the complete help directory path and add .html suffix. * Do not free the statically allocated result. */ { static char helpName[PATH_LEN]; /* This cfgOption comes from Todd Lowe's hgTrackUi.c addition (r1.230): */ char *helpDir = cfgOption("help.html"); if (helpDir != NULL) safef(helpName, sizeof(helpName), "%s/%s.html", helpDir, fileRoot); else safef(helpName, sizeof(helpName), "%s%s/%s.html", hDocumentRoot(), HELP_DIR, fileRoot); return helpName; } char *hFileContentsOrWarning(char *file) /* Return the contents of the html file, or a warning message. * The file path may begin with hDocumentRoot(); if it doesn't, it is * assumed to be relative and hDocumentRoot() will be prepended. */ { if (isEmpty(file)) return cloneString("
Program Error: Empty file name for include file" "
\n"); char path[PATH_LEN]; char *docRoot = hDocumentRoot(); if (startsWith(docRoot, file)) safecpy(path, sizeof path, file); else safef(path, sizeof path, "%s/%s", docRoot, file); if (! fileExists(path)) { char message[1024]; safef(message, sizeof(message), "
Program Error: Missing file %s
", path); return cloneString(message); } /* If the file is there but not readable, readInGulp will errAbort, * but I think that is serious enough that errAbort is OK. */ char *result; readInGulp(path, &result, NULL); return result; } char *hCgiRoot() /* get the path to the CGI directory. * Returns NULL when not running as a CGI (unless specified by browser.cgiRoot) */ { static char defaultDir[PATH_LEN]; char *scriptFilename = getenv("SCRIPT_FILENAME"); if (scriptFilename) { char dir[PATH_LEN], name[FILENAME_LEN], extension[FILEEXT_LEN]; dir[0] = 0; splitPath(scriptFilename, dir, name, extension); safef(defaultDir, sizeof(defaultDir), "%s", dir); int len = strlen(defaultDir); // Get rid of trailing slash to be consistent with hDocumentRoot if (defaultDir[len-1] == '/') defaultDir[len-1] = 0; } else { defaultDir[0] = 0; } return cfgOptionDefault("browser.cgiRoot", defaultDir); } char *hTrackUiForTrack(char *trackName) /* Relative URL to extended track UI, delegated to a track-specific UI if available. */ { if (trackName == NULL) return hgTrackUiName(); if (gtexIsGeneTrack(trackName)) return gtexTrackUiName(); if (gtexIsEqtlTrack(trackName)) return gtexTrackUiName(); return hgTrackUiName(); } /****** Some stuff for tables of controls ******/ struct controlGrid *startControlGrid(int columns, char *align) /* Start up a control grid. */ { struct controlGrid *cg; AllocVar(cg); cg->columns = columns; cg->align = cloneString(align); cg->rowOpen = FALSE; return cg; } void controlGridEndRow(struct controlGrid *cg) /* Force end of row. */ { printf(""); cg->rowOpen = FALSE; cg->columnIx = 0; } void controlGridStartCell(struct controlGrid *cg) /* Start a new cell in control grid. */ { if (cg->columnIx == cg->columns) controlGridEndRow(cg); if (!cg->rowOpen) { printf(""); cg->rowOpen = TRUE; } if (cg->align) printf("", cg->align); else printf(""); } void controlGridEndCell(struct controlGrid *cg) /* End cell in control grid. */ { printf(""); ++cg->columnIx; } void endControlGrid(struct controlGrid **pCg) /* Finish up a control grid. */ { struct controlGrid *cg = *pCg; if (cg != NULL) { int i; if (cg->columnIx != 0 && cg->columnIx < cg->columns) for( i = cg->columnIx; i <= cg->columns; i++) printf(" \n"); if (cg->rowOpen) printf("\n"); printf("\n"); freeMem(cg->align); freez(pCg); } } /****** Some stuff for hide/dense/full controls ******/ static char *hTvStrings[] = /* User interface strings for track visibility controls. */ { "hide", "dense", "full", "pack", "squish", "show" }; enum trackVisibility hTvFromStringNoAbort(char *s) // Given a string representation of track visibility, return as equivalent enum. { int vis = stringArrayIx(s, hTvStrings, ArraySize(hTvStrings)); if (vis < 0) { vis = 0; // don't generate bogus value on invalid input } return vis; } enum trackVisibility hTvFromString(char *s) // Given a string representation of track visibility, return as equivalent enum. { enum trackVisibility vis = hTvFromStringNoAbort(s); if ((int)vis < 0) errAbort("Unknown visibility %s. Use one of: hide, dense, squish, pack, full.", s); return vis; } char *hStringFromTv(enum trackVisibility vis) // Given enum representation convert to string. { return hTvStrings[vis]; } void hTvDropDownClassWithJavascript(char *varName, char *id, enum trackVisibility vis, boolean canPack, char *class, struct slPair *events) // Make track visibility drop down for varName with style class { static char *noPack[] = { "hide", "dense", "full", }; static char *pack[] = { "hide", "dense", "squish", "pack", "full", }; static int packIx[] = {tvHide,tvDense,tvSquish,tvPack,tvFull}; if (canPack) cgiMakeDropListClassWithIdStyleAndJavascript(varName, id, pack, ArraySize(pack), pack[packIx[vis]], class, TV_DROPDOWN_STYLE, events); else cgiMakeDropListClassWithIdStyleAndJavascript(varName, id, noPack, ArraySize(noPack), noPack[vis], class, TV_DROPDOWN_STYLE, events); } static char *denseOnly[] = { "hide", "dense", NULL }; static char *squishOnly[] = { "hide", "squish", NULL }; static char *packOnly[] = { "hide", "pack", NULL }; static char *fullOnly[] = { "hide", "full", NULL }; static char *noPack[] = { "hide", "dense", "full", NULL }; static char *pack[] = { "hide", "dense", "squish", "pack", "full", NULL }; enum trackVisibility tvFromVisOnlySetting(char *visOnly) /* Parse an onlyVisibility value. Deliberately mirrors hTvGetVizArr() below: matching is * case-insensitive, and an unrecognized value falls back to dense. Do NOT use * hTvFromString[NoAbort]() here - it is case sensitive and quietly answers tvHide for * anything it doesn't know, which would make the track vanish while the vis dropdown * built from the same setting still looked correct. */ { if (sameWord(visOnly,"dense")) return tvDense; else if (sameWord(visOnly,"squish")) return tvSquish; else if (sameWord(visOnly,"pack")) return tvPack; else if (sameWord(visOnly,"full")) return tvFull; else return tvDense; } char ** hTvGetVizArr(enum trackVisibility vis, boolean canPack, char* visOnly) /* return a NULL-terminated array of char* with possible track visibilities */ { if (visOnly != NULL) { if (sameWord(visOnly,"dense")) return denseOnly; else if (sameWord(visOnly,"squish")) return squishOnly; else if (sameWord(visOnly,"pack")) return packOnly; else if (sameWord(visOnly,"full")) return fullOnly; else /* default when not recognized */ return denseOnly; } else { if (canPack) return pack; else return noPack; } } void hTvDropDownClassVisOnlyAndExtraWithLabel(char *varName, enum trackVisibility vis, boolean canPack, char *class, char *visOnly, struct slPair *events, char *label) // Make track visibility drop down for varName with style class, optional aria-label, // and potentially limited to visOnly { char** vizArr = hTvGetVizArr(vis, canPack, visOnly); int vizArrLen = arrNullLen(vizArr); char* checked; // Same as hTvDropDownClassWithJavascript(): // Normal track with no special limits needs mapping to get back checked value static int packIx[] = {tvHide,tvDense,tvSquish,tvPack,tvFull}; if (visOnly != NULL) // Just hide and the one allowed vis, so a tv enum would index off the end of the array checked = (vis == tvHide ? vizArr[0] : vizArr[1]); else if (canPack) checked = vizArr[packIx[vis]]; else checked = vizArr[vis]; cgiMakeDropListClassWithIdStyleJavascriptAndLabel(varName, NULL, vizArr, vizArrLen, checked, class, TV_DROPDOWN_STYLE, events, label); } void hTvDropDownClassVisOnlyAndExtra(char *varName, enum trackVisibility vis, boolean canPack, char *class, char *visOnly, struct slPair *events) // Make track visibility drop down for varName with style class, and potentially limited to visOnly { hTvDropDownClassVisOnlyAndExtraWithLabel(varName, vis, canPack, class, visOnly, events, NULL); } void hideShowDropDownWithClassExtraAndLabel(char *varName, char *id, boolean show, char *class, struct slPair *events, char *ariaLabel) // Make hide/show dropdown for varName with optional aria-label { static char *hideShow[] = { "hide", "show" }; cgiMakeDropListClassWithIdStyleJavascriptAndLabel(varName, id, hideShow, ArraySize(hideShow), hideShow[show], class, TV_DROPDOWN_STYLE, events, ariaLabel); } void hideShowDropDownWithClassAndExtra(char *varName, char *id, boolean show, char *class, struct slPair *events) // Make hide/show dropdown for varName { hideShowDropDownWithClassExtraAndLabel(varName, id, show, class, events, NULL); } /****** Some stuff for stsMap related controls *******/ static char *stsMapOptions[] = { "All Genetic", "Genethon", "Marshfield", "deCODE", "GeneMap 99", "Whitehead YAC", "Whitehead RH", "Stanford TNG", }; enum stsMapOptEnum smoeStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, stsMapOptions); if (x < 0) errAbort("Unknown option %s", string); return x; } char *smoeEnumToString(enum stsMapOptEnum x) /* Convert from enum to string representation. */ { return stsMapOptions[x]; } void smoeDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, stsMapOptions, ArraySize(stsMapOptions), curVal); } /****** Some stuff for stsMapMouseNew related controls *******/ static char *stsMapMouseOptions[] = { "All Genetic", "WICGR Genetic Map", "MGD Genetic Map", "RH", }; enum stsMapMouseOptEnum smmoeStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, stsMapMouseOptions); if (x < 0) errAbort("Unknown option %s", string); return x; } char *smmoeEnumToString(enum stsMapMouseOptEnum x) /* Convert from enum to string representation. */ { return stsMapMouseOptions[x]; } void smmoeDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, stsMapMouseOptions, ArraySize(stsMapMouseOptions), curVal); } /****** Some stuff for stsMapRat related controls *******/ static char *stsMapRatOptions[] = { "All Genetic", "FHHxACI", "SHRSPxBN", "RH", }; enum stsMapRatOptEnum smroeStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, stsMapRatOptions); if (x < 0) errAbort("Unknown option %s", string); return x; } char *smroeEnumToString(enum stsMapRatOptEnum x) /* Convert from enum to string representation. */ { return stsMapRatOptions[x]; } void smroeDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, stsMapRatOptions, ArraySize(stsMapRatOptions), curVal); } /****** Some stuff for fishClones related controls *******/ static char *fishClonesOptions[] = { "Fred Hutchinson CRC", "National Cancer Institute", "Sanger Centre", "Roswell Park Cancer Institute", "Cedars-Sinai Medical Center", "Los Alamos National Lab", "UC San Francisco", }; enum fishClonesOptEnum fcoeStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, fishClonesOptions); if (x < 0) errAbort("Unknown option %s", string); return x; } char *fcoeEnumToString(enum fishClonesOptEnum x) /* Convert from enum to string representation. */ { return fishClonesOptions[x]; } void fcoeDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, fishClonesOptions, ArraySize(fishClonesOptions), curVal); } /****** Some stuff for recombRate related controls *******/ static char *recombRateOptions[] = { "deCODE Sex Averaged Distances", "deCODE Female Distances", "deCODE Male Distances", "Marshfield Sex Averaged Distances", "Marshfield Female Distances", "Marshfield Male Distances", "Genethon Sex Averaged Distances", "Genethon Female Distances", "Genethon Male Distances", }; enum recombRateOptEnum rroeStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, recombRateOptions); if (x < 0) errAbort("Unknown option %s", string); return x; } char *rroeEnumToString(enum recombRateOptEnum x) /* Convert from enum to string representation. */ { return recombRateOptions[x]; } void rroeDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, recombRateOptions, ArraySize(recombRateOptions), curVal); } /****** Some stuff for recombRateRat related controls *******/ static char *recombRateRatOptions[] = { "SHRSPxBN Sex Averaged Distances", "FHHxACI Sex Averaged Distances", }; enum recombRateRatOptEnum rrroeStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, recombRateRatOptions); if (x < 0) errAbort("Unknown option %s", string); return x; } char *rrroeEnumToString(enum recombRateRatOptEnum x) /* Convert from enum to string representation. */ { return recombRateRatOptions[x]; } void rrroeDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, recombRateRatOptions, ArraySize(recombRateRatOptions), curVal); } /****** Some stuff for recombRateMouse related controls *******/ static char *recombRateMouseOptions[] = { "WI Genetic Map Sex Averaged Distances", "MGD Genetic Map Sex Averaged Distances", }; enum recombRateMouseOptEnum rrmoeStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, recombRateMouseOptions); if (x < 0) errAbort("Unknown option %s", string); return x; } char *rrmoeEnumToString(enum recombRateMouseOptEnum x) /* Convert from enum to string representation. */ { return recombRateMouseOptions[x]; } void rrmoeDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, recombRateMouseOptions, ArraySize(recombRateMouseOptions), curVal); } /****** Some stuff for CGH NCI60 related controls *******/ static char *cghNci60Options[] = { "Tissue Averages", "BREAST", "CNS", "COLON", "LEUKEMIA", "LUNG", "MELANOMA", "OVARY", "PROSTATE", "RENAL", "All Cell Lines", }; enum cghNci60OptEnum cghoeStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, cghNci60Options); if (x < 0) errAbort("Unknown option %s", string); return x; } char *cghoeEnumToString(enum cghNci60OptEnum x) /* Convert from enum to string representation. */ { return cghNci60Options[x]; } void cghoeDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, cghNci60Options, ArraySize(cghNci60Options), curVal); } /****** Some stuff for nci60 related controls *******/ static char *nci60Options[] = { "Tissue Averages", "All Cell Lines", "BREAST", "CNS", "COLON", "LEUKEMIA", "MELANOMA", "OVARIAN", "PROSTATE", "RENAL", "NSCLC", "DUPLICATE", "UNKNOWN" }; enum nci60OptEnum nci60StringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, nci60Options); if (x < 0) errAbort("hui::nci60StringToEnum() - Unknown option %s", string); return x; } char *nci60EnumToString(enum nci60OptEnum x) /* Convert from enum to string representation. */ { return nci60Options[x]; } void nci60DropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, nci60Options, ArraySize(nci60Options), curVal); } /*** Control of base/codon coloring code: ***/ /* All options (parallel to enum baseColorDrawOpt): */ static char *baseColorDrawAllOptionLabels[] = { BASE_COLOR_DRAW_OFF_LABEL, BASE_COLOR_DRAW_GENOMIC_CODONS_LABEL, BASE_COLOR_DRAW_ITEM_CODONS_LABEL, BASE_COLOR_DRAW_DIFF_CODONS_LABEL, BASE_COLOR_DRAW_ITEM_BASES_CDS_LABEL, BASE_COLOR_DRAW_DIFF_BASES_CDS_LABEL, }; static char *baseColorDrawAllOptionValues[] = { BASE_COLOR_DRAW_OFF, BASE_COLOR_DRAW_GENOMIC_CODONS, BASE_COLOR_DRAW_ITEM_CODONS, BASE_COLOR_DRAW_DIFF_CODONS, BASE_COLOR_DRAW_ITEM_BASES, BASE_COLOR_DRAW_DIFF_BASES, }; /* Subset of options for tracks with CDS info but not item sequence: */ static char *baseColorDrawGenomicOptionLabels[] = { BASE_COLOR_DRAW_OFF_LABEL, BASE_COLOR_DRAW_GENOMIC_CODONS_LABEL, }; static char *baseColorDrawGenomicOptionValues[] = { BASE_COLOR_DRAW_OFF, BASE_COLOR_DRAW_GENOMIC_CODONS, }; /* Subset of options for tracks with aligned item sequence but not CDS: */ static char *baseColorDrawItemOptionLabels[] = { BASE_COLOR_DRAW_OFF_LABEL, BASE_COLOR_DRAW_ITEM_BASES_NC_LABEL, BASE_COLOR_DRAW_DIFF_BASES_NC_LABEL, }; static char *baseColorDrawItemOptionValues[] = { BASE_COLOR_DRAW_OFF, BASE_COLOR_DRAW_ITEM_BASES, BASE_COLOR_DRAW_DIFF_BASES, }; enum baseColorDrawOpt baseColorDrawOptStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, baseColorDrawAllOptionValues); if (x < 0) errAbort("hui::baseColorDrawOptStringToEnum() - Unknown option %s", string); return x; } static boolean baseColorGotCds(struct trackDb *tdb) /* Return true if this track has CDS info according to tdb (or is genePred). */ { boolean gotIt = FALSE; char *setting = trackDbSetting(tdb, BASE_COLOR_USE_CDS); if (isNotEmpty(setting)) { if (sameString(setting, "all") || sameString(setting, "given") || sameString(setting, "genbank") || startsWith("table", setting)) gotIt = TRUE; else if (! sameString(setting, "none")) errAbort("trackDb for %s, setting %s: unrecognized value \"%s\". " "must be one of {none, all, given, genbank, table}.", tdb->track, BASE_COLOR_USE_CDS, setting); } else if (startsWith("genePred", tdb->type) || startsWith("bigGenePred", tdb->type)) gotIt = TRUE; return gotIt; } static boolean baseColorGotSequence(struct trackDb *tdb) /* Return true if this track has aligned sequence according to tdb. */ { boolean gotIt = FALSE; char *setting = trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE); if (isNotEmpty(setting)) { if (sameString(setting, "genbank") || sameString(setting, "seq") || sameString(setting, "ss") || startsWith("extFile", setting) || sameString(setting, "hgPcrResult") || sameString(setting, "nameIsSequence") || sameString(setting, "seq1Seq2") || sameString(setting, "lfExtra") || sameString(setting, "lrg") || sameString(setting, "2bit") || startsWith("table ", setting) || startsWithWord("db", setting)) gotIt = TRUE; else if (differentString(setting, "none")) errAbort("trackDb for %s, setting %s: unrecognized value \"%s\". " "must be one of {none, genbank, seq, ss, extFile, nameIsSequence, seq1Seq2," "hgPcrResult, lfExtra, lrg, 2bit, table table}.", tdb->track, BASE_COLOR_USE_SEQUENCE, setting); } return gotIt; } static void baseColorDropLists(struct cart *cart, struct trackDb *tdb, char *name) /* draw the baseColor drop list options */ { enum baseColorDrawOpt curOpt = baseColorDrawOptEnabled(cart, tdb); char *curValue = baseColorDrawAllOptionValues[curOpt]; char var[512]; safef(var, sizeof(var), "%s." BASE_COLOR_VAR_SUFFIX, name); boolean gotCds = baseColorGotCds(tdb); boolean gotSeq = baseColorGotSequence(tdb); if (gotCds && gotSeq) { puts("

Color track by codons or bases:"); cgiMakeDropListFull(var, baseColorDrawAllOptionLabels, baseColorDrawAllOptionValues, ArraySize(baseColorDrawAllOptionLabels), curValue, NULL, NULL); printf("Help on mRNA coloring
", CDS_MRNA_HELP_PAGE); } else if (gotCds) { char buf[256]; char *disabled = NULL; safef(buf, sizeof(buf), "codonColoringChanged('%s');", name); puts("

Color track by codons:"); cgiMakeDropListFull(var, baseColorDrawGenomicOptionLabels, baseColorDrawGenomicOptionValues, ArraySize(baseColorDrawGenomicOptionLabels), curValue, "change", buf); printf("Help on codon coloring
", CDS_HELP_PAGE); safef(buf, sizeof(buf), "%s.%s", name, CODON_NUMBERING_SUFFIX); if (curOpt == baseColorDrawOff) disabled = "disabled"; printf("
Show codon numbering:\n", name, curOpt == baseColorDrawOff ? "class='disabled'" : ""); cgiMakeCheckBoxMore(buf, cartUsualBooleanClosestToHome(cart, tdb, FALSE, CODON_NUMBERING_SUFFIX, TRUE), disabled); } else if (gotSeq) { puts("

Color track by bases:"); cgiMakeDropListFull(var, baseColorDrawItemOptionLabels, baseColorDrawItemOptionValues, ArraySize(baseColorDrawItemOptionLabels), curValue, NULL, NULL); printf("Help on base coloring
", CDS_BASE_HELP_PAGE); } } void baseColorDrawOptDropDown(struct cart *cart, struct trackDb *tdb) /* Make appropriately labeled drop down of options if any are applicable.*/ { baseColorDropLists(cart, tdb, tdb->track); } static enum baseColorDrawOpt limitDrawOptForType(struct trackDb *tdb, enum baseColorDrawOpt drawOpt) /* If tdb->type is genePred, but something fancier like mRNA codons is enabled because the setting * is coming from a view that also includes a PSL track, downgrade it to genomic codons to avoid * drawing problems caused by the inappropriate setting. #21194 */ { if (startsWith("genePred", tdb->type) && drawOpt > baseColorDrawGenomicCodons) drawOpt = baseColorDrawGenomicCodons; return drawOpt; } enum baseColorDrawOpt baseColorDrawOptEnabled(struct cart *cart, struct trackDb *tdb) /* Query cart & trackDb to determine what drawing mode (if any) is enabled. */ { char *stringVal = NULL; assert(cart); assert(tdb); /* trackDb can override default of OFF; cart can override trackDb. */ stringVal = trackDbSettingClosestToHomeOrDefault(tdb, BASE_COLOR_DEFAULT, BASE_COLOR_DRAW_OFF); stringVal = cartUsualStringClosestToHome(cart, tdb, FALSE, BASE_COLOR_VAR_SUFFIX,stringVal); return limitDrawOptForType(tdb, baseColorDrawOptStringToEnum(stringVal)); } /*** Control of fancy indel display code: ***/ static boolean tdbOrCartBoolean(struct cart *cart, struct trackDb *tdb, char *settingName, char *defaultOnOff) /* Query cart & trackDb to determine if a boolean variable is set. */ { boolean alreadySet; alreadySet = !sameString("off",trackDbSettingOrDefault(tdb, settingName, defaultOnOff)); alreadySet = cartUsualBooleanClosestToHome(cart, tdb, FALSE, settingName, alreadySet); // NOTE: parentLevel=FALSE because tdb param already is at appropriate level return alreadySet; } static boolean indelAppropriate(struct trackDb *tdb) /* Return true if it makes sense to offer indel display options for tdb. */ { return (tdb && (startsWith("psl", tdb->type) || startsWith("bigPsl", tdb->type) || startsWithWord("chain", tdb->type) || startsWithWord("bigChain", tdb->type) || sameString("bam", tdb->type) || sameString("lrg", tdb->track))); } static void indelEnabledByName(struct cart *cart, struct trackDb *tdb, char *name, float basesPerPixel, boolean *retDoubleInsert, boolean *retQueryInsert, boolean *retPolyA) /* Query cart & trackDb to determine what indel display (if any) is enabled. Set * basesPerPixel to 0.0 to disable check for zoom level. */ { struct trackDb *tdbLevel = tdb; if (differentString(tdb->track, name) && tdb->parent != NULL) tdbLevel = tdb->parent; boolean apropos = indelAppropriate(tdb); if (apropos && (basesPerPixel > 0.0)) { // check indel max zoom float showIndelMaxZoom = trackDbFloatSettingOrDefault(tdbLevel, "showIndelMaxZoom", -1.0); if ((showIndelMaxZoom >= 0) && ((basesPerPixel > showIndelMaxZoom) || (showIndelMaxZoom == 0.0))) apropos = FALSE; } if (retDoubleInsert) *retDoubleInsert = apropos && tdbOrCartBoolean(cart, tdbLevel, INDEL_DOUBLE_INSERT, "off"); if (retQueryInsert) *retQueryInsert = apropos && tdbOrCartBoolean(cart, tdbLevel, INDEL_QUERY_INSERT, "off"); if (retPolyA) *retPolyA = apropos && tdbOrCartBoolean(cart, tdbLevel, INDEL_POLY_A, "off"); } void indelEnabled(struct cart *cart, struct trackDb *tdb, float basesPerPixel, boolean *retDoubleInsert, boolean *retQueryInsert, boolean *retPolyA) /* Query cart & trackDb to determine what indel display (if any) is enabled. Set * basesPerPixel to 0.0 to disable check for zoom level. */ { indelEnabledByName(cart,tdb,tdb->track,basesPerPixel,retDoubleInsert,retQueryInsert,retPolyA); } static void indelShowOptionsWithNameExt(struct cart *cart, struct trackDb *tdb, char *name, char *queryTerm, boolean includeDoubleInsert, boolean includePolyA) /* Make HTML inputs for indel display options if any are applicable. */ { if (indelAppropriate(tdb)) { boolean showDoubleInsert, showQueryInsert, showPolyA; char var[512]; indelEnabledByName(cart, tdb, name, 0.0, &showDoubleInsert, &showQueryInsert, &showPolyA); printf("\n\n\n" "\n", queryTerm); } } printf("
Alignment Gap/Insertion Display Options"); printf(" Help on display options
", INDEL_HELP_PAGE); if (includeDoubleInsert) { safef(var, sizeof(var), "%s.%s", name, INDEL_DOUBLE_INSERT); cgiMakeCheckBox(var, showDoubleInsert); printf(" Draw double horizontal lines when both genome and %s have " "an insertion
", queryTerm); } safef(var, sizeof(var), "%s.%s", name, INDEL_QUERY_INSERT); cgiMakeCheckBox(var, showQueryInsert); printf(" Draw a vertical purple line for an insertion at the beginning or " "end of the
%s, orange for insertion in the middle of the %s
", queryTerm, queryTerm); if (includePolyA) { safef(var, sizeof(var), "%s.%s", name, INDEL_POLY_A); /* We can highlight valid polyA's only if we have query sequence -- * so indelPolyA code piggiebacks on baseColor code: */ if (baseColorGotSequence(tdb)) { cgiMakeCheckBox(var, showPolyA); printf(" Draw a vertical green line where %s has a polyA tail " "insertion
\n"); } } static void indelShowOptionsWithName(struct cart *cart, struct trackDb *tdb, char *name) /* Make HTML inputs for indel display options if any are applicable. */ { indelShowOptionsWithNameExt(cart, tdb, name, "query", TRUE, TRUE); } void indelShowOptions(struct cart *cart, struct trackDb *tdb) /* Make HTML inputs for indel display options if any are applicable. */ { indelShowOptionsWithName(cart, tdb, tdb->track); } #define BAM_DEFAULT_SHOW_DIFF_BASES_MAX_ZOOM "100" void bamAddBaseAndIndelSettings(struct trackDb *tdb) /* Unless already set in tdb, add settings to enable base-level differences and indel display. */ { struct hash *settings = tdb->settingsHash; if (!hashLookup(settings, BASE_COLOR_USE_SEQUENCE)) hashAdd(settings, BASE_COLOR_USE_SEQUENCE, cloneString("lfExtra")); if (!hashLookup(settings, BASE_COLOR_DEFAULT)) hashAdd(settings, BASE_COLOR_DEFAULT, cloneString(BASE_COLOR_DRAW_DIFF_BASES)); if (!hashLookup(settings, SHOW_DIFF_BASES_ALL_SCALES)) hashAdd(settings, SHOW_DIFF_BASES_ALL_SCALES, cloneString(".")); if (!hashLookup(settings, INDEL_DOUBLE_INSERT)) hashAdd(settings, INDEL_DOUBLE_INSERT, cloneString("on")); if (!hashLookup(settings, INDEL_QUERY_INSERT)) hashAdd(settings, INDEL_QUERY_INSERT, cloneString("on")); if (!hashLookup(settings, INDEL_POLY_A)) hashAdd(settings, INDEL_POLY_A, cloneString("off")); if (!hashLookup(settings, "showDiffBasesMaxZoom")) hashAdd(settings, "showDiffBasesMaxZoom", cloneString(BAM_DEFAULT_SHOW_DIFF_BASES_MAX_ZOOM)); } /****** base position (ruler) controls *******/ static char *zoomOptions[] = { ZOOM_1PT5X, ZOOM_3X, ZOOM_10X, ZOOM_100X, ZOOM_BASE }; void zoomRadioButtons(char *var, char *curVal) /* Make a list of radio buttons for all zoom options */ { int i; int size = ArraySize(zoomOptions); for (i = 0; i < size; i++) { char *s = zoomOptions[i]; cgiMakeRadioButton(var, s, sameString(s, curVal)); printf(" %s ", s); } } /****** Some stuff for affy related controls *******/ static char *affyOptions[] = { "Chip Type", "Chip ID", "Tissue Averages" }; enum affyOptEnum affyStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, affyOptions); if (x < 0) errAbort("hui::affyStringToEnum() - Unknown option %s", string); return x; } char *affyEnumToString(enum affyOptEnum x) /* Convert from enum to string representation. */ { return affyOptions[x]; } void affyDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, affyOptions, ArraySize(affyOptions), curVal); } /****** Some stuff for affy all exon related controls *******/ static char *affyAllExonOptions[] = { "Chip", "Tissue Averages" }; enum affyAllExonOptEnum affyAllExonStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, affyAllExonOptions); if (x < 0) errAbort("hui::affyAllExonStringToEnum() - Unknown option %s", string); return x; } char *affyAllExonEnumToString(enum affyAllExonOptEnum x) /* Convert from enum to string representation. */ { return affyAllExonOptions[x]; } void affyAllExonDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, affyAllExonOptions, ArraySize(affyAllExonOptions), curVal); } /****** Some stuff for Rosetta related controls *******/ static char *rosettaOptions[] = { "All Experiments", "Common Reference and Other", "Common Reference", "Other Exps" }; static char *rosettaExonOptions[] = { "Confirmed Only", "Predicted Only", "All", }; enum rosettaOptEnum rosettaStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, rosettaOptions); if (x < 0) errAbort("hui::rosettaStringToEnum() - Unknown option %s", string); return x; } char *rosettaEnumToString(enum rosettaOptEnum x) /* Convert from enum to string representation. */ { return rosettaOptions[x]; } void rosettaDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, rosettaOptions, ArraySize(rosettaOptions), curVal); } enum rosettaExonOptEnum rosettaStringToExonEnum(char *string) /* Convert from string to enum representation of exon types. */ { int x = stringIx(string, rosettaExonOptions); if (x < 0) errAbort("hui::rosettaStringToExonEnum() - Unknown option %s", string); return x; } char *rosettaExonEnumToString(enum rosettaExonOptEnum x) /* Convert from enum to string representation of exon types. */ { return rosettaExonOptions[x]; } void rosettaExonDropDown(char *var, char *curVal) /* Make drop down of exon type options. */ { cgiMakeDropList(var, rosettaExonOptions, ArraySize(rosettaExonOptions), curVal); } /****** Options for the net track level display options *******/ static char *netLevelOptions[] = { NET_LEVEL_0, NET_LEVEL_1, NET_LEVEL_2, NET_LEVEL_3, NET_LEVEL_4, NET_LEVEL_5, NET_LEVEL_6 }; enum netLevelEnum netLevelStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, netLevelOptions); if (x < 0) errAbort("hui::netLevelStringToEnum() - Unknown option %s", string); return x; } char *netLevelEnumToString(enum netLevelEnum x) /* Convert from enum to string representation. */ { return netLevelOptions[x]; } void netLevelDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, netLevelOptions, ArraySize(netLevelOptions), curVal); } /****** Options for the net track color options *******/ static char *netColorOptions[] = { CHROM_COLORS, GRAY_SCALE }; enum netColorEnum netColorStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, netColorOptions); if (x < 0) errAbort("hui::netColorStringToEnum() - Unknown option %s", string); return x; } char *netColorEnumToString(enum netColorEnum x) /* Convert from enum to string representation. */ { return netColorOptions[x]; } void netColorDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, netColorOptions, ArraySize(netColorOptions), curVal); } /****** Options for the chain track color options *******/ static char *chainColorOptions[] = { CHROM_COLORS, SCORE_COLORS, NO_COLORS }; enum chainColorEnum chainColorStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, chainColorOptions); if (x < 0) errAbort("hui::chainColorStringToEnum() - Unknown option %s", string); return x; } char *chainColorEnumToString(enum chainColorEnum x) /* Convert from enum to string representation. */ { return chainColorOptions[x]; } void chainColorDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, chainColorOptions, ArraySize(chainColorOptions), curVal); } /****** Options for the wiggle track Windowing *******/ static char *wiggleWindowingOptions[] = { "mean+whiskers", "maximum", "mean", "minimum", "sum", }; enum wiggleWindowingEnum wiggleWindowingStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, wiggleWindowingOptions); if (x < 0) errAbort("hui::wiggleWindowingStringToEnum() - Unknown option %s", string); return x; } char *wiggleWindowingEnumToString(enum wiggleWindowingEnum x) /* Convert from enum to string representation. */ { return wiggleWindowingOptions[x]; } void wiggleWindowingDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, wiggleWindowingOptions, ArraySize(wiggleWindowingOptions), curVal); } /****** Options for the wiggle track Smoothing *******/ static char *wiggleSmoothingOptions[] = { "OFF", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16" }; enum wiggleSmoothingEnum wiggleSmoothingStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, wiggleSmoothingOptions); if (x < 0) errAbort("hui::wiggleSmoothingStringToEnum() - Unknown option %s", string); return x; } char *wiggleSmoothingEnumToString(enum wiggleSmoothingEnum x) /* Convert from enum to string representation. */ { return wiggleSmoothingOptions[x]; } void wiggleSmoothingDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, wiggleSmoothingOptions, ArraySize(wiggleSmoothingOptions), curVal); } /****** Options for the wiggle track y Line Mark On/Off *******/ static char *wiggleYLineMarkOptions[] = { "OFF", "ON" }; enum wiggleYLineMarkEnum wiggleYLineMarkStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, wiggleYLineMarkOptions); if (x < 0) errAbort("hui::wiggleYLineMarkStringToEnum() - Unknown option %s", string); return x; } char *wiggleYLineMarkEnumToString(enum wiggleYLineMarkEnum x) /* Convert from enum to string representation. */ { return wiggleYLineMarkOptions[x]; } void wiggleYLineMarkDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, wiggleYLineMarkOptions, ArraySize(wiggleYLineMarkOptions), curVal); } /****** Options for the wiggle track AutoScale *******/ static char *wiggleScaleOptionsParent[] = { "use vertical viewing range setting", "auto-scale to data view", "group auto-scale" }; static char *wiggleScaleOptions[] = { "use vertical viewing range setting", "auto-scale to data view" }; enum wiggleScaleOptEnum wiggleScaleStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, wiggleScaleOptionsParent); if (x < 0) errAbort("hui::wiggleScaleStringToEnum() - Unknown option %s", string); return x; } char *wiggleScaleEnumToString(enum wiggleScaleOptEnum x) /* Convert from enum to string representation. */ { return wiggleScaleOptionsParent[x]; } void wiggleScaleDropDownParent(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, wiggleScaleOptionsParent, ArraySize(wiggleScaleOptionsParent), curVal); } void wiggleScaleDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, wiggleScaleOptions, ArraySize(wiggleScaleOptions), curVal); } /****** Options for the wiggle track type of graph *******/ static char *wiggleGraphOptions[] = { "points", "bar", }; enum wiggleGraphOptEnum wiggleGraphStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, wiggleGraphOptions); if (x < 0) errAbort("hui::wiggleGraphStringToEnum() - Unknown option %s", string); return x; } char *wiggleGraphEnumToString(enum wiggleGraphOptEnum x) /* Convert from enum to string representation. */ { return wiggleGraphOptions[x]; } void wiggleGraphDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, wiggleGraphOptions, ArraySize(wiggleGraphOptions), curVal); } static char *aggregateExtraLabels[] = { "none", "transparent", "solid", "stacked", "add", "subtract", }; static char *aggregateExtraValues[] = { WIG_AGGREGATE_NONE, WIG_AGGREGATE_TRANSPARENT, WIG_AGGREGATE_SOLID, WIG_AGGREGATE_STACKED, WIG_AGGREGATE_ADD, WIG_AGGREGATE_SUBTRACT, }; static char *aggregateLabels[] = { "none", "transparent", "solid", "stacked", }; static char *aggregateValues[] = { WIG_AGGREGATE_NONE, WIG_AGGREGATE_TRANSPARENT, WIG_AGGREGATE_SOLID, WIG_AGGREGATE_STACKED, }; char *wiggleAggregateFunctionEnumToString(enum wiggleAggregateFunctionEnum x) /* Convert from enum to string representation. */ { return aggregateValues[x]; } enum wiggleAggregateFunctionEnum wiggleAggregateFunctionStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, aggregateExtraValues); if (x < 0) errAbort("hui::wiggleAggregateFunctionStringToEnum() - Unknown option %s", string); return x; } void aggregateExtraDropDown(char *var, char *curVal) /* Make drop down menu for aggregate plus strategy */ { cgiMakeDropListFull(var, aggregateExtraLabels, aggregateExtraValues, ArraySize(aggregateExtraValues), curVal, NULL, NULL); } void aggregateDropDown(char *var, char *curVal) /* Make drop down menu for aggregate strategy */ { cgiMakeDropListFull(var, aggregateLabels, aggregateValues, ArraySize(aggregateValues), curVal, NULL, NULL); } static char *viewFuncLabels[] = { "show all", "add all", "subtract from the first", }; static char *viewFuncValues[] = { WIG_VIEWFUNC_SHOW_ALL, WIG_VIEWFUNC_ADD_ALL, WIG_VIEWFUNC_SUBTRACT_ALL, }; char *wiggleViewFuncEnumToString(enum wiggleViewFuncEnum x) /* Convert from enum to string representation. */ { return viewFuncLabels[x]; } enum wiggleViewFuncEnum wiggleViewFuncStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, viewFuncValues); if (x < 0) errAbort("hui::wiggleViewFuncStringToEnum() - Unknown option %s", string); return x; } void viewFuncDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropListFull(var, viewFuncLabels, viewFuncValues, ArraySize(viewFuncValues), curVal, NULL, NULL); } static char *wiggleTransformFuncOptions[] = { "NONE", "LOG" }; static char *wiggleTransformFuncLabels[] = { "NONE", "LOG (ln(1+x))" }; enum wiggleTransformFuncEnum wiggleTransformFuncToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, wiggleTransformFuncOptions); if (x < 0) errAbort("hui::wiggleTransformFuncToEnum() - Unknown option %s", string); return x; } void wiggleTransformFuncDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropListFull(var, wiggleTransformFuncLabels, wiggleTransformFuncOptions, ArraySize(wiggleTransformFuncOptions), curVal, NULL, NULL); } static char *wiggleAlwaysZeroOptions[] = { "OFF", "ON" }; enum wiggleAlwaysZeroEnum wiggleAlwaysZeroToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, wiggleAlwaysZeroOptions); if (x < 0) errAbort("hui::wiggleAlwaysZeroToEnum() - Unknown option %s", string); return x; } void wiggleAlwaysZeroDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, wiggleAlwaysZeroOptions, ArraySize(wiggleAlwaysZeroOptions), curVal); } /****** Options for the wiggle track horizontal grid lines *******/ static char *wiggleGridOptions[] = { "ON", "OFF" }; enum wiggleGridOptEnum wiggleGridStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, wiggleGridOptions); if (x < 0) errAbort("hui::wiggleGridStringToEnum() - Unknown option %s", string); return x; } char *wiggleGridEnumToString(enum wiggleGridOptEnum x) /* Convert from enum to string representation. */ { return wiggleGridOptions[x]; } void wiggleGridDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, wiggleGridOptions, ArraySize(wiggleGridOptions), curVal); } /****** Some stuff for wiggle track related controls *******/ static char *wiggleOptions[] = { "samples only", "linear interpolation" }; enum wiggleOptEnum wiggleStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, wiggleOptions); if (x < 0) errAbort("hui::wiggleStringToEnum() - Unknown option %s", string); return x; } char *wiggleEnumToString(enum wiggleOptEnum x) /* Convert from enum to string representation. */ { return wiggleOptions[x]; } void wiggleDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, wiggleOptions, ArraySize(wiggleOptions), curVal); } /****** Some stuff for GCwiggle track related controls *******/ static char *GCwiggleOptions[] = { "samples only", "linear interpolation" }; enum GCwiggleOptEnum GCwiggleStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, GCwiggleOptions); if (x < 0) errAbort("hui::GCwiggleStringToEnum() - Unknown option %s", string); return x; } char *GCwiggleEnumToString(enum GCwiggleOptEnum x) /* Convert from enum to string representation. */ { return GCwiggleOptions[x]; } void GCwiggleDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, GCwiggleOptions, ArraySize(GCwiggleOptions), curVal); } /****** Some stuff for chimp track related controls *******/ static char *chimpOptions[] = { "samples only", "linear interpolation" }; enum chimpOptEnum chimpStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, chimpOptions); if (x < 0) errAbort("hui::chimpStringToEnum() - Unknown option %s", string); return x; } char *chimpEnumToString(enum chimpOptEnum x) /* Convert from enum to string representation. */ { return chimpOptions[x]; } void chimpDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, chimpOptions, ArraySize(chimpOptions), curVal); } /* #define POP_METHOD_AUTO "auto" #define POP_METHOD_MANUAL "manual" static char *popMethodLabels[] = { "auto", "manual", }; static char *popMethodValues[] = { POP_METHOD_AUTO, POP_METHOD_MANUAL, }; */ /****** Some stuff for mRNA and EST related controls *******/ static void addMrnaFilter(struct mrnaUiData *mud, char *track, char *label, char *key, char *table) /* Add an mrna filter */ { struct mrnaFilter *fil; AllocVar(fil); fil->label = label; fil->suffix = cloneString(key); fil->table = table; slAddTail(&mud->filterList, fil); } static struct mrnaUiData *newEmptyMrnaUiData(char *track) /* Make a new in extra-ui data structure for a bed. */ { struct mrnaUiData *mud; AllocVar(mud); mud->filterTypeSuffix = cloneString("Ft"); mud->logicTypeSuffix = cloneString("Lt"); return mud; } struct mrnaUiData *newBedUiData(char *track) /* Make a new in extra-ui data structure for a bed. */ { struct mrnaUiData *mud = newEmptyMrnaUiData(track); addMrnaFilter(mud, track, "name", "name",track); return mud; } struct mrnaUiData *newMrnaUiData(char *track, boolean isXeno) /* Make a new in extra-ui data structure for mRNA. */ { struct mrnaUiData *mud = newEmptyMrnaUiData(track); if (isXeno) addMrnaFilter(mud, track, "organism", "org", organismTable); addMrnaFilter(mud, track, "accession", "acc", "acc"); addMrnaFilter(mud, track, "author", "aut", authorTable); addMrnaFilter(mud, track, "library", "lib", libraryTable); addMrnaFilter(mud, track, "tissue", "tis", tissueTable); addMrnaFilter(mud, track, "cell", "cel", cellTable); addMrnaFilter(mud, track, "keyword", "key", keywordTable); addMrnaFilter(mud, track, "gene", "gen", geneNameTable); addMrnaFilter(mud, track, "product", "pro", productNameTable); addMrnaFilter(mud, track, "description", "des", descriptionTable); return mud; } int trackNameAndLabelCmp(const void *va, const void *vb) // Compare to sort on label. { const struct trackNameAndLabel *a = *((struct trackNameAndLabel **)va); const struct trackNameAndLabel *b = *((struct trackNameAndLabel **)vb); return strcmp(a->label, b->label); } char *trackFindLabel(struct trackNameAndLabel *list, char *label) // Try to find label in list. Return NULL if it's not there. { struct trackNameAndLabel *el; for (el = list; el != NULL; el = el->next) { if (sameString(el->label, label)) return label; } return NULL; } char *genePredDropDown(struct cart *cart, struct hash *trackHash, char *formName, char *varName) /* Make gene-prediction drop-down(). Return track name of * currently selected one. Return NULL if no gene tracks. * If formName isn't NULL, it's the form for auto submit (onchange attr). * If formName is NULL, no submit occurs when menu is changed */ { char *cartTrack = cartOptionalString(cart, varName); struct hashEl *trackList, *trackEl; char *selectedName = NULL; struct trackNameAndLabel *nameList = NULL, *name; char *trackName = NULL; /* Make alphabetized list of all genePred track names. */ trackList = hashElListHash(trackHash); for (trackEl = trackList; trackEl != NULL; trackEl = trackEl->next) { struct trackDb *tdb = trackEl->val; char *dupe = cloneString(tdb->type); char *type = firstWordInLine(dupe); if ((sameString(type, "genePred")) && (!sameString(tdb->table, "tigrGeneIndex") && !tdbIsComposite(tdb) && !tdbIsCompositeView(tdb))) { AllocVar(name); name->name = tdb->track; name->label = tdb->longLabel; slAddHead(&nameList, name); } freez(&dupe); } slSort(&nameList, trackNameAndLabelCmp); /* No gene tracks - not much we can do. */ if (nameList == NULL) { slFreeList(&trackList); return NULL; } /* Try to find current track - from cart first, then * knownGenes, then refGenes. */ if (cartTrack != NULL) selectedName = trackFindLabel(nameList, cartTrack); if (selectedName == NULL) selectedName = trackFindLabel(nameList, "Known Genes"); if (selectedName == NULL) selectedName = trackFindLabel(nameList, "SGD Genes"); if (selectedName == NULL) selectedName = trackFindLabel(nameList, "BDGP Genes"); if (selectedName == NULL) selectedName = trackFindLabel(nameList, "WormBase Genes"); if (selectedName == NULL) selectedName = trackFindLabel(nameList, "RefSeq Genes"); if (selectedName == NULL) selectedName = nameList->name; /* Make drop-down list. */ { char javascript[SMALLBUF], *autoSubmit, *event; int nameCount = slCount(nameList); char **menu; int i; AllocArray(menu, nameCount); for (name = nameList, i=0; name != NULL; name = name->next, ++i) { menu[i] = name->label; } if (formName == NULL) { autoSubmit = NULL; event = NULL; } else { safef(javascript, sizeof(javascript), "document.%s.submit();", formName); autoSubmit = javascript; event = "change"; } cgiMakeDropListFull(varName, menu, menu, nameCount, selectedName, event, autoSubmit); freez(&menu); } /* Convert to track name */ for (name = nameList; name != NULL; name = name->next) { if (sameString(selectedName, name->label)) trackName = name->name; } /* Clean up and return. */ slFreeList(&nameList); slFreeList(&trackList); return trackName; } void rAddTrackListToHash(struct hash *trackHash, struct trackDb *tdbList, char *chrom, boolean leafOnly) /* Recursively add trackList to trackHash */ { struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { if (hTrackOnChrom(tdb, chrom)) { if (tdb->subtracks == NULL || !leafOnly) hashAdd(trackHash, tdb->track, tdb); } rAddTrackListToHash(trackHash, tdb->subtracks, chrom, leafOnly); } } struct hash *trackHashMakeWithComposites(char *db,char *chrom,struct trackDb **tdbList, bool withComposites) // Make hash of trackDb items for this chromosome, including composites, not just the subtracks. // May pass in prepopulated trackDb list, or may receive the trackDb list as an inout. { struct trackDb *theTdbs = NULL; if (tdbList == NULL || *tdbList == NULL) { theTdbs = hTrackDb(db); if (tdbList != NULL) *tdbList = theTdbs; } else theTdbs = *tdbList; struct hash *trackHash = newHash(7); rAddTrackListToHash(trackHash, theTdbs, chrom, !withComposites); return trackHash; } /****** Stuff for acembly related options *******/ static char *acemblyOptions[] = { "all genes", "main", "putative", }; enum acemblyOptEnum acemblyStringToEnum(char *string) /* Convert from string to enum representation. */ { int x = stringIx(string, acemblyOptions); if (x < 0) errAbort("hui::acemblyStringToEnum() - Unknown option %s", string); return x; } char *acemblyEnumToString(enum acemblyOptEnum x) /* Convert from enum to string representation. */ { return acemblyOptions[x]; } void acemblyDropDown(char *var, char *curVal) /* Make drop down of options. */ { cgiMakeDropList(var, acemblyOptions, ArraySize(acemblyOptions), curVal); } static boolean parseAssignment(char *words, char **name, char **value) /* parse =, destroying input words in the process */ { char *p; if ((p = index(words, '=')) == NULL) return FALSE; *p++ = 0; if (name) *name = words; if (value) *value = p; return TRUE; } static char *getPrimaryType(char *primarySubtrack, struct trackDb *tdb) /* Do not free when done. */ { char *type = NULL; if (primarySubtrack) { struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendants(tdb->subtracks); for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *subtrack = tdbRef->val; if (sameString(subtrack->track, primarySubtrack)) { type = subtrack->type; break; } } slFreeList(&tdbRefList); } return type; } boolean hSameTrackDbType(char *type1, char *type2) // Compare type strings: identical first word or allowed compatibilities { // OLD_CODE //return (sameString(type1, type2) || // (startsWith("wig ", type1) && startsWith("wig ", type2))); int wordLength = strlen(type1); // Many types have additional args which should not interfere (e.g. "bigWig 0 20") // Note: beds of different size are ok char *firstWhite = skipToSpaces(type1); if (firstWhite != NULL) wordLength = (firstWhite - type1) + 1; // include white space if (sameStringN(type1, type2,wordLength)) return TRUE; // Allow these cross overs? Why not? (see redmine #7588) if (startsWith("wig ",type1) && startsWith("bigWig ",type2)) // tested return TRUE; if (startsWith("bigWig ",type1) && startsWith("wig ",type2)) // tested return TRUE; // Many flavors of bed that could be merged... if (( startsWith("bed ",type1) // bed to Peak and vis-versa tested || startsWith("broadPeak",type1) || startsWith("narrowPeak",type1)) && ( startsWith("bed ",type2) || startsWith("broadPeak",type2) || startsWith("narrowPeak",type2))) return TRUE; // bigBed to bed and vis-versa fails! //if (( startsWith("bed ",type1) // || startsWith("bigBed ",type1) // || startsWith("broadPeak",type1) // || startsWith("narrowPeak",type1)) //&& ( startsWith("bed ",type2) // || startsWith("bigBed ",type2) // || startsWith("broadPeak",type2) // || startsWith("narrowPeak",type2))) // return TRUE; return FALSE; } static char *labelRoot(char *label, char** suffix) /* Parses a label which may be split with a into root and suffix Always free labelRoot. suffix, which may be null does not need to be freed. */ { char *root = cloneString(label); char *extra=strstrNoCase(root," "); // mean don't include the reset as part of the link if ((long)(extra)==-1) extra=NULL; if (extra!=NULL) { *extra='\0'; if (suffix != NULL) { extra+=5; *extra=' '; // Converts the to ' ' and include the ' ' *suffix = extra; } } return root; } typedef struct _dividers { int count; char**subgroups; char* setting; } dividers_t; static dividers_t *dividersSettingGet(struct trackDb *parentTdb) // Parses any dividers setting in parent of subtracks { dividers_t *dividers = needMem(sizeof(dividers_t)); dividers->setting = cloneString(trackDbSetting(parentTdb, "dividers")); if (dividers->setting == NULL) { freeMem(dividers); return NULL; } dividers->subgroups = needMem(24*sizeof(char*)); dividers->count = chopByWhite(dividers->setting, dividers->subgroups,24); return dividers; } static void dividersFree(dividers_t **dividers) // frees any previously obtained dividers setting { if (dividers && *dividers) { freeMem((*dividers)->subgroups); freeMem((*dividers)->setting); freez(dividers); } } typedef struct _hierarchy { int count; char* subgroup; char**membership; int* indents; char* setting; } hierarchy_t; static hierarchy_t *hierarchySettingGet(struct trackDb *parentTdb) // Parses any list hierachy instructions setting in parent of subtracks { hierarchy_t *hierarchy = needMem(sizeof(hierarchy_t)); hierarchy->setting = cloneString(trackDbSetting(parentTdb, "hierarchy")); // To be freed later if (hierarchy->setting == NULL) { freeMem(hierarchy); return NULL; } int cnt,ix; char *words[SMALLBUF]; cnt = chopLine(hierarchy->setting, words); assert(cnt<=ArraySize(words)); if (cnt <= 1) { freeMem(hierarchy->setting); freeMem(hierarchy); return NULL; } hierarchy->membership = needMem(cnt*sizeof(char*)); hierarchy->indents = needMem(cnt*sizeof(int)); hierarchy->subgroup = words[0]; char *name,*value; for (ix = 1,hierarchy->count=0; ix < cnt; ix++) { if (parseAssignment(words[ix], &name, &value)) { hierarchy->membership[hierarchy->count] = name; hierarchy->indents[hierarchy->count] = sqlUnsigned(value); hierarchy->count++; } } return hierarchy; } static void hierarchyFree(hierarchy_t **hierarchy) // frees any previously obtained hierachy settings { if (hierarchy && *hierarchy) { freeMem((*hierarchy)->setting); freeMem((*hierarchy)->membership); freeMem((*hierarchy)->indents); freez(hierarchy); } } // Four State checkboxes can be checked/unchecked by enable/disabled // NOTE: fourState is not a bitmap because it is manipulated in javascript and // int seemed easier at the time #define FOUR_STATE_EMPTY TDB_EXTRAS_EMPTY_STATE //#define FOUR_STATE_UNCHECKED 0 //#define FOUR_STATE_CHECKED 1 //#define FOUR_STATE_CHECKED_DISABLED -1 #define FOUR_STATE_DISABLE(val) {while ((val) >= 0) (val) -= 2;} #define FOUR_STATE_ENABLE(val) {while ((val) < 0) (val) += 2;} int subtrackFourStateChecked(struct trackDb *subtrack, struct cart *cart) // Returns the four state checked state of the subtrack { char * setting = NULL; char objName[SMALLBUF]; int fourState = (int)tdbExtrasFourState(subtrack); if (fourState != FOUR_STATE_EMPTY) return fourState; fourState = FOUR_STATE_UNCHECKED; // default to unchecked, enabled if ((setting = trackDbLocalSetting(subtrack, "parent")) != NULL) { if (findWordByDelimiter("off",' ',setting) == NULL) fourState = FOUR_STATE_CHECKED; } // Now check visibility enum trackVisibility vis = tdbLocalVisibility(cart, subtrack, NULL); if (vis == tvHide) { if (tdbIsCompositeView(subtrack->parent)) { if (tdbLocalVisibility(cart, subtrack->parent, NULL) == tvHide) FOUR_STATE_DISABLE(fourState); } } safef(objName, sizeof(objName), "%s_sel", subtrack->track); setting = cartOptionalString(cart, objName); if (setting == NULL) setting = cartOptionalString(cart, trackHubSkipHubName(objName)); if (setting != NULL) { if (sameWord("on",setting)) // ouch! cartUsualInt was interpreting "on" as 0, which was bad bug! fourState = 1; else fourState = atoi(setting); } tdbExtrasFourStateSet(subtrack,fourState); return fourState; } void subtrackFourStateCheckedSet(struct trackDb *subtrack, struct cart *cart,boolean checked, boolean enabled) // Sets the fourState Checked in the cart and updates cached state { int fourState = ( checked ? FOUR_STATE_CHECKED : FOUR_STATE_UNCHECKED ); if (!enabled) FOUR_STATE_DISABLE(fourState); char objName[SMALLBUF]; char objVal[5]; safef(objName, sizeof(objName), "%s_sel", subtrack->track); safef(objVal, sizeof(objVal), "%d", fourState); cartSetString(cart, objName, objVal); tdbExtrasFourStateSet(subtrack,fourState); } static char *tagEncode(char *name) // Turns out css classes cannot begin with a number. So prepend 'A' // If this were more widely used, could move to cheapcgi.c. { if (!isdigit(*name)) return name; char *newName = needMem(strlen(name)+2); *newName = 'A'; strcpy(newName+1,name); return newName; } boolean dimensionsExist(struct trackDb *parentTdb) // Does this parent track contain dimensions? { return (trackDbSetting(parentTdb, "dimensions") != NULL); } static dimensions_t *dimensionSettingsGet(struct trackDb *parentTdb) // Parses any dimemnions setting in parent of subtracks { dimensions_t *dimensions = needMem(sizeof(dimensions_t)); dimensions->setting = cloneString(trackDbSetting(parentTdb, "dimensions")); // To be freed later if (dimensions->setting == NULL) { freeMem(dimensions); return NULL; } int cnt,ix; char *words[SMALLBUF]; cnt = chopLine(dimensions->setting,words); assert(cnt<=ArraySize(words)); if (cnt <= 0) { freeMem(dimensions->setting); freeMem(dimensions); return NULL; } dimensions->names = needMem(cnt*sizeof(char*)); dimensions->subgroups = needMem(cnt*sizeof(char*)); char *name,*value; for (ix = 0,dimensions->count=0; ix < cnt; ix++) { if (parseAssignment(words[ix], &name, &value)) { dimensions->names[dimensions->count] = name; dimensions->subgroups[dimensions->count] = tagEncode(value); dimensions->count++; } } return dimensions; } static void dimensionsFree(dimensions_t **dimensions) // frees any previously obtained dividers setting { if (dimensions && *dimensions) { freeMem((*dimensions)->setting); freeMem((*dimensions)->names); freeMem((*dimensions)->subgroups); freez(dimensions); } } #define SUBGROUP_MAX 9 int subgroupCount(struct trackDb *parentTdb) // How many subGroup setting does this parent have? { int ix; int count = 0; for (ix=1;ix<=SUBGROUP_MAX;ix++) { char subGrp[16]; safef(subGrp, ArraySize(subGrp), "subGroup%d",ix); if (trackDbSetting(parentTdb, subGrp) != NULL) count++; } return count; } char * subgroupSettingByTagOrName(struct trackDb *parentTdb, char *groupNameOrTag) // look for a subGroup by name (ie subGroup1) or tag (ie view) and return an unallocated char* { struct trackDb *ancestor; for (ancestor = parentTdb; ancestor != NULL; ancestor = ancestor->parent) { char *setting = NULL; if (startsWith("subGroup",groupNameOrTag)) { setting = trackDbSetting(ancestor, groupNameOrTag); if (setting != NULL) return setting; } // these views are cached at trackDb read time setting = trackDbViewSetting(ancestor, groupNameOrTag); if (setting != NULL) return setting; } return NULL; } boolean subgroupingExists(struct trackDb *parentTdb, char *groupNameOrTag) // Does this parent track contain a particular subgrouping? { return (subgroupSettingByTagOrName(parentTdb,groupNameOrTag) != NULL); } static members_t *subgroupMembersGet(struct trackDb *parentTdb, char *groupNameOrTag) // Parse a subGroup setting line into tag,title, names(optional) and values(optional), // returning the count of members or 0 { static members_t nullMember; // place holder for NULL members_t *members = tdbExtrasMembers(parentTdb, groupNameOrTag); if (members != NULL) { if (members == &nullMember) return NULL; return members; } int ix,count; char *setting = subgroupSettingByTagOrName(parentTdb, groupNameOrTag); if (setting == NULL) { tdbExtrasMembersSet(parentTdb, groupNameOrTag, &nullMember); return NULL; } members = needMem(sizeof(members_t)); members->setting = cloneString(setting); #define MAX_SUBGROUP_MEMBERS 2000 char *words[MAX_SUBGROUP_MEMBERS+3]; // members preceded by tag and title, one extra to detect count = chopLine(members->setting, words); if (count == ArraySize(words)) warn("Subgroup %s exceeds maximum %d members", words[1], MAX_SUBGROUP_MEMBERS); if (count <= 1) { freeMem(members->setting); freeMem(members); tdbExtrasMembersSet(parentTdb, groupNameOrTag, &nullMember); return NULL; } // A subGroup label from a track hub is text from a stranger and is printed into the page in // a dozen places, so escape it here, once. Only for hub tracks: our own trackDb puts real // HTML entities in these labels on purpose (the ENCODE composites use and &alpha), // and escaping those would show the entity text instead of the character. boolean escapeLabels = isHubTrack(parentTdb->track); members->groupTag = words[0]; members->groupTitle = strSwapChar(words[1],'_',' '); // Titles replace '_' with space if (escapeLabels) members->groupTitle = htmlEncode(members->groupTitle); members->tags = needMem(count*sizeof(char*)); members->titles = needMem(count*sizeof(char*)); for (ix = 2,members->count=0; ix < count; ix++) { char *name,*value; if (parseAssignment(words[ix], &name, &value)) { members->tags[members->count] = tagEncode(name); members->titles[members->count] = strSwapChar(value,'_',' '); if (escapeLabels) members->titles[members->count] = htmlEncode(members->titles[members->count]); members->count++; } else { warn("Subgroup \"%s\" is missing a tag=val pair", words[1]); } } tdbExtrasMembersSet(parentTdb, groupNameOrTag, members); return members; } static int membersSubGroupIx(members_t* members, char *tag) // Returns the index of the subgroup within the members struct (or -1) { int ix = 0; for (ix=0;ixcount;ix++) { if (members->tags[ix] != NULL && sameString(members->tags[ix],tag)) return ix; } return -1; } static void subgroupMembersFree(members_t **members) // frees memory for subgroupMembers lists { if (members && *members) { // This should only get set through membersForAll which should not be freed. if ((*members)->selected != NULL || (*members)->subtrackList != NULL) return; freeMem((*members)->setting); freeMem((*members)->tags); freeMem((*members)->titles); freez(members); } } static members_t *subgroupMembersWeedOutEmpties(struct trackDb *parentTdb, members_t *members, struct cart *cart) // Weed out members of a subgroup without any subtracks, alters memory in place! { if (members->count == 0) { warn("%s: No subtracks in group: %s. This indicates a problem in the subGroup line for this group.", parentTdb->track, members->groupTitle); return members; } // First tally all subtrack counts int ixIn=0; struct slRef *subtrackRef, *subtrackRefList = trackDbListGetRefsToDescendantLeaves(parentTdb->subtracks); struct trackDb *subtrack; members->subtrackCount = needMem(members->count * sizeof(int)); members->currentlyVisible = needMem(members->count * sizeof(int)); members->subtrackList = needMem(members->count * sizeof(struct slRef *)); for (subtrackRef = subtrackRefList; subtrackRef != NULL; subtrackRef = subtrackRef->next) { subtrack = subtrackRef->val; char *belongsTo =NULL; if (subgroupFind(subtrack,members->groupTag,&belongsTo)) { if (-1 != (ixIn = stringArrayIx(belongsTo, members->tags, members->count))) { members->subtrackCount[ixIn]++; if (cart && fourStateVisible(subtrackFourStateChecked(subtrack,cart))) members->currentlyVisible[ixIn]++; refAdd(&(members->subtrackList[ixIn]), subtrack); } } } // Now weed out empty subgroup tags. Can do this in place since new count <= old count // NOTE: Don't I wish I had made these as an slList ages ago! (tim) int ixOut=0; for (ixIn=ixOut;ixIncount;ixIn++) { if (members->subtrackCount[ixIn] > 0) { if (ixOut < ixIn) { members->tags[ixOut] = members->tags[ixIn]; members->titles[ixOut] = members->titles[ixIn]; members->subtrackCount[ixOut] = members->subtrackCount[ixIn]; members->currentlyVisible[ixOut] = members->currentlyVisible[ixIn]; members->subtrackList[ixOut] = members->subtrackList[ixIn]; if (members->selected != NULL) members->selected[ixOut] = members->selected[ixIn]; } ixOut++; } else { members->tags[ixIn] = NULL; members->titles[ixIn] = NULL; members->subtrackCount[ixIn] = 0; members->currentlyVisible[ixIn] = 0; //slFreeList(&members->subtrackList[ixIn]); // No freeing at this moment members->subtrackList[ixIn] = NULL; if (members->selected != NULL) members->selected[ixIn] = FALSE; } } members->count = ixOut; if (members->count == 0) // No members of this subgroup had a subtrack { //subgroupMembersFree(&members); // don't bother freeing return NULL; } return members; } enum { dimV=0, // View first dimX=1, // X & Y next dimY=2, dimA=3, // dimA is start of first of the optional non-matrix, non-view dimensions }; static char* abcMembersChecked(struct trackDb *parentTdb, struct cart *cart, members_t* members, char letter) // returns a string of subGroup tags which are currently checked { char settingName[SMALLBUF]; int mIx; if (members->selected == NULL) members->selected = needMem(members->count * sizeof(boolean)); safef(settingName, sizeof(settingName), "%s.filterComp.%s",parentTdb->track,members->groupTag); struct slName *options = cartOptionalSlNameList(cart,settingName); if (options != NULL) { if (sameWord(options->name,"All")) // filterComp returns "All" meaning every option selected { slNameFreeList(&options); options = slNameListFromStringArray(members->tags, members->count); assert(options != NULL); } struct slName *option; for (option=options;option!=NULL;option=option->next) { mIx = membersSubGroupIx(members, option->name); if (mIx >= 0) members->selected[mIx] = TRUE; } return slNameListToString(options,','); } struct dyString *currentlyCheckedTags = NULL; // Need a string of subGroup tags which are currently checked safef(settingName,sizeof(settingName),"dimension%cchecked",letter); char *dimCheckedDefaults = trackDbSettingOrDefault(parentTdb,settingName,"All"); char *checkedDefaults[12]; int defaultCount = 0; if (dimCheckedDefaults != NULL && differentWord(dimCheckedDefaults,"All") && differentWord(dimCheckedDefaults,"Any")) { defaultCount = chopCommas(dimCheckedDefaults, checkedDefaults); int dIx = 0; for (;dIx < defaultCount;dIx++) checkedDefaults[dIx] = tagEncode(checkedDefaults[dIx]); // encode these before compare! } // Will leak, but this is a tiny amount for (mIx=0;mIxcount;mIx++) { safef(settingName, sizeof(settingName), "%s.mat_%s_dim%c_cb", parentTdb->track,members->tags[mIx],letter); members->selected[mIx] = TRUE; if (defaultCount > 0) members->selected[mIx] = (-1 != stringArrayIx(members->tags[mIx],checkedDefaults,defaultCount)); members->selected[mIx] = cartUsualBoolean(cart,settingName,members->selected[mIx]); if (members->selected[mIx]) { if (currentlyCheckedTags == NULL) currentlyCheckedTags = dyStringCreate("%s",members->tags[mIx]); else dyStringPrintf(currentlyCheckedTags,",%s",members->tags[mIx]); } } if (currentlyCheckedTags) return dyStringCannibalize(¤tlyCheckedTags); return NULL; } static membersForAll_t *membersForAllSubGroupsWeedOutEmpties(struct trackDb *parentTdb, membersForAll_t *membersForAll, struct cart *cart) // Weed through members, tossing those without subtracks { // View is always first if (membersForAll->members[dimV] != NULL) membersForAll->members[dimV] = subgroupMembersWeedOutEmpties(parentTdb, membersForAll->members[dimV],cart); // X and Y are special if (membersForAll->members[dimX] != NULL) membersForAll->members[dimX] = subgroupMembersWeedOutEmpties(parentTdb, membersForAll->members[dimX],cart); if (membersForAll->members[dimY] != NULL) membersForAll->members[dimY] = subgroupMembersWeedOutEmpties(parentTdb, membersForAll->members[dimY],cart); // Handle the ABC dimensions int ixIn,ixOut=dimA; for (ixIn=ixOut;ixIndimMax;ixIn++) { if (membersForAll->members[ixIn] != NULL) membersForAll->members[ixIn] = subgroupMembersWeedOutEmpties(parentTdb, membersForAll->members[ixIn],cart); if (membersForAll->members[ixIn] == NULL) membersForAll->checkedTags[ixOut] = NULL; else { if (ixOut < ixIn) // Collapse if necessary { // NOTE: Don't I wish I had made these as an slList ages ago! (tim) membersForAll->members[ixOut] = membersForAll->members[ixIn]; membersForAll->checkedTags[ixOut] = membersForAll->checkedTags[ixIn]; membersForAll->letters[ixOut] = membersForAll->letters[ixIn]; } ixOut++; } } membersForAll->dimMax = ixOut; membersForAll->abcCount = membersForAll->dimMax - dimA; return membersForAll; } membersForAll_t* membersForAllSubGroupsGet(struct trackDb *parentTdb, struct cart *cart) // Returns all the parents subGroups and members { membersForAll_t *membersForAll = tdbExtrasMembersForAll(parentTdb); if (membersForAll != NULL) return membersForAll; // Already retrieved, so don't do it again int ix; membersForAll = needMem(sizeof(membersForAll_t)); if (tdbIsCompositeView(parentTdb->subtracks)) // view must have viewInMidle tdb in tree membersForAll->members[dimV]=subgroupMembersGet(parentTdb,"view"); membersForAll->letters[dimV]='V'; membersForAll->dimMax=dimA; // This can expand, depending upon ABC dimensions membersForAll->dimensions = dimensionSettingsGet(parentTdb); if (membersForAll->dimensions != NULL) { for (ix=0;ixdimensions->count;ix++) { char letter = lastChar(membersForAll->dimensions->names[ix]); if (letter != 'X' && letter != 'Y') { membersForAll->members[membersForAll->dimMax] = subgroupMembersGet(parentTdb, membersForAll->dimensions->subgroups[ix]); membersForAll->letters[membersForAll->dimMax] = letter; if (cart != NULL) membersForAll->checkedTags[membersForAll->dimMax] = abcMembersChecked( parentTdb,cart,membersForAll->members[membersForAll->dimMax],letter); membersForAll->dimMax++; } else if (letter == 'X') { membersForAll->members[dimX] = subgroupMembersGet(parentTdb, membersForAll->dimensions->subgroups[ix]); membersForAll->letters[dimX] = letter; } else { membersForAll->members[dimY] = subgroupMembersGet(parentTdb, membersForAll->dimensions->subgroups[ix]); membersForAll->letters[dimY] = letter; } } } else // No 'dimensions" setting: treat any subGroups as abc dimensions { char letter = 'A'; // walk through numbered subgroups for (ix=1;ixmembers[dimV] && sameWord(tag,"view")) continue; // View should have already been handled. NOTE: extremely unlikely case membersForAll->members[membersForAll->dimMax]=subgroupMembersGet(parentTdb, tag); membersForAll->letters[membersForAll->dimMax]=letter; if (cart != NULL) membersForAll->checkedTags[membersForAll->dimMax] = abcMembersChecked( parentTdb,cart,membersForAll->members[membersForAll->dimMax],letter); membersForAll->dimMax++; letter++; } } } membersForAll->abcCount = membersForAll->dimMax - dimA; membersForAll = membersForAllSubGroupsWeedOutEmpties(parentTdb, membersForAll, cart); // NOTE: Dimensions must be defined for filterComposite. Filter dimensioms are all and only ABCs. // Use dimensionAchecked to define selected char *filtering = trackDbSettingOrDefault(parentTdb,"filterComposite",NULL); if (filtering && !sameWord(filtering,"off")) { if (membersForAll->dimensions == NULL) errAbort("If 'filterComposite' defined, must define 'dimensions' also."); membersForAll->filters = TRUE; // Default all to multi for (ix=dimA;ixdimMax;ix++) { if (membersForAll->members[ix] != NULL) membersForAll->members[ix]->fcType = fctMulti; } if (!sameWord(filtering,"on")) { // Example tdb setting: "filterComposite on" OR // "filterComposite dimA=one dimB=multi dimC=onlyOne" // FIXME: do we even support anything but multi??? char *filterGroups[27]; int count = chopLine(filtering,filterGroups); for (ix=0;ixdimMax && membersForAll->letters[abcIx] != letter;abcIx++) ; // Advance to correct letter if (abcIx >= membersForAll->dimMax) errAbort("Invalid 'filterComposite' trackDb setting. Dimension '%s' not found.", dim); if (sameWord(filterGroups[ix],"one")) membersForAll->members[abcIx]->fcType = fctOne; else if (sameWord(filterGroups[ix],"onlyOne") || sameWord(filterGroups[ix],"oneOnly")) membersForAll->members[abcIx]->fcType = fctOneOnly; } } } if (cart != NULL) // Only save this if it is fully populated! tdbExtrasMembersForAllSet(parentTdb,membersForAll); return membersForAll; } static int membersForAllFindSubGroupIx(membersForAll_t* membersForAll, char *tag) { // Returns the index of the subgroups member struct within membersForAll (or -1) int ix = 0; for (ix=0;ixdimMax;ix++) { if (membersForAll->members[ix] != NULL && sameString(membersForAll->members[ix]->groupTag,tag)) return ix; } return -1; } const members_t*membersFindByTag(struct trackDb *parentTdb, char *tag) { // Uses membersForAll which may be in tdbExtraCache. Do not free membersForAll_t* membersForAll = membersForAllSubGroupsGet(parentTdb,NULL); if (membersForAll == NULL) return NULL; int ix = membersForAllFindSubGroupIx(membersForAll,tag); if (ix >= 0) return membersForAll->members[ix]; return NULL; } static void membersForAllSubGroupsFree(struct trackDb *parentTdb, membersForAll_t** membersForAllPtr) // frees memory for membersForAllSubGroups struct { return; // don't bother freeing things, just takes time for no benefit if (membersForAllPtr && *membersForAllPtr) { if (parentTdb != NULL) { if (*membersForAllPtr == tdbExtrasMembersForAll(parentTdb)) return; // Don't free something saved to the tdbExtras! } membersForAll_t* membersForAll = *membersForAllPtr; subgroupMembersFree(&(membersForAll->members[dimX])); subgroupMembersFree(&(membersForAll->members[dimY])); subgroupMembersFree(&(membersForAll->members[dimV])); int ix; for (ix=dimA;ixdimMax;ix++) { //ASSERT(membersForAll->members[ix] != NULL); subgroupMembersFree(&(membersForAll->members[ix])); if (membersForAll->checkedTags[ix]) freeMem(membersForAll->checkedTags[ix]); } dimensionsFree(&(membersForAll->dimensions)); freez(membersForAllPtr); } } int multViewCount(struct trackDb *parentTdb) // returns the number of multiView views declared { char *setting = subgroupSettingByTagOrName(parentTdb,"view"); if (setting == NULL) return 0; setting = cloneString(setting); int cnt; char *words[32]; cnt = chopLine(setting, words); freeMem(setting); return (cnt - 1); } membership_t *subgroupMembershipGet(struct trackDb *childTdb) // gets all the subgroup membership for a child track { membership_t *membership = tdbExtrasMembership(childTdb); if (membership != NULL) return membership; // Already retrieved, so don't do it again membership = needMem(sizeof(membership_t)); membership->setting = cloneString(trackDbSetting(childTdb, "subGroups")); if (membership->setting == NULL) { freeMem(membership); return NULL; } int ix,cnt; char *words[SMALLBUF]; cnt = chopLine(membership->setting, words); assert(cnt < ArraySize(words)); if (cnt <= 0) { freeMem(membership->setting); freeMem(membership); return NULL; } membership->subgroups = needMem(cnt*sizeof(char*)); membership->membership = needMem(cnt*sizeof(char*)); membership->titles = needMem(cnt*sizeof(char*)); for (ix = 0,membership->count=0; ix < cnt; ix++) { char *name,*value; if (parseAssignment(words[ix], &name, &value)) { membership->subgroups[membership->count] = name; membership->membership[membership->count] = tagEncode(value); // tags will be used as classes by js members_t* members = subgroupMembersGet(childTdb->parent, name); membership->titles[membership->count] = NULL; // default if (members != NULL) { int ix2 = stringArrayIx(membership->membership[membership->count],members->tags, members->count); if (ix2 != -1) membership->titles[membership->count] = strSwapChar(cloneString(members->titles[ix2]),'_',' '); // subgroupMembersFree(&members); /// don't bother freeing } membership->count++; } } tdbExtrasMembershipSet(childTdb,membership); return membership; } static boolean membershipInAllCurrentABCs(membership_t *membership,membersForAll_t*membersForAll) // looks for a match between a membership set and ABC dimensions currently checked { int mIx,aIx,tIx; for (aIx = dimA; aIx < membersForAll->dimMax; aIx++) // for each ABC subGroup { assert(membersForAll->members[aIx]->selected); // must find atleast one selected tag that we have membership in boolean matched = FALSE; for (mIx = 0; mIx members[aIx]->count;mIx++) // for each tag of that subgroup { if (membersForAll->members[aIx]->selected[mIx]) // The particular subgroup tag is selected { for (tIx=0;tIxcount;tIx++) // what we are members of { // subTrack belongs to subGroup and tags match if (sameString(membersForAll->members[aIx]->groupTag, membership->subgroups[tIx]) && sameWord(membersForAll->members[aIx]->tags[mIx],membership->membership[tIx])) { matched = TRUE; break; } } } } if (!matched) return FALSE; } return TRUE; // passed all tests so must be on all } char *compositeGroupLabel(struct trackDb *tdb, char *group, char *id) // Given ID from group, return corresponding label, looking through parent's subGroupN's // Given group ID, return group label, looking through parent's subGroupN's { members_t *members = subgroupMembersGet(tdb, group); char *result = NULL; int i; for (i=0; icount; ++i) { if (sameString(members->tags[i], id)) result = cloneString(members->titles[i]); } //subgroupMembersFree(&members); /// don't bother freeing return result; } char *compositeGroupId(struct trackDb *tdb, char *group, char *label) // Given label, return id, looking through parent's subGroupN's { members_t *members = subgroupMembersGet(tdb, group); char *result = NULL; int i; for (i=0; icount; ++i) { if (sameString(members->titles[i], label)) result = cloneString(members->tags[i]); } //subgroupMembersFree(&members); /// don't bother freeing return result; } static boolean subtrackInAllCurrentABCs(struct trackDb *childTdb,membersForAll_t*membersForAll) // looks for a match between a membership set and ABC dimensions currently checked { membership_t *membership = subgroupMembershipGet(childTdb); if (membership == NULL) return FALSE; boolean found = membershipInAllCurrentABCs(membership,membersForAll); return found; } boolean subgroupFind(struct trackDb *childTdb, char *name,char **value) // looks for a single tag in a child track's subGroups setting { if (value != NULL) *value = NULL; membership_t *membership = subgroupMembershipGet(childTdb); if (membership != NULL) { int ix; for (ix=0;ixcount;ix++) { if (sameString(name,membership->subgroups[ix])) { if (value != NULL) *value = cloneString(membership->membership[ix]); return TRUE; } } } return FALSE; } static char *subtrackColorToCompare(struct trackDb *subtrack) /* Convert RGB color to string with scaled hue, suitable for alpha sort */ { struct rgbColor rgbColor; rgbColor.r = subtrack->colorR; rgbColor.g = subtrack->colorG; rgbColor.b = subtrack->colorB; rgbColor.a = 255; struct hslColor hslColor = mgRgbToHsl(rgbColor); int hue = hslColor.h * 10; char buf[5]; safef(buf, 5, "%04d", hue); return cloneString(buf); } boolean subgroupFindTitle(struct trackDb *parentTdb, char *name,char **value) // looks for a a subgroup matching the name and returns the title if found { if (value != (void*)NULL) *value = NULL; members_t*members=subgroupMembersGet(parentTdb, name); //const members_t *members = membersFindByTag(parentTdb,name); // Can't use because of dimension dependence if (members==NULL) return FALSE; *value = cloneString(members->groupTitle); //subgroupMembersFree(&members); return TRUE; } void subgroupFree(char **value) // frees subgroup memory { if (value && *value) freez(value); } boolean subgroupRequired(char *value) /* Returns whether subgroup much be specified for each track. * Generally true. Exceptions are specially defined subgroups */ { return differentString(SUBTRACK_COLOR_SUBGROUP, value); } #define SORT_ON_TRACK_NAME "trackName" #define SORT_ON_RESTRICTED "dateUnrestricted" sortOrder_t *sortOrderGet(struct cart *cart,struct trackDb *parentTdb) // Parses any list sort order instructions for parent of subtracks (from cart or trackDb) // Some trickiness here. sortOrder->sortOrder is from cart (changed by user action), // as is sortOrder->order, But columns are in original tdb order (unchanging)! // However, if cart is null, all is from trackDb.ra { int ix; char *setting = trackDbSetting(parentTdb, "sortOrder"); if (setting == NULL) // Must be in trackDb or not a sortable table return NULL; sortOrder_t *sortOrder = needMem(sizeof(sortOrder_t)); sortOrder->htmlId = needMem(strlen(parentTdb->track)+15); safef(sortOrder->htmlId, (strlen(parentTdb->track)+15), "%s.sortOrder", parentTdb->track); char *cartSetting = NULL; if (cart != NULL) cartSetting = cartCgiUsualString(cart, sortOrder->htmlId, setting); // If setting is bigger than cartSetting, then it may be due to a trackDb change if (cart != NULL && strlen(cartSetting) > strlen(setting)) sortOrder->sortOrder = cloneString(cartSetting); // cart order else sortOrder->sortOrder = cloneString(setting); // old cart value is abandoned! /* parse setting into sortOrder */ sortOrder->setting = cloneString(setting); sortOrder->count = chopByWhite(sortOrder->setting,NULL,0); // Get size if (cart && !stringIn(SORT_ON_TRACK_NAME,setting)) sortOrder->count += 1; if (cart && !stringIn(SORT_ON_RESTRICTED,setting)) sortOrder->count += 1; sortOrder->column = needMem(sortOrder->count*sizeof(char*)); int foundColumns = chopByWhite(sortOrder->setting, sortOrder->column,sortOrder->count); sortOrder->title = needMem(sortOrder->count*sizeof(char*)); sortOrder->forward = needMem(sortOrder->count*sizeof(boolean)); sortOrder->order = needMem(sortOrder->count*sizeof(int)); if (cart && foundColumns < sortOrder->count) { int columnCount = foundColumns; int size = 0; char *moreOrder = NULL; if (cart && columnCount < sortOrder->count && !stringIn(SORT_ON_TRACK_NAME,setting)) { assert(sortOrder->column[columnCount] == NULL); sortOrder->column[columnCount] = cloneString(SORT_ON_TRACK_NAME "=+"); if (!stringIn(SORT_ON_TRACK_NAME,sortOrder->sortOrder)) { // little bit more size = strlen(sortOrder->sortOrder) + strlen(sortOrder->column[columnCount]) + 5; moreOrder = needMem(size); safef(moreOrder,size,"%s %s",sortOrder->sortOrder, sortOrder->column[columnCount]); freeMem(sortOrder->sortOrder); sortOrder->sortOrder = moreOrder; } columnCount++; } if (cart && columnCount < sortOrder->count && !stringIn(SORT_ON_RESTRICTED,setting)) { assert(sortOrder->column[columnCount] == NULL); sortOrder->column[columnCount] = cloneString(SORT_ON_RESTRICTED "=+"); if (!stringIn(SORT_ON_RESTRICTED,sortOrder->sortOrder)) { size = strlen(sortOrder->sortOrder) + strlen(sortOrder->column[columnCount]) + 5; moreOrder = needMem(size); safef(moreOrder,size,"%s %s",sortOrder->sortOrder, sortOrder->column[columnCount]); freeMem(sortOrder->sortOrder); sortOrder->sortOrder = moreOrder; } columnCount++; } } for (ix = 0; ixcount; ix++) { strSwapChar(sortOrder->column[ix],'=',0); // Don't want 'CEL=+' but 'CEL' and '+' // find tdb substr in cart current order string char *pos = stringIn(sortOrder->column[ix], sortOrder->sortOrder); //assert(pos != NULL && pos[strlen(sortOrder->column[ix])] == '='); if (pos != NULL && pos[strlen(sortOrder->column[ix])] == '=') { int ord=1; char* pos2 = sortOrder->sortOrder; for (;*pos2 && pos2 < pos;pos2++) { if (*pos2 == '=') // Discovering sort order in cart ord++; } sortOrder->forward[ix] = (pos[strlen(sortOrder->column[ix]) + 1] == '+'); sortOrder->order[ix] = ord; } else // give up on cartSetting { sortOrder->forward[ix] = TRUE; sortOrder->order[ix] = ix+1; } if (ix < foundColumns) { subgroupFindTitle(parentTdb,sortOrder->column[ix],&(sortOrder->title[ix])); } } return sortOrder; // NOTE cloneString:words[0]==*sortOrder->column[0] } // and will be freed when sortOrder is freed void sortOrderFree(sortOrder_t **sortOrder) // frees any previously obtained sortOrder settings { if (sortOrder && *sortOrder) { int ix; for (ix=0;ix<(*sortOrder)->count;ix++) { subgroupFree(&((*sortOrder)->title[ix])); } freeMem((*sortOrder)->sortOrder); freeMem((*sortOrder)->htmlId); freeMem((*sortOrder)->column); freeMem((*sortOrder)->forward); freeMem((*sortOrder)->order); freeMem((*sortOrder)->setting); freez(sortOrder); } } sortableTdbItem *sortableTdbItemCreate(struct trackDb *tdbChild,sortOrder_t *sortOrder) // creates a sortable tdb item struct, given a child tdb and its parent's sort table // Errors in interpreting a passed in sortOrder will return NULL { sortableTdbItem *item = NULL; if (tdbChild == NULL || tdbChild->shortLabel == NULL) return NULL; AllocVar(item); item->tdb = tdbChild; if (sortOrder != NULL) // Add some sort buttons { int sIx=0; for (sIx=sortOrder->count - 1;sIx>=0;sIx--) // walk backwards to ensure sort order in columns { sortColumn *column = NULL; AllocVar(column); column->fwd = sortOrder->forward[sIx]; char *col = sortOrder->column[sIx]; if (!subgroupFind(item->tdb, col, &(column->value))) { if (sameString(col, SUBTRACK_COLOR_SUBGROUP)) { // convert RGB color to hue so alpha sort can compare column->value = subtrackColorToCompare(tdbChild); } else { char *setting = trackDbSetting(item->tdb,col); if (setting != NULL) column->value = cloneString(setting); // No subgroup, assume there is a matching setting (eg longLabel) } } if (column->value != NULL) slAddHead(&(item->columns), column); else { freez(&column); if (item->columns != NULL) slFreeList(&(item->columns)); freeMem(item); return NULL; // sortOrder setting doesn't match items to be sorted. } } } return item; } static int sortableTdbItemsCmp(const void *va, const void *vb) // Compare two sortable tdb items based upon sort columns. { const sortableTdbItem *a = *((sortableTdbItem **)va); const sortableTdbItem *b = *((sortableTdbItem **)vb); sortColumn *colA = a->columns; sortColumn *colB = b->columns; int compared = 0; for (;compared==0 && colA!=NULL && colB!=NULL;colA=colA->next,colB=colB->next) { if (colA->value != NULL && colB->value != NULL) compared = strcmp(colA->value, colB->value) * (colA->fwd? 1: -1); } if (compared != 0) return compared; return strcasecmp(a->tdb->shortLabel, b->tdb->shortLabel); // Last chance } void sortTdbItemsAndUpdatePriorities(sortableTdbItem **items) // sort items in list and then update priorities of item tdbs { if (items != NULL && *items != NULL) { slSort(items, sortableTdbItemsCmp); int priority=1; sortableTdbItem *item; for (item = *items; item != NULL; item = item->next) item->tdb->priority = (float)priority++; } } void sortableTdbItemsFree(sortableTdbItem **items) // Frees all memory associated with a list of sortable tdb items { if (items != NULL && *items != NULL) { sortableTdbItem *item; for (item = *items; item != NULL; item = item->next) { sortColumn *column; for (column = item->columns; column != NULL; column = column->next) freeMem(column->value); slFreeList(&(item->columns)); } slFreeList(items); } } static boolean colonPairToStrings(char * colonPair,char **first,char **second) // Will set *first and *second to NULL. Must free any string returned! // No colon: value goes to *first { if (first) *first =NULL; // default to NULL ! if (second) *second=NULL; if (colonPair != NULL) { if (strchr(colonPair,':')) { if (second) *second = cloneString(strchr(colonPair,':') + 1); if (first) *first = strSwapChar(cloneString(colonPair),':',0); } else if (first) *first = cloneString(colonPair); return (*first != NULL || *second != NULL); } return FALSE; } boolean colonPairToInts(char * colonPair,int *first,int *second) { // Non-destructive. Only sets values if found. No colon: value goes to *first char *a=NULL; char *b=NULL; if (colonPairToStrings(colonPair,&a,&b)) { if (a!=NULL) { if (first) *first = atoi(a); freeMem(a); } if (b!=NULL) { if (second) *second = atoi(b); freeMem(b); } return TRUE; } return FALSE; } boolean colonPairToDoubles(char * colonPair,double *first,double *second) { // Non-destructive. Only sets values if found. No colon: value goes to *first char *a=NULL; char *b=NULL; if (colonPairToStrings(colonPair,&a,&b)) { if (a!=NULL) { if (first) *first = strtod(a,NULL); freeMem(a); } if (b!=NULL) { if (second) *second = strtod(b,NULL); freeMem(b); } return TRUE; } return FALSE; } static void chopUpValues(filterBy_t *filterBy) /* Chop up strings in filterBy or FilterValues statement. We look for optional labels * and optional CSS inside curly braces. */ { struct slName *val = filterBy->slValues; for (;val!=NULL;val=val->next) { // chip the style off the end of value or value|label char *chipper = strrchr(val->name,'{'); if (chipper != NULL) { if (val == filterBy->slValues) // First one { filterBy->styleFollows = (lastChar(chipper) == '}'); if (filterBy->styleFollows == FALSE) // Must be closed at the end of the string or filterBy->styleFollows = (*(chipper + 1) == '#'); // Legacy: color only } if (filterBy->styleFollows == FALSE) errAbort("filterBy values either all end in {CSS style} or none do."); *chipper++ = 0; // delimit by null char *end = chipper + (strlen(chipper) - 1); if (*end == '}') *end = 0; else if (*(chipper + 1) != '#') // Legacy: Could be color only definition errAbort("filterBy values ending in style must be enclosed in {curly brackets}."); } else if (filterBy->styleFollows) errAbort("filterBy values either all end in {CSS style} or none do."); if (filterBy->useIndex) strSwapChar(val->name,'_',' '); // value is a label so swap underscores else { // now chip the label off the end of value name chipper =strchr(val->name,'|'); if (chipper != NULL) { if (val == filterBy->slValues) // First one filterBy->valueAndLabel = TRUE; if (filterBy->valueAndLabel == FALSE) errAbort("filterBy values either all have labels (as value|label) " "or none do."); *chipper++ = 0; // The label is found inside filters->svValues as the next string strSwapChar(chipper,'_',' '); // Title does not have underscores } else if (filterBy->valueAndLabel) errAbort("filterBy values either all have labels in form of value|label " "or none do."); } } } char *extractFieldNameNew(char *trackDbVariable, char *filterType) /* Extract field name from a filter trackDb variable. Variables are filter*.column */ { char *ptr = strchr(trackDbVariable, '.'); if (ptr == NULL) errAbort("%s doesn't have a '.' in it", trackDbVariable); return ptr + 1; } char *extractFieldNameOld(char *trackDbVariable, char *filterType) /* Extract field name from a filter trackDb variable. Variables can either be * Filter* or .Filter* */ { char *field = cloneString(trackDbVariable); int ix = strlen(field) - strlen(filterType); field[ix] = '\0'; if (field[ix - 1] == '.') field[ix - 1] = '\0'; return field; } static char *getFilterValueDefaultsSetting(struct cart *cart, struct trackDb *tdb, char *field) // grab the default setting for a filterValues statement { char defaultsSetting[4096]; safef(defaultsSetting, sizeof defaultsSetting, "%s.%s", FILTER_VALUES_DEFAULT_NAME_LOW, field); char *defaults = cartOrTdbString(cart, tdb, defaultsSetting, NULL); if (defaults == NULL) { safef(defaultsSetting, sizeof defaultsSetting, "%s.%s", field, FILTER_VALUES_DEFAULT_NAME_CAP); defaults = cartOrTdbString(cart, tdb, defaultsSetting, NULL); } if (defaults == NULL) { safef(defaultsSetting, sizeof defaultsSetting, "%s%s", field, FILTER_VALUES_DEFAULT_NAME_CAP); defaults = cartOrTdbString(cart, tdb, defaultsSetting, NULL); } return defaults; } static char *getLabelSetting(struct cart *cart, struct trackDb *tdb, char *field) { char labelSetting[4096]; safef(labelSetting, sizeof labelSetting, "%s.%s", FILTER_LABEL_NAME_LOW, field); char *trackDbLabel = cartOrTdbString(cart, tdb, labelSetting, NULL); if (trackDbLabel == NULL) { safef(labelSetting, sizeof labelSetting, "%s.%s", field, FILTER_LABEL_NAME_CAP); trackDbLabel = cartOrTdbString(cart, tdb, labelSetting, NULL); } if (trackDbLabel == NULL) { safef(labelSetting, sizeof labelSetting, "%s%s", field, FILTER_LABEL_NAME_CAP); trackDbLabel = cartOrTdbString(cart, tdb, labelSetting, NULL); } return trackDbLabel; } static filterBy_t *buildFilterBy(struct trackDb *tdb, struct cart *cart, struct asObject *as, struct trackDbFilter *tdbFilter, char *name) /* Build a filterBy_t structure from a FilterValues statement. */ { boolean isHighlight = startsWith("highlightValues.", tdbFilter->name); char *field = tdbFilter->fieldName; if (isEmpty(tdbFilter->setting)) errAbort("track %s: FilterValues setting of field '%s' must have a value.", tdb->track, tdbFilter->fieldName); char *value = cartUsualStringClosestToHome(cart, tdb, FALSE, tdbFilter->name, tdbFilter->setting); filterBy_t *filterBy; AllocVar(filterBy); filterBy->column = cloneString(field); filterBy->title = cloneString(field); /// title should come from AS file, or trackDb variable struct asColumn *asCol = (as != NULL) ? asColumnFind(as, field) : NULL; if (asCol != NULL) filterBy->title = asCol->comment; else if (as != NULL) { // We have autoSql but the field is missing — that's a typo or an // outdated trackDb. Emit a visible warning so a hub maker reading the // page sees a clear hint, then abort. (The as==NULL case is reserved // for superTracks/noData tdbs that legitimately declare filterValues // on virtual fields they only aggregate over.) warn("Track %s: filter on field '%s' is not in the autoSql file. " "Check the field name in your trackDb filterValues.* / " "filterByRange.* settings against the .as schema.", tdb->track, field); errAbort("Track %s: Building filter on field %s which is not in AS file.", tdb->track, field); } char *trackDbLabel = getLabelSetting(cart, tdb, field); if (trackDbLabel) filterBy->title = trackDbLabel; filterBy->useIndex = FALSE; filterBy->slValues = slNameListFromCommaEscaped(value); chopUpValues(filterBy); if (cart != NULL) { char suffix[256]; safef(suffix, sizeof(suffix), "%s.%s", isHighlight ? "highlightBy" : "filterBy", filterBy->column); boolean parentLevel = isNameAtParentLevel(tdb,tdb->track); if (cartLookUpVariableClosestToHome(cart,tdb,parentLevel,suffix,&(filterBy->htmlName))) { filterBy->slChoices = cartOptionalSlNameList(cart,filterBy->htmlName); freeMem(filterBy->htmlName); } } if (filterBy->slChoices == NULL) // no settings in cart, initialize from trackDb { char *setting = getFilterValueDefaultsSetting(cart, tdb, field); filterBy->slChoices = slNameListFromCommaEscaped(setting); } struct dyString *dy = dyStringNew(128); dyStringPrintf(dy, "%s.%s.%s", name, isHighlight ? "highlightBy": "filterBy", filterBy->column); filterBy->htmlName = dy->string; return filterBy; } filterBy_t *filterByValues(struct trackDb *tdb, struct cart *cart, struct trackDbFilter *trackDbFilters, char *name) /* Build a filterBy_t list from tdb variables of the form *FilterValues */ { // Not every tdb has an autoSql: superTracks and tracks pointing at a // bigData file that isn't reachable at UI time both return NULL here. // That's fine for filterValues.* settings as long as a filterLabel.* // override is provided; buildFilterBy() already tolerates a NULL `as`. struct asObject *as = asForTdb(NULL, tdb); filterBy_t *filterByList = NULL, *filter; struct trackDbFilter *fieldFilter; while ((fieldFilter = slPopHead(&trackDbFilters)) != NULL) { // slAddTail (not slAddHead) keeps the priority-sorted order from tdbGetTrackFilters // since filterBySetCfgUi displays the list head-to-tail. if ((filter = buildFilterBy(tdb, cart, as, fieldFilter, name)) != NULL) slAddTail(&filterByList, filter); } return filterByList; } filterBy_t *filterBySetGetGuts(struct trackDb *tdb, struct cart *cart, char *name, char *subName, char *settingName) // Gets one or more "filterBy" settings (ClosestToHome). returns NULL if not found { // first check to see if this tdb is using "new" FilterValues cart variables if (differentString(subName, "highlightBy")) { struct trackDbFilter *trackDbFilters = tdbGetTrackFilterByFilters( tdb); if (trackDbFilters) return filterByValues(tdb, cart, trackDbFilters, name); } else { struct trackDbFilter *trackDbHighlights = tdbGetTrackHighlightByHighlights(tdb); if (trackDbHighlights) return filterByValues(tdb, cart, trackDbHighlights, name); } filterBy_t *filterBySet = NULL; char *setting = trackDbSettingClosestToHome(tdb, settingName); if(setting == NULL) return NULL; if ( name == NULL ) name = tdb->track; setting = cloneString(setting); char *filters[10]; // multiple filterBys are delimited by space but spaces inside filter can be protected "by quotes" int filterCount = chopByWhiteRespectDoubleQuotes(setting, filters, ArraySize(filters)); int ix; for (ix=0;ixcolumn = filter; filter += strlen(filter) + 1; first = strchr(filter,'='); if (first != NULL) *first = '\0'; else errAbort("filterBySetGet() expected '=' divider between table column and options list: %s", filters[ix]); filterBy->title = strSwapChar(filter,'_',' '); // Title does not have underscores filter += strlen(filter) + 1; // Are values indexes to the string titles? if (filter[0] == '+') { filter += 1; filterBy->useIndex = TRUE; } // Now set up each of the values which may have 1-3 parts (value|label{style}) // the slName list will have the 3 parts delimited by null value\0label\0style\0 stripString(filter, "\""); // Remove any double quotes now and chop by commmas filterBy->slValues = slNameListFromComma(filter); chopUpValues(filterBy); slAddTail(&filterBySet,filterBy); // Keep them in order (only a few) if (cart != NULL) { char suffix[256]; safef(suffix, sizeof(suffix), "%s.%s", subName, filterBy->column); boolean parentLevel = isNameAtParentLevel(tdb,name); if (cartLookUpVariableClosestToHome(cart,tdb,parentLevel,suffix,&(filterBy->htmlName))) { filterBy->slChoices = cartOptionalSlNameList(cart,filterBy->htmlName); freeMem(filterBy->htmlName); } } // Note: cannot use found name above because that may be at a higher (composite/view) level int len = strlen(name) + strlen(filterBy->column) + 15; filterBy->htmlName = needMem(len); safef(filterBy->htmlName, len, "%s.%s.%s", name,subName,filterBy->column); } freeMem(setting); return filterBySet; } filterBy_t *filterBySetGet(struct trackDb *tdb, struct cart *cart, char *name) /* Gets one or more "filterBy" settings (ClosestToHome). returns NULL if not found */ { return filterBySetGetGuts(tdb, cart, name, "filterBy", FILTER_BY); } filterBy_t *highlightBySetGet(struct trackDb *tdb, struct cart *cart, char *name) /* Gets one or more "highlightBy" settings (ClosestToHome). returns NULL if not found */ { return filterBySetGetGuts(tdb, cart, name, "highlightBy", HIGHLIGHT_BY); } void filterBySetFree(filterBy_t **filterBySet) // Free a set of filterBy structs { if (filterBySet != NULL) { while (*filterBySet != NULL) { filterBy_t *filterBy = slPopHead(filterBySet); if (filterBy->slValues != NULL) slNameFreeList(filterBy->slValues); if (filterBy->slChoices != NULL) slNameFreeList(filterBy->slChoices); if (filterBy->htmlName != NULL) freeMem(filterBy->htmlName); freeMem(filterBy->column); freeMem(filterBy); } } } static char *filterByClauseStd(filterBy_t *filterBy) // returns the SQL where clause for a single filterBy struct in the standard cases { int count = slCount(filterBy->slChoices); struct dyString *dyClause = dyStringNew(256); sqlDyStringPrintf(dyClause, "%s", filterBy->column); if (count == 1) sqlDyStringPrintf(dyClause, " = "); else sqlDyStringPrintf(dyClause, " in ("); struct slName *slChoice = NULL; boolean first = TRUE; for (slChoice = filterBy->slChoices;slChoice != NULL;slChoice=slChoice->next) { if (!first) sqlDyStringPrintf(dyClause, ","); first = FALSE; if (filterBy->useIndex) sqlDyStringPrintf(dyClause, "%d",atoi(slChoice->name)); // a number converted to a string else sqlDyStringPrintf(dyClause, "\"%s\"",slChoice->name); } if (dyStringLen(dyClause) == 0) { dyStringFree(&dyClause); return NULL; } if (count > 1) sqlDyStringPrintf(dyClause, ")"); return dyStringCannibalize(&dyClause); } char *filterByClause(filterBy_t *filterBy) // returns the SQL where clause for a single filterBy struct { if (filterByAllChosen(filterBy)) return NULL; else return filterByClauseStd(filterBy); } struct dyString *dyAddFilterByClause(struct cart *cart, struct trackDb *tdb, struct dyString *extraWhere,char *column, boolean *and) // creates the where clause condition to support a filterBy setting. // Format: filterBy column:Title=value,value [column:Title=value|label,value|label,value|label]) // filterBy filters are multiselect's so could have multiple values selected. // thus returns the "column1 in (...) and column2 in (...)" clause. // if 'column' is provided, and there are multiple filterBy columns, only the named column's // clause is returned. // The 'and' param and dyString in/out allows stringing multiple where clauses together { filterBy_t *filterBySet = filterBySetGet(tdb, cart,NULL); if (filterBySet== NULL) return extraWhere; filterBy_t *filterBy = filterBySet; for (;filterBy != NULL; filterBy = filterBy->next) { if (column != NULL && differentString(column,filterBy->column)) continue; char *clause = filterByClause(filterBy); if (clause != NULL) { if (*and) sqlDyStringPrintf(extraWhere, " AND "); sqlDyStringPrintf(extraWhere,"%-s", clause); freeMem(clause); *and = TRUE; } } filterBySetFree(&filterBySet); return extraWhere; } char *filterBySetClause(filterBy_t *filterBySet) // returns the "column1 in (...) and column2 in (...)" clause for a set of filterBy structs { struct dyString *dyClause = dyStringNew(256); boolean notFirst = FALSE; filterBy_t *filterBy = NULL; for (filterBy = filterBySet;filterBy != NULL; filterBy = filterBy->next) { char *clause = filterByClause(filterBy); if (clause != NULL) { if (notFirst) sqlDyStringPrintf(dyClause, " AND "); sqlDyStringPrintf(dyClause,"%-s", clause); freeMem(clause); notFirst = TRUE; } } if (dyStringLen(dyClause) == 0) { dyStringFree(&dyClause); return NULL; } return dyStringCannibalize(&dyClause); } void filterBySetCfgUiOption(filterBy_t *filterBy, struct slName *slValue, int ix) /* output one option for filterBy UI */ { char varName[32]; char *label = NULL; char *name = NULL; if (filterBy->useIndex) { safef(varName, sizeof(varName), "%d",ix); name = varName; label = slValue->name; } else { label = (filterBy->valueAndLabel? slValue->name + strlen(slValue->name)+1: slValue->name); name = slValue->name; } printf("slChoices != NULL && slNameInList(filterBy->slChoices,name)) printf(" SELECTED"); if (filterBy->useIndex || filterBy->valueAndLabel) printf(" value='%s'",name); if (filterBy->styleFollows) { char *styler = label + strlen(label)+1; if (*styler != '\0') { if (*styler == '#') // Legacy: just the color that follows printf(" style='color: %s;'",styler); else printf(" style='%s'",styler); } } printf(">%s\n",label); } static boolean filterByColumnIsMultiple(struct cart *cart, struct trackDb *tdb, char *setting) /* Is this filter setting expecting multiple items (e.g. has checkboxes in the UI) */ { return (sameString(setting, FILTERBY_MULTIPLE) || sameString(setting, FILTERBY_MULTIPLE_LIST_OR) || sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_OR) || sameString(setting, FILTERBY_MULTIPLE_LIST_ONLY_AND) || sameString(setting, FILTERBY_MULTIPLE_LIST_AND)); } static boolean advancedFilter(struct cart *cart, struct trackDb *tdb, char *setting) { if (!tdbIsBigBed(tdb)) return FALSE; return sameString(setting, FILTERBY_MULTIPLE_LIST_OR) || sameString(setting, FILTERBY_MULTIPLE_LIST_AND); } void filterBySetCfgUiGuts(struct cart *cart, struct trackDb *tdb, filterBy_t *filterBySet, boolean onOneLine, char *filterTypeTitle, char *selectIdPrefix, char *allLabel, char *prefix, boolean isHighlight) // Does the UI for a list of filterBy structure for either filterBy or highlightBy controls // isHighlight controls the variable name for the cart { if (filterBySet == NULL) return; #define FILTERBY_HELP_LINK "Help" int count = slCount(filterBySet); if (count == 1) puts(""); else printf("%s items by: (select multiple categories and items - %s) " "
\n",filterTypeTitle,FILTERBY_HELP_LINK); jsInlineF("$(function () { " "$('#filterClearButton').click( " " function(ev) { ev.preventDefault(); " " $('.filterBy option[value=\"All\"]').removeAttr(\"selected\");" " $('.filterBy option[Value=\"All\"]').attr('selected', 'selected');" " $('.filterBy').dropdownchecklist('refresh'); " " }); " "});"); #ifdef ADVANCED_BUTTON if (tdbIsBigBed(tdb)) { char varName[1024]; safef(varName, sizeof(varName), "%s.doAdvanced", tdb->track); puts(" "); printf("%s" ,varName,"Advanced "); printf("
"); jsInlineF("$(function () { advancedSearchOnChange('%s'); });\n", varName); } #endif // ADVANCED_BUTTON filterBy_t *filterBy = NULL; if (cartOptionalString(cart, "ajax") == NULL) { webIncludeResourceFile("ui.dropdownchecklist.css"); jsIncludeFile("ui.dropdownchecklist.js",NULL); jsIncludeFile("ddcl.js",NULL); } // TODO: columnCount (Number of filterBoxes per row) should be configurable through tdb setting for (filterBy = filterBySet; filterBy != NULL; filterBy = filterBy->next) { puts(""); } puts(""); for (filterBy = filterBySet; filterBy != NULL; filterBy = filterBy->next) { puts(""); } puts(""); int ix=0; for (filterBy = filterBySet; filterBy != NULL; filterBy = filterBy->next, ix++) { char *setting = getFilterType(cart, tdb, filterBy->column, FILTERBY_DEFAULT); puts(""); } puts("
"); char selectStatement[4096]; char *setting = getFilterType(cart, tdb, filterBy->column, FILTERBY_DEFAULT); if (filterByColumnIsMultiple(cart, tdb, setting)) safef(selectStatement, sizeof selectStatement, " (select multiple items - %s)", FILTERBY_HELP_LINK); else selectStatement[0] = 0; // the title is filterLabel. or an autoSql column comment, both hub supplied if(count == 1) printf("%s by %s%s",filterTypeTitle,htmlEncode(filterBy->title),selectStatement); else printf("%s",htmlEncode(filterBy->title)); puts("
"); char *setting = getFilterType(cart, tdb, filterBy->column, FILTERBY_DEFAULT); if (advancedFilter(cart, tdb, setting)) { char cartSettingString[4096]; if (isHighlight) { safef(cartSettingString, sizeof cartSettingString, "%s.%s.%s", prefix,HIGHLIGHT_TYPE_NAME_LOW, filterBy->column); printf("
Highlight if "); // ADVANCED BUTTON printf("
Match if "); cgiMakeRadioButton(cartSettingString, HIGHLIGHTBY_MULTIPLE_LIST_AND, sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_AND)); printf(" all "); cgiMakeRadioButton(cartSettingString, HIGHLIGHTBY_MULTIPLE_LIST_OR, sameString(setting, HIGHLIGHTBY_MULTIPLE_LIST_OR)); printf(" one or more match
"); } else { safef(cartSettingString, sizeof cartSettingString, "%s.%s.%s", prefix,FILTER_TYPE_NAME_LOW, filterBy->column); printf("
Match if "); // ADVANCED BUTTON printf("
Match if "); cgiMakeRadioButton(cartSettingString, FILTERBY_MULTIPLE_LIST_AND, sameString(setting, FILTERBY_MULTIPLE_LIST_AND)); printf(" all "); cgiMakeRadioButton(cartSettingString, FILTERBY_MULTIPLE_LIST_OR, sameString(setting, FILTERBY_MULTIPLE_LIST_OR)); printf(" one or more match
"); } } puts("
"); // value is always "All", even if label is different, to simplify javascript code int valIx = 1; // htmlName holds the field name, which for a hub bigBed comes from the hub's autoSql if (filterByColumnIsMultiple(cart, tdb, setting)) printf( "\n", selectIdPrefix,ix,htmlEncode(filterBy->htmlName)); printf("%s\n", (filterByAllChosen(filterBy)?" SELECTED":""), allLabel); struct slName *slValue; for (slValue=filterBy->slValues;slValue!=NULL;slValue=slValue->next,valIx++) { char varName[32]; char *label = NULL; char *name = NULL; if (filterBy->useIndex) { safef(varName, sizeof(varName), "%d",valIx); name = varName; label = slValue->name; } else { label = (filterBy->valueAndLabel ? slValue->name + strlen(slValue->name)+1 : slValue->name); name = slValue->name; } printf("slChoices != NULL && slNameInList(filterBy->slChoices,name)) printf(" SELECTED"); if (filterBy->useIndex || filterBy->valueAndLabel) printf(" value='%s'",htmlEncode(name)); // filterValues are hub supplied if (filterBy->styleFollows) { char *styler = label + strlen(label)+1; if (*styler != '\0') { if (*styler == '#') // Legacy: just the color that follows printf(" style='color: %s;'",styler); else printf(" style='%s'",styler); } } printf(">%s\n",htmlEncode(label)); // filterValues are hub supplied } printf("\n"); puts("
"); } void filterBySetCfgUi(struct cart *cart, struct trackDb *tdb, filterBy_t *filterBySet, boolean onOneLine, char *prefix) /* Does the filter UI for a list of filterBy structure */ { char selectIdPrefix[4096]; safef(selectIdPrefix, sizeof(selectIdPrefix), "fbc_%s", prefix); // Our checklists use ddcl.js, which doesn't seem to play nicely when elements have id strings that include '.' replaceChar(selectIdPrefix, '.', '_'); filterBySetCfgUiGuts(cart, tdb, filterBySet, onOneLine, "Filter", selectIdPrefix, "All", prefix, FALSE); } void highlightBySetCfgUi(struct cart *cart, struct trackDb *tdb, filterBy_t *filterBySet, boolean onOneLine, char *prefix, boolean isHighlight) /* Does the highlight UI for a list of filterBy structure */ { char selectIdPrefix[4096]; safef(selectIdPrefix, sizeof(selectIdPrefix), "hbc_%s", prefix); // Our checklists use ddcl.js, which doesn't seem to play nicely when elements have id strings that include '.' replaceChar(selectIdPrefix, '.', '_'); filterBySetCfgUiGuts(cart, tdb, filterBySet, onOneLine, "Highlight", selectIdPrefix, "None", prefix, TRUE); } #define COLOR_BG_DEFAULT_IX 0 #define COLOR_BG_ALTDEFAULT_IX 1 #define DIVIDING_LINE "

\n" #define DIVIDER_PRINT(color) printf(DIVIDING_LINE,COLOR_BG_DEFAULT,(color)) static boolean divisionIfNeeded(char **lastDivide,dividers_t *dividers,membership_t *membership) // Keeps track of location within subtracks in order to provide requested division lines { boolean division = FALSE; if (dividers) { if (lastDivide != NULL) { int ix; for (ix=0;ixcount;ix++) { int sIx = stringArrayIx(dividers->subgroups[ix],membership->subgroups, membership->count); if ((lastDivide[ix] == (void*)NULL && sIx >= 0) || (lastDivide[ix] != (void*)NULL && sIx < 0) || (strcmp(lastDivide[ix],membership->membership[sIx]) != 0) ) { division = TRUE; if (lastDivide[ix] != (void*)NULL) freeMem(lastDivide[ix]); lastDivide[ix] = (sIx<0 ? (void*)NULL : cloneString(membership->membership[sIx])); } } } //if (division) // DIVIDER_PRINT(COLOR_DARKGREEN); } return division; } static void indentIfNeeded(hierarchy_t*hierarchy,membership_t *membership) // inserts any needed indents { int indent = 0; if (hierarchy && hierarchy->count>0) { int ix; for (ix=0;ixcount;ix++) { int iIx = stringArrayIx(membership->membership[ix], hierarchy->membership, hierarchy->count); if (iIx >= 0) { indent = hierarchy->indents[iIx]; break; // Only one } } } for (;indent>0;indent--) puts(" "); } // FIXME FIXME Should be able to use membersForAll struct to set default sort order from subGroups // FIXME FIXME This should be done in hgTrackDb at load time and should change tag values to // FIXME FIXME ensure js still works boolean tdbAddPrioritiesFromCart(struct cart *cart, struct trackDb *tdbList) // Updates the tdb->priority from cart for all tracks in list and their descendents. { char htmlIdentifier[1024]; struct trackDb *tdb; boolean cartPriorities = FALSE; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { safef(htmlIdentifier, sizeof(htmlIdentifier), "%s.priority", tdb->track); char *cartHas = cartOptionalString(cart,htmlIdentifier); if (cartHas != NULL) { tdb->priority = atof(cartHas); cartPriorities = TRUE; } if (tdbAddPrioritiesFromCart(cart, tdb->subtracks)) cartPriorities = TRUE; } return cartPriorities; } boolean tdbSortPrioritiesFromCart(struct cart *cart, struct trackDb **tdbList) // Updates the tdb->priority from cart then sorts the list anew. // Returns TRUE if priorities obtained from cart { boolean cartPriorities = tdbAddPrioritiesFromCart(cart, *tdbList); slSort(tdbList, trackDbCmp); return cartPriorities; } boolean tdbRefSortPrioritiesFromCart(struct cart *cart, struct slRef **tdbRefList) // Updates the tdb->priority from cart then sorts the list anew. // Returns TRUE if priorities obtained from cart { char htmlIdentifier[128]; struct slRef *tdbRef; boolean cartPriorities = FALSE; for (tdbRef = *tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *tdb = tdbRef->val; safef(htmlIdentifier, sizeof(htmlIdentifier), "%s.priority", tdb->track); char *cartHas = cartOptionalString(cart,htmlIdentifier); if (cartHas != NULL) { tdb->priority = atof(cartHas); cartPriorities = TRUE; } } slSort(tdbRefList, trackDbRefCmp); return cartPriorities; } void bigRmskCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* UI for the bigRmsk track */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); boolean showUnalignedExtents = cartUsualBoolean(cart, BIGRMSK_SHOW_UNALIGNED_EXTENTS, BIGRMSK_SHOW_UNALIGNED_EXTENTS_DEFAULT); boolean showLabels = cartUsualBoolean(cart, BIGRMSK_SHOW_LABELS, BIGRMSK_SHOW_LABELS_DEFAULT); boolean origPackViz = cartUsualBoolean(cart, BIGRMSK_ORIG_PACKVIZ, BIGRMSK_ORIG_PACKVIZ_DEFAULT); boolean regexpFilter = cartUsualBoolean(cart, BIGRMSK_REGEXP_FILTER, BIGRMSK_REGEXP_FILTER_DEFAULT); char * nameFilter = cartUsualString(cart, BIGRMSK_NAME_FILTER, BIGRMSK_NAME_FILTER_DEFAULT); puts("
"); printf("Filter by 'name#class/subclass' field (e.g. '*Alu*' would match 'FRAM#SINE/Alu'): "); cgiMakeTextVar(BIGRMSK_NAME_FILTER, cartUsualString(cart, BIGRMSK_NAME_FILTER, nameFilter), 20); cgiMakeCheckBox(BIGRMSK_REGEXP_FILTER, regexpFilter); puts(" regular expression

"); cgiMakeCheckBox(BIGRMSK_SHOW_UNALIGNED_EXTENTS, showUnalignedExtents); puts(" Show unaligned repeat regions

"); cgiMakeCheckBox(BIGRMSK_SHOW_LABELS, showLabels); puts(" Show annotation labels

"); cgiMakeCheckBox(BIGRMSK_ORIG_PACKVIZ, origPackViz); puts(" Display original pack visualization

"); cfgEndBox(boxed); } void lollyCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* UI for the wiggle track */ { int maxHeightPixels; int minHeightPixels; char option[256]; int defaultHeight; /* pixels per item */ int settingsDefault; #define MIN_HEIGHT_LOLLY 32 cartTdbFetchMinMaxPixels(cart, tdb, MIN_HEIGHT_LOLLY, atoi(DEFAULT_HEIGHT_PER), atoi(DEFAULT_HEIGHT_PER), &minHeightPixels, &maxHeightPixels, &settingsDefault, &defaultHeight); boxed = cfgBeginBoxAndTitle(tdb, boxed, title); printf(""); printf(""); double minY; /* from trackDb or cart */ double maxY; /* from trackDb or cart */ double tDbMinY; /* data range limits from trackDb type line */ double tDbMaxY; /* data range limits from trackDb type line */ char *words[8]; /* to parse the trackDb type line */ int wordCount = 0; /* to parse the trackDb type line */ wigFetchMinMaxYWithCart(cart, tdb, name, &minY, &maxY, &tDbMinY, &tDbMaxY, wordCount, words); printf("" ""); printf("

Track height:	"); safef(option, sizeof(option), "%s.%s", name, HEIGHTPER ); cgiMakeIntVarWithLimits(option, defaultHeight, "Track height",0, minHeightPixels, maxHeightPixels); printf("pixels (range: %d to %d)", minHeightPixels, maxHeightPixels); char *autoScale; wigFetchAutoScaleWithCart(cart,tdb,name, &autoScale); printf("
Data view scaling:	"); safef(option, sizeof(option), "%s.%s", name, AUTOSCALE ); wiggleScaleDropDown(option, autoScale); void wiggleScaleDropDownJavascript(char *name); wiggleScaleDropDownJavascript(name); puts("
Vertical viewing range:	min: ", name); safef(option, sizeof(option), "%s.%s", name, MIN_Y ); cgiMakeDoubleVarWithLimits(option, minY, "Range min", 0, NO_VALUE, NO_VALUE); printf("	max: "); safef(option, sizeof(option), "%s.%s", name, MAX_Y ); cgiMakeDoubleVarWithLimits(option, maxY, "Range max", 0, NO_VALUE, NO_VALUE); /* printf("
Drawing method:	"); safef(option, sizeof(option), "%s.%s", name, POPMETHOD); char popMethodVal = cartOrTdbString(cart, tdb, "popMethod", NULL); cgiMakeDropListFull(option, popMethodLabels, popMethodValues, ArraySize(popMethodValues), popMethodVal, NULL, NULL); / puts("

"); cfgEndBox(boxed); // N.B. scoreCfgUi maybe creates a box, so this is called after cfgEndBox // unclear what the logic is with box creation here scoreCfgUi(db, cart,tdb,name,title,1000,boxed); } void labelMakeCheckBox(struct cart *cart, struct trackDb *tdb, char *sym, char *desc, boolean defaultOn) /* add a checkbox for the user to select a component of a label (e.g. ID, name, other info). * NOTE: This does not have a track name argument, so the correct tdb must be passed in: * if setting is at composite level, then pass in composite tdb, likewise for view. */ { char suffix[512]; safef(suffix, sizeof(suffix), "label.%s", sym); boolean option = cartUsualBooleanClosestToHome(cart, tdb, FALSE, suffix, defaultOn); char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.%s", trackHubSkipHubName(tdb->track), suffix); cgiMakeCheckBox(cartVar, option); printf(" %s ", desc); } void geneTrackMakeCheckBox(struct cart *cart, struct trackDb *tdb, char *sym, char *desc, boolean defaultOn) /* add a checkbox for the user to select a component of a label (e.g. ID, name, other info). * NOTE: This does not have a track name argument, so the correct tdb must be passed in: * if setting is at composite level, then pass in composite tdb, likewise for view. */ { char suffix[512]; safef(suffix, sizeof(suffix), "geneTrack.%s", sym); boolean option = cartUsualBooleanClosestToHome(cart, tdb, FALSE, suffix, defaultOn); char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.%s", tdb->track, suffix); cgiMakeCheckBox(cartVar, option); printf(" %s ", desc); } static void freqSourceSelect(struct cart *cart, struct trackDb *tdb, char *name) /* Make a select input for preferred source of allele frequencies from * trackDb setting freqSourceOrder. */ { char *freqSourceOrder = cloneString(trackDbSetting(tdb, "freqSourceOrder")); if (isEmpty(freqSourceOrder)) return; int fsCount = countSeparatedItems(freqSourceOrder, ','); char *values[fsCount]; chopCommas(freqSourceOrder, values); char *menu[fsCount]; int i; for (i = 0; i < fsCount; i++) { // Change label of GnomAD to "GnomAD genomes" for clarity when "GnomAD_exomes" is present. if (sameString(values[i], "GnomAD") && stringIx("GnomAD_exomes", values) >= 0) menu[i] = "GnomAD genomes"; else { menu[i] = cloneString(values[i]); strSwapChar(menu[i], '_', ' '); } } boolean parentLevel = isNameAtParentLevel(tdb, name); char *freqProj = cartOptionalStringClosestToHome(cart, tdb, parentLevel, "freqProj"); puts("Frequency source/project to use for Minor Allele Frequency (MAF):"); char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.freqProj", name); cgiMakeDropListWithVals(cartVar, menu, values, ArraySize(menu), freqProj); puts("
"); } struct trackDb *tdbOrAncestorByName(struct trackDb *tdb, char *name) /* For reasons Angie cannot fathom, if a composite or view is passed to cfgByCfgType then * cfgByCfgType passes a leaf subtrack to its callees like bigDbSnpCfgUi. That is why we * see so many calls to isNameAtParentLevel, which returns true if the tdb was originally * at the composite or view level, which we can only tell by comparing with the original track name. * labelMakeCheckBox, called by many handlers in hgTrackUi that must be always top-level * (or have a special handler that bypasses cfgByCfgType like refSeqComposite), * is blissfully unaware of this. It uses the same tdb for looking in cart ClosestToHome * and for making the HTML element's cart var name, trusting that the correct tdb has been * handed to it. * So in order for a callee of cfgByCfgType to call labelMakeCheckBox with the correct tdb, * we need to walk back up comparing name like isNameAtParentLevel does. * If name doesn't match tdb or any of its ancestors then this returns NULL. */ { struct trackDb *correctTdb; for (correctTdb = tdb; correctTdb != NULL; correctTdb = correctTdb->parent) if (startsWithWordByDelimiter(correctTdb->track, '.', name)) return correctTdb; return NULL; } void snp153MakeCheckboxGroupSetClearButton(char *buttonVar, boolean isSet) /* Make a button for setting or clearing a set of checkboxes with the same name. * Uses only javascript to change the checkboxes, no resubmit. */ { char id[256]; char javascript[256]; safef(javascript, sizeof(javascript), "$(\"input:checkbox[name^='%s']\").each(function(){this.checked = %s;$(this).trigger('change');})", buttonVar, isSet ? "true" : "false"); safef(id, sizeof id, "%s_grp%sBut", buttonVar, isSet ? "Set" : "Clr"); cgiMakeOnClickButton(id, javascript, isSet ? JS_SET_ALL_BUTTON_LABEL : JS_CLEAR_ALL_BUTTON_LABEL); } struct trackDb *snp125FetchGeneTracks(char *database, struct cart *cart) /* Get a list of genePred tracks. */ { struct trackDb *tdbList = NULL; struct hash *trackHash = trackHashMakeWithComposites(database,NULL,&tdbList,FALSE); struct sqlConnection *conn = hAllocConn(database); struct slName *justGenePredTables = hTrackTablesOfType(conn, "genePred%%"), *gt; struct slName *bigGenePredTables = hTrackTablesOfType(conn, "bigGenePred%%"); struct slName *genePredTables = slCat(justGenePredTables,bigGenePredTables); struct trackDb *geneTdbList = NULL, *gTdb; if (genePredTables != NULL) { for (gt = genePredTables; gt != NULL; gt = gt->next) { gTdb = hashFindVal(trackHash, gt->name); if (gTdb && sameString(gTdb->grp, "genes")) { // We are going to overwrite gTdb's next pointer and possibly its priority, // so make a shallow copy: gTdb = CloneVar(gTdb); if (gTdb->parent) gTdb->priority = (gTdb->parent->priority + gTdb->priority/1000); slAddHead(&geneTdbList, gTdb); } } slSort(&geneTdbList, trackDbCmp); } hFreeConn(&conn); return geneTdbList; } void snp153OfferGeneTracksForFunction(char *database, struct cart *cart, char *name, struct trackDb *tdb, struct trackDb *correctTdb) /* Get a list of genePred tracks and make checkboxes to enable hgc's functional * annotations. */ { struct trackDb *geneTdbList = NULL, *gTdb; geneTdbList = snp125FetchGeneTracks(database, cart); if (geneTdbList) { char sectionVar[256]; safef(sectionVar, sizeof(sectionVar), "%s.geneTracks", name); jsBeginCollapsibleSection(cart, name, sectionVar, "Use Gene Tracks for Functional Annotation", FALSE); printf("
On details page, show function and coding differences relative to: \n"); char buttonVarPrefix[256]; safef(buttonVarPrefix, sizeof(buttonVarPrefix), "%s.geneTrack", name); snp153MakeCheckboxGroupSetClearButton(buttonVarPrefix, TRUE); snp153MakeCheckboxGroupSetClearButton(buttonVarPrefix, FALSE); struct slName *defaultGeneTracks = slNameListFromComma(trackDbSetting(tdb, "defaultGeneTracks")); int i; int numCols = 4; int menuSize = slCount(geneTdbList); char **values = needMem(menuSize*sizeof(char *)); char **labels = needMem(menuSize*sizeof(char *)); for (i = 0, gTdb = geneTdbList; i < menuSize && gTdb != NULL; i++, gTdb = gTdb->next) { values[i] = gTdb->track; if (gTdb->parent != NULL) { struct dyString *dy = dyStringNew(0); if (gTdb->parent->parent != NULL && !startsWith(gTdb->parent->parent->shortLabel, gTdb->parent->shortLabel)) dyStringPrintf(dy, "%s: ", gTdb->parent->parent->shortLabel); if (!startsWith(gTdb->parent->shortLabel, gTdb->shortLabel)) dyStringPrintf(dy, "%s: ", gTdb->parent->shortLabel); dyStringPrintf(dy, "%s", gTdb->shortLabel); labels[i] = dyStringCannibalize(&dy); } else labels[i] = gTdb->shortLabel; } printf("
\n"); puts(""); for (i = 0; i < menuSize; ++i) { if (i > 0 && (i % numCols) == 0) printf(""); printf(""); } if ((i % numCols) != 0) while ((i++ % numCols) != 0) printf(""); puts("

"); geneTrackMakeCheckBox(cart, correctTdb, values[i], labels[i], slNameInList(defaultGeneTracks, values[i]) ); printf("

"); jsEndCollapsibleSection(); } } void bigDbSnpCfgUi(char *db, struct cart *cart, struct trackDb *leafTdb, char *name, char *title, boolean boxed) /* UI for bigDbSnp a.k.a. "dbSNP 2.0". */ { boxed = cfgBeginBoxAndTitle(leafTdb, boxed, title); freqSourceSelect(cart, leafTdb, name); puts("
"); puts("Label:"); struct trackDb *correctTdb = tdbOrAncestorByName(leafTdb, name); labelMakeCheckBox(cart, correctTdb, "rsId", "rs# identifier", TRUE); labelMakeCheckBox(cart, correctTdb, "refAlt", "reference/alternate allele", TRUE); labelMakeCheckBox(cart, correctTdb, "majMin", "major/minor allele", FALSE); labelMakeCheckBox(cart, correctTdb, "maf", "MAF if available", FALSE); labelMakeCheckBox(cart, correctTdb, "func", "Most severe functional impact on gene if any", FALSE); puts("
"); scoreCfgUi(db, cart, leafTdb, name, "", 0, FALSE); puts("For more information about the "Interesting or anomalous properties", " "see below."); puts("

"); puts("Minimum MAF:"); boolean parentLevel = isNameAtParentLevel(leafTdb, name); double minMaf = cartUsualDoubleClosestToHome(cart, leafTdb, parentLevel, "minMaf", 0.0); char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.minMaf", name); cgiMakeDoubleVarWithLimits(cartVar, minMaf, "MAF", 0, 0.0, 0.5); puts("range: 0.0 - 0.5
"); // Make wrapper table for collapsible sections: puts(""); snp153OfferGeneTracksForFunction(db, cart, name, leafTdb, correctTdb); // End wrapper table for collapsible sections: puts("

"); wigOption(cart, name, title, leafTdb); cfgEndBox(boxed); } void cfgByCfgType(eCfgType cType,char *db, struct cart *cart, struct trackDb *tdb,char *prefix, char *title, boolean boxed) // Methods for putting up type specific cfgs used by composites/subtracks in hui.c { // When only one subtrack, then show it's cfg settings instead of composite/view level settings // This simplifies the UI where hgTrackUi won't have 2 levels of cfg, // while hgTracks still supports rightClick cfg of the subtrack. // Don't do this if noParentConfig is specified in the composite parent boolean noParentConfig = tdb && trackDbSetting(tdb, "noParentConfig"); if (!noParentConfig && (configurableByAjax(tdb,cType) > 0)) // Only if subtrack's configurable by ajax do we { // consider this option if (tdbIsComposite(tdb) // called for the composite && !isCustomComposite(tdb) && !tdbIsCompositeView(tdb->subtracks) // and there is no view level && slCount(tdb->subtracks) == 1) // and there is only one subtrack { tdb = tdb->subtracks; // show subtrack cfg instead prefix = tdb->track; } else if (tdbIsSubtrack(tdb) // called with subtrack && tdbIsCompositeView(tdb->parent) // subtrack has view && differentString(prefix,tdb->track) // and this has been called FOR the view && slCount(tdb->parent->subtracks) == 1) // and view has only one subtrack prefix = tdb->track; // removes reference to view level } // Cfg could be explicitly blocked, but if tdb is example subtrack // then blocking should have occurred before we got here. if (!tdbIsSubtrack(tdb) && trackDbSettingBlocksConfiguration(tdb,FALSE)) return; // composite/view must pass in example subtrack // NOTE: if subtrack types vary then there shouldn't be cfg at composite/view level! while (tdb->subtracks) tdb = tdb->subtracks; switch(cType) { case cfgBedScore: bedScoreCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgPeak: encodePeakCfgUi(cart,tdb,prefix,title,boxed); break; case cfgWig: wigCfgUi(cart,tdb,prefix,title,boxed); break; case cfgWigMaf: wigMafCfgUi(cart,tdb,prefix,title,boxed, db); break; case cfgGenePred: genePredCfgUi(db, cart,tdb,prefix,title,boxed); break; case cfgChain: chainCfgUi(db,cart,tdb,prefix,title,boxed, NULL); break; case cfgNetAlign: netAlignCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgBedFilt: bedFiltCfgUi(cart,tdb,prefix,title, boxed); break; case cfgBam: bamCfgUi(cart, tdb, prefix, title, boxed); break; case cfgVcf: vcfCfgUi(cart, tdb, prefix, title, boxed); break; case cfgLong: longRangeCfgUi(cart, tdb, prefix, title, boxed); break; case cfgSnake: snakeCfgUi(cart, tdb, prefix, title, boxed); break; case cfgPsl: pslCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgBarChart: barChartCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgInteract: interactCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgBigRmsk: bigRmskCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgLollipop: lollyCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgHic: hicCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgBigDbSnp: bigDbSnpCfgUi(db, cart, tdb, prefix, title, boxed); break; default: warn("Track type is not known to multi-view composites. type is: %d ", cType); break; } } char *encodeRestrictionDate(char *db,struct trackDb *trackDb,boolean excludePast) // Create a string for ENCODE restriction date of this track // if return is not null, then free it after use { if (!trackDb) return NULL; char *date = NULL; if (metadataForTable(db,trackDb,NULL) != NULL) { date = cloneString((char *)metadataFindValue(trackDb,"dateUnrestricted")); if (date != NULL) date = strSwapChar(date, ' ', 0); // Truncate time (not expected, but just in case) if (excludePast && !isEmpty(date) && dateIsOld(date, MDB_ENCODE_DATE_FORMAT)) freez(&date); } return date; } /* Subtrack configuration settings */ struct subtrackConfigSettings { sortOrder_t *sortOrder; /* from trackDb setting */ boolean useDragAndDrop; /* from trackDb setting */ boolean restrictions; /* from metadata ? */ boolean colorPatch; /* from trackDb setting */ boolean displayAll; /* from radiobutton */ int bgColorIx; /* from logic over other settings */ int columnCount; /* determined from trackDb settings */ }; #define LARGE_COMPOSITE_CUTOFF 30 static void printSubtrackListRadioButtons(char *parentTrack, int subCount, boolean displayAll) // Print radio buttons for all/select { printf("List subtracks: "); char javascript[JBUFSIZE]; safef(javascript, sizeof(javascript), "showOrHideSelectedSubtracks(true);"); char buffer[SMALLBUF]; if (subCount > LARGE_COMPOSITE_CUTOFF) safef(buffer,SMALLBUF,"%s.displaySubtracks", parentTrack); else safecpy(buffer,SMALLBUF,"displaySubtracks"); cgiMakeOnEventRadioButtonWithClass(buffer, "selected", !displayAll, "allOrOnly", "click", javascript); puts("only selected/visible "); safef(javascript, sizeof(javascript), "showOrHideSelectedSubtracks(false);"); cgiMakeOnEventRadioButtonWithClass(buffer, "all", displayAll, "allOrOnly", "click", javascript); printf("all"); if (subCount > 5) printf(" ()"); } static void printSubtrackTableHeader(struct trackDb *parentTdb, struct slRef *subtrackRefList, struct subtrackConfigSettings *settings) /* Print header of subtrack table, including classes describing display appearance and behavior. Return number of columns */ { boolean useDragAndDrop = settings->useDragAndDrop; sortOrder_t *sortOrder = settings->sortOrder; if (sortOrder != NULL) puts(""); else puts(""); int colspan = 3; if (sortOrder != NULL) colspan = sortOrder->count+2; else if (!tdbIsMultiTrack(parentTdb)) // An extra column for subVis/wrench so dragAndDrop works colspan++; if (settings->colorPatch) colspan++; int columnCount = 0; if (sortOrder != NULL) printf("\n", useDragAndDrop ? " nodrop nodrag" : ""); else { printf("", useDragAndDrop ? " id='noDrag' class='nodrop nodrag'" : ""); // First table row contains the display "selected/visible" or "all" radio buttons // NOTE: list subtrack radio buttons are inside tracklist table header if // there are no sort columns. The reason is to ensure spacing of lines // column headers when the only column header is "Restricted Until" printf("", colspan); int subCount = slCount(subtrackRefList); printSubtrackListRadioButtons(parentTdb->track, subCount, settings->displayAll); puts(""); columnCount = colspan; } // Add column headers which are sort button links if (sortOrder != NULL) { printf(" \n", sortOrder->htmlId, sortOrder->sortOrder); // keeing track of sortOrder columnCount++; if (!tdbIsMultiTrack(parentTdb)) // An extra column for subVis/wrench so dragAndDrop works { printf("\n"); columnCount++; } // Columns in tdb order (unchanging), sort in cart order (changed by user action) int sIx=0; for (sIx=0;sIxcount;sIx++) { if (sameString(SORT_ON_TRACK_NAME,sortOrder->column[sIx])) break; // All wrangler requested sort orders have been done. if (sameString(SORT_ON_RESTRICTED,sortOrder->column[sIx])) break; // All wrangler requested sort orders have been done. printf("%s", sortOrder->column[sIx], (sortOrder->forward[sIx] ? "" : " sortRev"),sortOrder->order[sIx], sortOrder->title[sIx]); jsOnEventById("click", sortOrder->column[sIx], "tableSortAtButtonPress(this);"); printf("^{%s",(sortOrder->forward[sIx]?"↓":"↑"));
if (sortOrder->count > 1)
printf("%d",sortOrder->order[sIx]);
printf("}"); puts(""); columnCount++; } // longLabel column assert(sameString(SORT_ON_TRACK_NAME,sortOrder->column[sIx])); printf(" Track Name", sortOrder->column[sIx],(sortOrder->forward[sIx]?"":" sortRev"),sortOrder->order[sIx]); jsOnEventById("click", sortOrder->column[sIx], "tableSortAtButtonPress(this);"); printf("^%s%d",(sortOrder->forward[sIx]?"↓":"↑"),sortOrder->order[sIx]); puts(""); columnCount++; } puts(" "); // schema column columnCount++; // Finally there may be a restricted until column if (settings->restrictions) { if (sortOrder != NULL) { int sIx=sortOrder->count-1; assert(sameString(SORT_ON_RESTRICTED,sortOrder->column[sIx])); printf(" Restricted Until", sortOrder->column[sIx], (sortOrder->forward[sIx]?"":" sortRev"),sortOrder->order[sIx]); jsOnEventById("click", sortOrder->column[sIx], "tableSortAtButtonPress(this);"); printf("^%s%d",(sortOrder->forward[sIx] ? "↓" : "↑"), sortOrder->order[sIx]); puts(""); } else { printf(" "); printf("Restricted Until", ENCODE_DATA_RELEASE_POLICY); puts(" "); } columnCount++; } puts(""); // The end of the header section. settings->columnCount = columnCount; } static void printSubtrackTableFooter(int subCount, struct subtrackConfigSettings *settings) /* Print footer with restriction policy if needed */ { boolean restrictions = settings->restrictions; sortOrder_t *sortOrder = settings->sortOrder; int columnCount = settings->columnCount; if (subCount > 5 || (restrictions && sortOrder != NULL)) { printf("", COLOR_BG_DEFAULT_DARKER); if (restrictions && sortOrder != NULL) printf(" ",columnCount-1); else printf(" ",columnCount); // Count of subtracks is filled in by javascript. if (subCount > 5) printf("\n"); printf("\n"); // Restriction policy needs a link if (restrictions && sortOrder != NULL) printf("Restriction Policy", ENCODE_DATA_RELEASE_POLICY); printf("\n"); } } /********************/ /* Basic info for a controlled vocabulary term */ struct vocabBasic { struct vocabBasic *next; char *term; char *description; char *url; }; boolean vocabSettingIsEncode(char *setting) /* Distinguish ENCODE controlled vocab settings (first arg is cv.ra filename) from non-ENCODE (table-based vocabs) */ { if (setting && (strchr(cloneFirstWord(setting), '=') == NULL)) return TRUE; return FALSE; } char *vocabLink(struct hash *vocabFieldHash, char *term, char *title) /* Make an anchor with mouseover containing description and link if present */ { struct vocabBasic *vocab = hashFindVal(vocabFieldHash, term); if (vocab == NULL) return NULL; struct dyString *ds = dyStringNew(0); if (vocab->url == NULL || strlen(vocab->url) == 0) dyStringPrintf(ds, "%s", vocab->description, term); else dyStringPrintf(ds, "%s\n", vocab->description, vocab->url, term); return dyStringCannibalize(&ds); } struct hash *vocabBasicFromSetting(struct trackDb *parentTdb, struct cart *cart) /* Get description and URL for all vocabTables. Returns a hash of hashes */ { char *spec = trackDbSetting(parentTdb, "controlledVocabulary"); if (!spec) return NULL; // Not yet implemented for ENCODE-style CV if (vocabSettingIsEncode(spec)) return NULL; struct slPair *vocabTables = slPairFromString(spec); struct slPair *vocabTable = NULL; struct hash *tableHash = hashNew(0); struct sqlResult *sr; char **row; char query[256]; char *database = cartString(cart, "db"); for (vocabTable = vocabTables; vocabTable != NULL; vocabTable = vocabTable->next) { char *db = database; char *tableSpec = (char *)vocabTable->val; char *tableName = chopPrefix(tableSpec); if (differentString(tableName, tableSpec)) { chopSuffix(tableSpec); db = tableSpec; } struct sqlConnection *conn = hAllocConn(db); boolean hasUrl = FALSE; struct hash *subgroupHash = hashNew(0); hashAdd(tableHash, vocabTable->name, subgroupHash); if (hHasField(db, tableName, "url")) { sqlSafef(query, sizeof(query), "select term, description, url from %s", tableName); hasUrl = TRUE; } else sqlSafef(query, sizeof(query), "select term, description from %s", tableName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct vocabBasic *vocab = NULL; AllocVar(vocab); vocab->term = cloneString(row[0]); vocab->description = cloneString(row[1]); if (hasUrl) vocab->url = cloneString(row[2]); hashAdd(subgroupHash, vocab->term, vocab); } sqlFreeResult(&sr); hFreeConn(&conn); } return tableHash; } static void printSubtrackTableBody(struct trackDb *parentTdb, struct slRef *subtrackRefList, struct subtrackConfigSettings *settings, struct cart *cart) /* Print list of subtracks */ { sortOrder_t *sortOrder = settings->sortOrder; boolean useDragAndDrop = settings->useDragAndDrop; boolean restrictions = settings->restrictions; struct dyString *dyHtml = dyStringNew(SMALLBUF); char buffer[SMALLBUF]; char id[SMALLBUF]; char *db = cartString(cart, "db"); // The subtracks need to be sorted by priority but only sortable and dragable will have // non-default (cart) priorities to sort on if (sortOrder != NULL || useDragAndDrop) { // preserves user's prev sort/drags, ignore returned value about where // priorities come from (void) tdbRefSortPrioritiesFromCart(cart, &subtrackRefList); printf("\n", (sortOrder != NULL ? "sortable " : "") ); } else { slSort(&subtrackRefList, trackDbRefCmp); // straight from trackDb.ra puts(""); } // Finally the big "for loop" to list each subtrack as a table row. printf("\n\n"); membersForAll_t* membersForAll = membersForAllSubGroupsGet(parentTdb,NULL); struct hash *vocabHash = vocabBasicFromSetting(parentTdb, cart); struct slRef *subtrackRef; /* Color handling ?? */ //char *colors[2] = { COLOR_BG_DEFAULT, // COLOR_BG_ALTDEFAULT }; char *colors[2] = { "bgLevel1", "bgLevel1" }; int colorIx = settings->bgColorIx; boolean noParentConfig = parentTdb && trackDbSetting(parentTdb, "noParentConfig"); for (subtrackRef = subtrackRefList; subtrackRef != NULL; subtrackRef = subtrackRef->next) { struct trackDb *subtrack = subtrackRef->val; int ix; // Determine whether subtrack is checked, visible, configurable, has group membership, etc. int fourState = subtrackFourStateChecked(subtrack,cart); boolean checkedCB = fourStateChecked(fourState); boolean enabledCB = fourStateEnabled(fourState); boolean visibleCB = fourStateVisible(fourState); membership_t *membership = subgroupMembershipGet(subtrack); eCfgType cType = cfgNone; if (!tdbIsMultiTrack(parentTdb)) // MultiTracks never have configurable subtracks! cType = cfgTypeFromTdb(subtrack,FALSE); if (cType != cfgNone) { // Turn off configuring for certain track type or if explicitly turned off int cfgSubtrack = configurableByAjax(subtrack,cType); if (cfgSubtrack <= cfgNone) cType = cfgNone; else if (membersForAll->members[dimV] && membership != NULL) { // subtrack only configurable if more than one subtrack in view // find "view" in subgroup membership: e.g. "signal" if (-1 != (ix = stringArrayIx(membersForAll->members[dimV]->groupTag, membership->subgroups, membership->count))) { int ix2; // find "signal" in set of all views if (-1 != (ix2 = stringArrayIx(membership->membership[ix], membersForAll->members[dimV]->tags, membersForAll->members[dimV]->count))) { if (membersForAll->members[dimV]->subtrackCount[ix2] < 2) cType = cfgNone; } } } else if (!noParentConfig && slCount(subtrackRefList) < 2 // don't bother if there is a single subtrack without noParentConfig in the composite header && cfgTypeFromTdb(parentTdb,FALSE) != cfgNone) // but the composite is configurable. cType = cfgNone; } if (sortOrder == NULL && !useDragAndDrop) { char **lastDivide = NULL; dividers_t *dividers = dividersSettingGet(parentTdb); if (dividers) lastDivide = needMem(sizeof(char*)*dividers->count); if (membership && divisionIfNeeded(lastDivide,dividers,membership) ) colorIx = (colorIx == COLOR_BG_DEFAULT_IX ? COLOR_BG_ALTDEFAULT_IX : COLOR_BG_DEFAULT_IX); dividersFree(÷rs); } safef(id, sizeof(id), "%s_sel", subtrack->track); printf("\n",id,(!visibleCB && !settings->displayAll?" style='display:none'":"")); // Now the TD that holds the checkbox printf("", (enabledCB?"":" title='view is hidden'"), (useDragAndDrop?" class='dragHandle' title='Drag to reorder'":"")); // A hidden field to keep track of subtrack order if it could change if (sortOrder != NULL || useDragAndDrop) { safef(buffer, sizeof(buffer), "%s.priority", subtrack->track); float priority = (float)cartUsualDouble(cart, buffer, subtrack->priority); printf("", buffer, priority); // keeing track of priority } // The checkbox has identifying classes including subCB and the tag for each dimension // (e.g. class='subCB GM12878 CTCF Peak') dyStringClear(dyHtml); dyStringAppend(dyHtml, "subCB"); // always first int di; if (membersForAll->dimensions && membership != NULL) { for (di=dimX;didimMax;di++) { if (membersForAll->members[di] && -1 != (ix = stringArrayIx(membersForAll->members[di]->groupTag, membership->subgroups, membership->count))) dyStringPrintf(dyHtml," %s",htmlEncode(membership->membership[ix])); } } else if (membersForAll->abcCount && membership != NULL) // "dimensions" don't exist but may be subgroups anyway { for (di=dimA;didimMax;di++) { if (membersForAll->members[di] && -1 != (ix = stringArrayIx(membersForAll->members[di]->groupTag, membership->subgroups, membership->count))) dyStringPrintf(dyHtml," %s",htmlEncode(membership->membership[ix])); } } if (membersForAll->members[dimV] && membership != NULL && -1 != (ix = stringArrayIx(membersForAll->members[dimV]->groupTag, membership->subgroups, membership->count))) dyStringPrintf(dyHtml, " %s",htmlEncode(membership->membership[ix])); // Saved view for last // And finally the checkBox is made! safef(buffer, sizeof(buffer), "%s_sel", subtrack->track); if (!enabledCB) { dyStringAppend(dyHtml, " disabled"); cgiMakeCheckBoxFourWay(buffer,checkedCB,enabledCB,id,dyStringContents(dyHtml), "style='cursor:pointer' title='view is hidden'"); jsOnEventById("click", id, "matSubCbClick(this);"); } else { cgiMakeCheckBoxFourWay(buffer,checkedCB,enabledCB,id,dyStringContents(dyHtml), "style='cursor:pointer'"); jsOnEventById("click", id, "matSubCbClick(this);"); } if (useDragAndDrop) printf(" "); if (!tdbIsMultiTrack(parentTdb)) // MultiTracks never have independent vis { printf(""); // An extra column for subVis/wrench so dragAndDrop works enum trackVisibility vis = tdbVisLimitedByAncestors(cart,subtrack,FALSE,FALSE); char *view = NULL; if (membersForAll->members[dimV] && membership !=NULL && -1 != (ix = stringArrayIx(membersForAll->members[dimV]->groupTag, membership->subgroups, membership->count))) view = membership->membership[ix]; char classList[256]; if (view != NULL) safef(classList,sizeof(classList),"clickable fauxInput%s subVisDD %s", (visibleCB ? "":" disabled"),view); // view should be last! else safef(classList,sizeof(classList),"clickable fauxInput%s subVisDD", (visibleCB ? "":" disabled")); #define SUBTRACK_CFG_VIS "

%c%s

\n" char* visString = hStringFromTv(vis); printf(SUBTRACK_CFG_VIS,subtrack->track,classList, toupper((unsigned char)visString[0]), visString+1); char id[256]; safef(id, sizeof id, "%s_faux", subtrack->track); jsOnEventByIdF("click", id, "return subCfg.replaceWithVis(this,\"%s\",true);", subtrack->track); if (cType != cfgNone) // make a wrench { safef(id, sizeof id, "%s_toggle", subtrack->track); #define SUBTRACK_CFG_WRENCH "

" \ " Configure\n" printf(SUBTRACK_CFG_WRENCH,id, (visibleCB ? "":" disabled")); jsOnEventByIdF("click", id, "return subCfg.cfgToggle(this,\"%s\");", subtrack->track); } } printf(""); // If sortable, then there must be a column per sortable dimension if (sortOrder != NULL) { int sIx=0; for (sIx=0; sIx count; sIx++) { ix = -1; char *col = sortOrder->column[sIx]; if (membership) ix = stringArrayIx(col, membership->subgroups, membership->count); // TODO: Sort needs to expand from subGroups to labels as well // only print the warning message for trackDb errors and not for the // default sortable columns of trackName and dateUnrestricted if ( (!membership || (membership && ix == -1) ) && !(sameString(col, "trackName") || sameString(col, "dateUnrestricted") || sameString(col, "subtrackColor")) ) { printf("Missing subgroup"); } else { if (ix >= 0) { char *term = membership->membership[ix]; char *title = membership->titles[ix]; char *titleRoot=NULL; if (cvTermIsEmpty(col, title)) titleRoot = cloneString(" "); else titleRoot = labelRoot(title, NULL); // Each sortable column requires hidden goop (in the "abbr" field currently) // which is the actual sort on value printf("", subtrack->track, col, htmlEncode(term)); printf(" "); char *link = NULL; if (vocabHash) { struct hash *colHash = hashFindVal(vocabHash, col); if (colHash) link = vocabLink(colHash, term, titleRoot); } printf("%s", link ? link : titleRoot); puts(""); freeMem(titleRoot); } else if (sameString(col, SUBTRACK_COLOR_SUBGROUP)) { char *hue = subtrackColorToCompare(subtrack); printf("" " ", subtrack->track, col, hue, subtrack->colorR, subtrack->colorG, subtrack->colorB); } } } } else // Non-sortable tables do not have sort by columns but will display a short label { // (which may be a configurable link) if (settings->colorPatch) { printf(" ", subtrack->colorR, subtrack->colorG, subtrack->colorB); } printf(" "); hierarchy_t *hierarchy = hierarchySettingGet(parentTdb); indentIfNeeded(hierarchy,membership); hierarchyFree(&hierarchy); printf("%s",htmlEncode(subtrack->shortLabel)); puts(""); } // The long label column (note that it may have a metadata dropdown) printf(" %s", htmlEncode(subtrack->longLabel)); if (trackDbSetting(parentTdb, "wgEncode") && trackDbSetting(subtrack, "accession")) printf(" [GEO:%s]", trackDbSetting(subtrack, "accession")); compositeMetadataToggle(db,subtrack,NULL,TRUE,FALSE); printf(" "); // Embedded cfg dialogs are within the TD that contains the longLabel. // This allows a wide item to be embedded in the table if (cType != cfgNone) { // How to make this thing float to the left? Container is overflow:visible // and contained (made in js) is position:relative; left: -{some pixels} #define CFG_SUBTRACK_DIV "" #define MAKE_CFG_SUBTRACK_DIV(table,view) \ printf(CFG_SUBTRACK_DIV,(table),(view)?(view):"noView") char * view = NULL; if (membersForAll->members[dimV] && membership != NULL && -1 != (ix = stringArrayIx(membersForAll->members[dimV]->groupTag, membership->subgroups, membership->count))) view = membership->membership[ix]; MAKE_CFG_SUBTRACK_DIV(subtrack->track,view); } // A schema link for each track printf("\n "); makeSchemaLink(db,subtrack,"Data format"); printf(" "); // Do we have a restricted until date? if (restrictions) { char *dateDisplay = encodeRestrictionDate(db,subtrack,FALSE); // includes dates in the past if (dateDisplay) { if (dateIsOld(dateDisplay, MDB_ENCODE_DATE_FORMAT)) printf("\n %s ", dateDisplay); else printf("\n %s ", dateDisplay); } } // End of row and free ourselves of this subtrack puts("\n"); boolean showCfg = trackDbSettingOn(subtrack, "showCfg"); if (showCfg) jsInlineF(" subCfg.cfgToggle(document.getElementById(\"%s_toggle\"),\"%s\");", subtrack->track, subtrack->track); } // End of the table puts(""); dyStringFree(&dyHtml); membersForAllSubGroupsFree(parentTdb,&membersForAll); } static boolean membersHaveMatrix(membersForAll_t *membersForAll) /* Check for matrix */ { if (membersForAll->members[dimX] == NULL && membersForAll->members[dimY] == NULL) return FALSE; return TRUE; } static void printSubtrackTable(struct trackDb *parentTdb, struct slRef *subtrackRefList, struct subtrackConfigSettings *settings, struct cart *cart) /* Print table of subtracks */ { // Print table tag printf("\nsortOrder != NULL) dyStringPrintf(dyHtml, "sortable"); if (settings->useDragAndDrop) { if (dyStringLen(dyHtml) > 0) dyStringAppendC(dyHtml,' '); dyStringPrintf(dyHtml, "tableWithDragAndDrop"); } printf(" class='subtracks"); if (dyStringLen(dyHtml) > 0) { printf(" bglevel1 %s'",dyStringContents(dyHtml)); settings->bgColorIx = COLOR_BG_ALTDEFAULT_IX; } else settings->bgColorIx = COLOR_BG_DEFAULT_IX; // Start with non-default allows alternation puts("'>"); dyStringFree(&dyHtml); // save count of subtracks for use by footer code int subCount = slCount(subtrackRefList); printSubtrackTableHeader(parentTdb, subtrackRefList, settings); printSubtrackTableBody(parentTdb, subtrackRefList, settings, cart); printSubtrackTableFooter(subCount, settings); puts("

"); } boolean compositeHideEmptySubtracksSetting(struct trackDb *tdb, boolean *retDefault, char **retMultiBedFile, char **retSubtrackIdFile) /* Parse hideEmptySubtracks settings * Format: hideEmptySubtracks on|off * Optional index files for performance: * hideEmptySubtracksMultiBedUrl multiBed.bigBed * hideEmptySubtracksSourceUrl subtrackIds.tab * MultiBed.bed is a bed3Sources bigBed, generated with UCSC tool trackDbIndexBb * (for single view subtracks, can use bedtools multiinter * post-processed by UCSC multiBed.pl tool) * subtrackIds.tab is a tab-sep file: id subtrackName * * Return TRUE if setting is present. retDefault is TRUE if set to 'on', o/w FALSE */ { if (!tdbIsComposite(tdb)) return FALSE; char *hideEmpties = cloneString(trackDbSetting(tdb, SUBTRACK_HIDE_EMPTY)); if (!hideEmpties) return FALSE; boolean deflt = FALSE; if (sameString(hideEmpties, "on")) deflt = TRUE; else if (differentString(hideEmpties, "off")) { warn("Track %s %s setting invalid: %s", tdb->track, SUBTRACK_HIDE_EMPTY, hideEmpties); return FALSE; } if (retDefault) *retDefault = deflt; if (retMultiBedFile != NULL && retSubtrackIdFile != NULL) { char *file = cloneString(trackDbSetting(tdb, SUBTRACK_HIDE_EMPTY_MULTIBED_URL)); if (file != NULL) { // multi-bed specified to speed display *retMultiBedFile = cloneString(hReplaceGbdb(file)); file = cloneString(trackDbSetting(tdb, SUBTRACK_HIDE_EMPTY_SOURCES_URL)); if (file == NULL) { warn("Track %s missing setting: %s", tdb->track, SUBTRACK_HIDE_EMPTY_SOURCES_URL); return FALSE; } *retSubtrackIdFile = cloneString(hReplaceGbdb(file)); } } return TRUE; } boolean compositeHideEmptySubtracks(struct cart *cart, struct trackDb *tdb, char **retMultiBedFile, char **retSubtrackIdFile) /* Parse hideEmptySubtracks setting and check cart * Return TRUE if we should hide empties */ { boolean deflt = FALSE; if (!compositeHideEmptySubtracksSetting(tdb, &deflt, retMultiBedFile, retSubtrackIdFile)) return FALSE; char buf[128]; safef(buf, sizeof buf, "%s.%s", tdb->track, SUBTRACK_HIDE_EMPTY); return cartUsualBoolean(cart, buf, deflt); } boolean compositeChildHideEmptySubtracks(struct cart *cart, struct trackDb *childTdb, char **retMultiBedFile, char **retSubtrackIdFile) /* Parse hideEmptySubtracks setting and check cart * Return TRUE if we should hide empties */ { struct trackDb *tdb = tdbGetComposite(childTdb); if (!tdb) return FALSE; return compositeHideEmptySubtracks(cart, tdb, retMultiBedFile, retSubtrackIdFile); } void compositeHideEmptySubtracksUi(struct cart *cart, struct trackDb *tdb) /* Print the checkbox controlling the hideEmptySubtracks setting, for composites that * have it. Prints nothing for the ones that don't. */ { boolean hideSubtracksDefault; // TODO: Gray out or otherwise suppress when in multi-region mode if (!compositeHideEmptySubtracksSetting(tdb, &hideSubtracksDefault, NULL, NULL)) return; char *hideLabel = "Hide empty subtracks"; hideLabel = trackDbSettingOrDefault(tdb, SUBTRACK_HIDE_EMPTY_LABEL, hideLabel); printf("

%s: ", hideLabel); char buf[128]; safef(buf, sizeof buf, "%s.%s", tdb->track, SUBTRACK_HIDE_EMPTY); boolean doHideEmpties = compositeHideEmptySubtracks(cart, tdb, NULL, NULL); cgiMakeCheckBox(buf, doHideEmpties); // info icon with explanatory text on mouseover char *info = "Subtracks with no data in the browser window are hidden. Changing the browser window" " by zooming or scrolling may result in display of a different selection of tracks."; printInfoIcon(info); printf("

"); } static void compositeUiSubtracks(char *db, struct cart *cart, struct trackDb *parentTdb) // Display list of subtracks and descriptions with checkboxes to control visibility and // possibly other nice things including links to schema and metadata and a release date. { char buffer[SMALLBUF]; struct trackDb *subtrack; // Get list of leaf subtracks to work with struct slRef *subtrackRef, *subtrackRefList = trackDbListGetRefsToDescendantLeaves(parentTdb->subtracks); membersForAll_t* membersForAll = membersForAllSubGroupsGet(parentTdb,NULL); sortOrder_t* sortOrder = sortOrderGet(cart, parentTdb); char *displaySubs = NULL; int subCount = slCount(subtrackRefList); if (subCount > LARGE_COMPOSITE_CUTOFF && membersForAll->dimensions != NULL) { // ignore displaySubtracks setting for large composites with a matrix as // matrix effectively shows all safef(buffer, SMALLBUF,"%s.displaySubtracks", parentTdb->track); displaySubs = cartUsualString(cart, buffer,"some"); // track specific defaults to only selected } else { displaySubs = cartUsualString(cart, "displaySubtracks", "all"); // browser wide defaults to all } boolean displayAll = sameString(displaySubs, "all"); // Table wraps around entire list so that "Top" link can float to the correct place. cgiDown(0.7); printf("

"); printf(""); if (sortOrder != NULL) { // First table row contains the display "selected/visible" or "all" radio buttons // NOTE: list subtrack radio buttons are inside tracklist table header if // there are no sort columns. The reason is to ensure spacing of lines // column headers when the only column header is "Restricted Until" printSubtrackListRadioButtons(parentTdb->track, subCount, displayAll); if (membersHaveMatrix(membersForAll)) makeTopLink(parentTdb); printf("

"); } else { if (membersHaveMatrix(membersForAll)) makeTopLink(parentTdb); } // Get info for subtrack list struct subtrackConfigSettings *settings = NULL; AllocVar(settings); // Determine whether there is a restricted until date column settings->restrictions = FALSE; for (subtrackRef = subtrackRefList; subtrackRef != NULL; subtrackRef = subtrackRef->next) { subtrack = subtrackRef->val; (void)metadataForTable(db,subtrack,NULL); if (NULL != metadataFindValue(subtrack,"dateUnrestricted")) { settings->restrictions = TRUE; break; } } settings->useDragAndDrop = sameOk("subTracks",trackDbSetting(parentTdb, "dragAndDrop")); settings->sortOrder = sortOrder; settings->displayAll = displayAll; settings->colorPatch = (trackDbSetting(parentTdb, SUBTRACK_COLOR_PATCH) != NULL); printSubtrackTable(parentTdb, subtrackRefList, settings, cart); if (sortOrder == NULL) printf(""); membersForAllSubGroupsFree(parentTdb,&membersForAll); sortOrderFree(&sortOrder); } static void compositeUiSubtracksMatchingPrimary(char *db, struct cart *cart, struct trackDb *parentTdb,char *primarySubtrack) // Display list of subtracks associated with a primary subtrack for the hgTables merge function { assert(primarySubtrack != NULL); char *primaryType = getPrimaryType(primarySubtrack, parentTdb); char htmlIdentifier[SMALLBUF]; // Get list of leaf subtracks to work with and sort them struct slRef *subtrackRef, *subtrackRefList = trackDbListGetRefsToDescendantLeaves(parentTdb->subtracks); if (NULL != trackDbSetting(parentTdb, "sortOrder") || NULL != trackDbSetting(parentTdb, "dragAndDrop")) tdbRefSortPrioritiesFromCart(cart, &subtrackRefList); // preserves user's prev sort/drags else slSort(&subtrackRefList, trackDbRefCmp); // straight from trackDb.ra // Now we can start in on the table of subtracks printf("\n" "\n\n",parentTdb->track); for (subtrackRef = subtrackRefList; subtrackRef != NULL; subtrackRef = subtrackRef->next) { struct trackDb *subtrack = subtrackRef->val; int fourState = subtrackFourStateChecked(subtrack,cart); boolean checkedCB = fourStateChecked(fourState); boolean enabledCB = fourStateEnabled(fourState); safef(htmlIdentifier, sizeof(htmlIdentifier), "%s_sel", subtrack->track); if (sameString(subtrack->track, primarySubtrack)) { puts("\n", subtrack->longLabel); } else if (hSameTrackDbType(primaryType, subtrack->type)) { puts("\n", subtrack->longLabel); } } puts(""); puts("

"); cgiMakeHiddenBoolean(htmlIdentifier, TRUE); puts("[on] "); printf("	%s [selected on main page]
"); cgiMakeCheckBox(htmlIdentifier, checkedCB && enabledCB); printf("	%s

"); if (slCount(subtrackRefList) > 5) puts(" "); puts("

"); if (!primarySubtrack) jsInline("matInitializeMatrix();\n"); } static void makeAddClearButtonPair(char *idPrefix, char *class,char *separator) // Print an [Add][Clear] button pair that uses javascript to check subtracks { char buf[256]; if (class) safef(buf, sizeof buf,"matSetMatrixCheckBoxes(true,CSS.escape('%s')); return false;", class); else safef(buf, sizeof buf,"matSetMatrixCheckBoxes(true); return false;"); char id[256]; safef(id, sizeof id, "%s_add", idPrefix); cgiMakeOnClickButton(id, buf, ADD_BUTTON_LABEL); if (separator) printf("%s",separator); if (class) safef(buf, sizeof buf,"matSetMatrixCheckBoxes(false,CSS.escape('%s')); return false;", class); else safef(buf, sizeof buf,"matSetMatrixCheckBoxes(false); return false;"); safef(id, sizeof id, "%s_clr", idPrefix); cgiMakeOnClickButton(id, buf, CLEAR_BUTTON_LABEL); } #define MANY_SUBTRACKS 8 #define WIGGLE_HELP_PAGE "../goldenPath/help/hgWiggleTrackHelp.html" boolean cfgBeginBoxAndTitle(struct trackDb *tdb, boolean boxed, char *title) // Handle start of box and title for individual track type settings { if (!boxed) { boxed = trackDbSettingOn(tdb,"boxedCfg"); if (boxed) printf("
"); } if (boxed) { printf("
", COLOR_BG_ALTDEFAULT); if (title) printf("%s Configuration\n", title); } else if (title) printf("
%s ", title ); else printf("
"); return boxed; } void cfgEndBox(boolean boxed) // Handle end of box and title for individual track type settings { if (boxed) puts("
"); } void snakeOption(struct cart *cart, char *name, char *title, struct trackDb *tdb) /* let the user choose to see the track in snake mode */ { if (!cfgOptionBooleanDefault("canSnake", TRUE)) return; printf("
Display data as a rearrangement graph: "); boolean option = cartOrTdbBoolean(cart, tdb, "doSnake", FALSE); char varName[1024]; safef(varName, sizeof(varName), "%s.doSnake", name); cgiMakeCheckBox(varName, option); printf("
\n"); //char *style = option ? "display:block" : "display:none"; //printf("

\n", style); //printf("

\n\n"); jsInlineF("$(\"input[name='%s']\").click( function() { $('#snakeGraphOptions').toggle();} );\n" , varName); // XSS FILTER? } void squishyPackOption(struct cart *cart, char *name, char *title, struct trackDb *tdb) /* let the user choose to see the track in wiggle mode */ { char option[256]; char buffer[4096]; char *field = trackDbSetting(tdb, "squishyPackField"); if (field == NULL) return; char *fieldLabel = trackDbSetting(tdb, "squishyPackLabel"); if (fieldLabel == NULL) { fieldLabel = buffer; safef(buffer, sizeof buffer, "Reduce (squish) the height of items that have a %s value greater than", field); } double squishyPackPoint = cartOrTdbDouble(cart, tdb, "squishyPackPoint", 999); printf("
%s ", fieldLabel); safef(option, sizeof(option), "%s.%s", name, "squishyPackPoint" ); cgiMakeDoubleVarWithLimits(option, squishyPackPoint, "Range min", 0, NO_VALUE, NO_VALUE); } void wigOption(struct cart *cart, char *name, char *title, struct trackDb *tdb) /* let the user choose to see the track in wiggle mode */ { printf("

Display data as a density graph: "); boolean option = cartOrTdbBoolean(cart, tdb, "doWiggle", FALSE); char varName[1024]; safef(varName, sizeof(varName), "%s.doWiggle", name); cgiMakeCheckBox(varName, option); printf("
\n"); char *style = option ? "display:block" : "display:none"; printf("

\n", name, style); // we need to fool the wiggle dialog into defaulting to autoscale and maximum char *origType = tdb->type; tdb->type = "bedGraph"; if (hashFindVal(tdb->settingsHash, AUTOSCALE) == NULL) hashAdd(tdb->settingsHash, AUTOSCALE, "on"); if (hashFindVal(tdb->settingsHash, WINDOWINGFUNCTION) == NULL) hashAdd(tdb->settingsHash, WINDOWINGFUNCTION, wiggleWindowingEnumToString( wiggleWindowingMean)); wigCfgUi(cart,tdb,name,title,TRUE); tdb->type = origType; printf("

\n\n"); jsInlineF("$(\"input[name='%s']\").click( function() { $('#densGraphOptions%s').toggle();} );\n" , varName, name); // XSS FILTER? } void filterNameOption(struct cart *cart, char *name, struct trackDb *tdb) /* filter by feature names text input box */ { printf("

Show only transcripts with these accessions: "); char varName[1024]; safef(varName, sizeof(varName), "%s.nameFilter", name); char *onlyTransStr = cartUsualString(cart, varName, ""); cgiMakeTextVar(varName, onlyTransStr, 60); printInfoIcon("Enter the primary accession of the track, so RefSeq IDs for the RefSeq track, Gencode IDs for the Gencode track, etc. Separate multiple accessions with commas."); puts("

\n\n"); } boolean tdbSupportsColorOverride(struct trackDb *tdb) /* Return TRUE if this track type supports the color override feature. */ { if (!cfgOptionBooleanDefault("showColorPicker", FALSE)) return FALSE; char *type = tdb->type; char *track = tdb->track; // Blacklist tracks that use custom rendering incompatible with color override if (startsWith("gtexGene", track) || startsWith("gtexEqtlCluster", track) || startsWith("gtexEqtlTissue", track)) return FALSE; return !tdbIsComposite(tdb) && (startsWithWord("bed", type) || startsWithWord("bigBed", type) || startsWithWord("genePred", type) || startsWithWord("bigGenePred", type) || startsWithWord("wig", type) || startsWithWord("bigWig", type) || startsWithWord("rmsk", type) || startsWithWord("interact", type) || startsWithWord("bigInteract", type) || startsWithWord("bigLolly", type) || startsWithWord("vcfTabix", type) || startsWithWord("vcf", type) || startsWithWord("bigDbSnp", type)); } void colorTrackOption(struct cart *cart, char *name, struct trackDb *tdb) /* color picker for overriding track color */ { char varName[1024]; safef(varName, sizeof(varName), "%s.colorOverride", name); char defaultColor[16]; safef(defaultColor, sizeof(defaultColor), "#%02x%02x%02x", tdb->colorR, tdb->colorG, tdb->colorB); char *rawCartValue = cartOptionalString(cart, varName); boolean hasOverride = (rawCartValue != NULL && rawCartValue[0] != '\0'); char *colorValue = hasOverride ? rawCartValue : defaultColor; char checkVar[1024]; safef(checkVar, sizeof(checkVar), "%s.colorOverrideOn", name); boolean isOn = cartUsualBoolean(cart, checkVar, hasOverride); printf("
Override track color: "); cgiMakeCheckBox(checkVar, isOn); printf(" ", varName, varName, htmlEncode(colorValue)); // colorValue may be a cart override, escape printf(" \n", varName); jsInlineF( "(function() {\n" " var textEl = document.getElementById('%s_text');\n" " var pickerEl = document.getElementById('%s_picker');\n" " var checkEl = document.querySelector('input[type=checkbox][name=\"%s\"]');\n" " $(pickerEl).spectrum({\n" " color: textEl.value,\n" " showPalette: true,\n" " showSelectionPalette: true,\n" " showInitial:true,\n" " showInput: true,\n" " preferredFormat: 'hex',\n" " hideAfterPaletteSelect: true,\n" " change: function(color) { textEl.value = color.toHexString(); checkEl.checked = true; }\n" " });\n" " textEl.addEventListener('change', function() {\n" " $(pickerEl).spectrum('set', textEl.value);\n" " checkEl.checked = true;\n" " });\n" "})();\n", varName, varName, checkVar); puts("\n"); } void wiggleScaleDropDownJavascript(char *name) /* print some js that deactivates the min/max range if autoscaling is activated */ { struct dyString *dy = dyStringNew(1024); dyStringPrintf(dy, " $(\"[name='%s.autoScale']\").change(function()\n", name); dyStringPrintf(dy, " {\n"); dyStringPrintf(dy, " val= $(this).find(':selected').val(); \n"); dyStringPrintf(dy, " if (val!=\"use vertical viewing range setting\")\n"); dyStringPrintf(dy, " {\n"); dyStringPrintf(dy, " $(\"[name='%s.minY']\")[0].disabled=true;\n", name); dyStringPrintf(dy, " $(\"[name='%s.maxY']\")[0].disabled=true;\n", name); dyStringPrintf(dy, " $(\".%sAutoScaleDesc\").attr('style', 'color:grey;');\n", name); dyStringPrintf(dy, " }\n"); dyStringPrintf(dy, " else\n"); dyStringPrintf(dy, " {\n"); dyStringPrintf(dy, " $(\"[name='%s.minY']\")[0].disabled=false;\n", name); dyStringPrintf(dy, " $(\"[name='%s.maxY']\")[0].disabled=false;\n", name); dyStringPrintf(dy, " $(\".%sAutoScaleDesc\").attr('style', 'color:black;');\n", name); dyStringPrintf(dy, " }\n"); dyStringPrintf(dy, " });\n"); dyStringPrintf(dy, "\n"); dyStringPrintf(dy, " $( document ).ready(function()\n"); dyStringPrintf(dy, " {\n"); dyStringPrintf(dy, " val= $(\"[name='%s.autoScale']\").find(':selected').val(); \n", name); dyStringPrintf(dy, " if (val==\"auto-scale to data view\")\n"); dyStringPrintf(dy, " {\n"); dyStringPrintf(dy, " $(\"[name='%s.minY']\")[0].disabled=true;\n", name); dyStringPrintf(dy, " $(\"[name='%s.maxY']\")[0].disabled=true;\n", name); dyStringPrintf(dy, " $(\".%sAutoScaleDesc\").attr('style', 'color:grey;');\n", name); dyStringPrintf(dy, " }\n"); dyStringPrintf(dy, " });\n"); jsInline(dy->string); dyStringFree(&dy); } void wigCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* UI for the wiggle track */ { char *typeLine = NULL; /* to parse the trackDb type line */ char *words[8]; /* to parse the trackDb type line */ int wordCount = 0; /* to parse the trackDb type line */ char option[256]; double minY; /* from trackDb or cart */ double maxY; /* from trackDb or cart */ double tDbMinY; /* data range limits from trackDb type line */ double tDbMaxY; /* data range limits from trackDb type line */ char *horizontalGrid = NULL; /* Grid lines, off by default */ char *transformFunc = NULL; /* function to transform data points */ char *alwaysZero = NULL; /* Always include 0 in range */ char *lineBar; /* Line or Bar graph */ char *autoScale; /* Auto scaling on or off */ char *windowingFunction; /* Maximum, Mean, or Minimum */ char *smoothingWindow; /* OFF or [2:16] */ char *yLineMarkOnOff; /* user defined Y marker line to draw */ double yLineMark; /* from trackDb or cart */ int maxHeightPixels = atoi(DEFAULT_HEIGHT_PER); int minHeightPixels = MIN_HEIGHT_PER; int defaultHeight = maxHeightPixels; /* pixels per item */ boxed = cfgBeginBoxAndTitle(tdb, boxed, title); wigFetchMinMaxPixelsWithCart(cart,tdb,name,&minHeightPixels, &maxHeightPixels, &defaultHeight); typeLine = cloneString(tdb->type); wordCount = chopLine(typeLine,words); wigFetchMinMaxYWithCart(cart, tdb, name, &minY, &maxY, &tDbMinY, &tDbMaxY, wordCount, words); freeMem(typeLine); wigFetchTransformFuncWithCart(cart,tdb,name, &transformFunc); wigFetchAlwaysZeroWithCart(cart,tdb,name, &alwaysZero); wigFetchHorizontalGridWithCart(cart,tdb,name, &horizontalGrid); wigFetchAutoScaleWithCart(cart,tdb,name, &autoScale); wigFetchGraphTypeWithCart(cart,tdb,name, &lineBar); wigFetchWindowingFunctionWithCart(cart,tdb,name, &windowingFunction); wigFetchSmoothingWindowWithCart(cart,tdb,name, &smoothingWindow); wigFetchYLineMarkWithCart(cart,tdb,name, &yLineMarkOnOff); wigFetchYLineMarkValueWithCart(cart,tdb,name, &yLineMark); boolean doNegative = wigFetchDoNegativeWithCart(cart,tdb,tdb->track, (char **) NULL); boolean doSequenceLogo = wigFetchDoSequenceLogoWithCart(cart,tdb,tdb->track, (char **) NULL); printf(""); boolean isLogo = ((tdb->parent != NULL) && trackDbSetting(tdb->parent, "logo") != NULL); boolean parentLevel = isNameAtParentLevel(tdb, name); boolean didAggregate = FALSE; if (parentLevel && !isLogo) { assert(tdb->parent != NULL); char *aggregate = trackDbSetting(tdb->parent, "aggregate"); if (aggregate != NULL && parentLevel) { char *aggregateVal = cartOrTdbString(cart, tdb->parent, "aggregate", NULL); safef(option, sizeof(option), "%s.%s", name, AGGREGATE); if (isCustomComposite(tdb)) { printf(""); if (sameString(aggregateVal, WIG_AGGREGATE_STACKED) && sameString(windowingFunction, "mean+whiskers")) { windowingFunction = "maximum"; } didAggregate = TRUE; } if (isCustomComposite(tdb)) { /* char *viewFuncVal = cartOrTdbString(cart, tdb->parent, "viewFunc", NULL); printf(""); } printf(""); printf(""); } printf("" ""); printf(""); if (!isLogo) { printf(""); printf(""); printf(""); printf(""); printf("" "" "

Merge method:	"); aggregateExtraDropDown(option, aggregateVal); } else { printf("
Overlay method:	"); aggregateDropDown(option, aggregateVal); } puts("
Math method:	"); safef(option, sizeof(option), "%s.%s", name, VIEWFUNC); viewFuncDropDown(option, viewFuncVal); */ printf("
Missing data treatment:	"); char *missingMethodVal = cartOrTdbString(cart, tdb->parent, "missingMethod", NULL); boolean missingIsZero = (missingMethodVal == NULL) \|\| differentString(missingMethodVal, "missing"); char buffer[1024]; safef(buffer, sizeof buffer, "%s.missingMethod",name); cgiMakeOnEventRadioButtonWithClass(buffer, "zero", missingIsZero, "allOrOnly", "click", NULL); puts("missing is zero "); cgiMakeOnEventRadioButtonWithClass(buffer, "missing", !missingIsZero, "allOrOnly", "click", NULL); printf("math with missing values is missing"); } } if (!isLogo) { printf("
Type of graph:	"); safef( option, sizeof(option), "%s.%s", name, LINEBAR ); wiggleGraphDropDown(option, lineBar); if (boxed) { printf("	"); printf("Graph configuration help",WIGGLE_HELP_PAGE); } puts("
Track height:	"); safef(option, sizeof(option), "%s.%s", name, HEIGHTPER ); cgiMakeIntVarWithLimits(option, defaultHeight, "Track height",0, minHeightPixels, maxHeightPixels); printf("pixels (range: %d to %d)", minHeightPixels, maxHeightPixels); puts("
Data view scaling:	"); safef(option, sizeof(option), "%s.%s", name, AUTOSCALE ); if (tdb->parent \|\| tdb->subtracks) wiggleScaleDropDownParent(option, autoScale); else wiggleScaleDropDown(option, autoScale); wiggleScaleDropDownJavascript(name); if (!isLogo) { safef(option, sizeof(option), "%s.%s", name, ALWAYSZERO); printf("Always include zero: "); wiggleAlwaysZeroDropDown(option, alwaysZero); puts("
Vertical viewing range:	min: ", name); safef(option, sizeof(option), "%s.%s", name, MIN_Y ); cgiMakeDoubleVarWithLimits(option, minY, "Range min", 0, NO_VALUE, NO_VALUE); printf("	max: "); safef(option, sizeof(option), "%s.%s", name, MAX_Y ); cgiMakeDoubleVarWithLimits(option, maxY, "Range max", 0, NO_VALUE, NO_VALUE); if (!isCustomComposite(tdb)) printf(" (range: %g to %g)", tDbMinY, tDbMaxY); puts("
Transform function:	"); safef(option, sizeof(option), "%s.%s", name, TRANSFORMFUNC); printf("Transform data points by: "); wiggleTransformFuncDropDown(option, transformFunc); puts("
Windowing function:	"); safef(option, sizeof(option), "%s.%s", name, WINDOWINGFUNCTION ); wiggleWindowingDropDown(option, windowingFunction); puts("	Smoothing window:	"); safef(option, sizeof(option), "%s.%s", name, SMOOTHINGWINDOW ); wiggleSmoothingDropDown(option, smoothingWindow); puts(" pixels
Negate values:	"); safef(option, sizeof(option), "%s.%s", name, DONEGATIVEMODE ); cgiMakeCheckBox(option, doNegative); puts("
Draw y indicator lines:	"); printf("at y = 0.0:"); safef(option, sizeof(option), "%s.%s", name, HORIZGRID ); wiggleGridDropDown(option, horizontalGrid); printf(" at y ="); safef(option, sizeof(option), "%s.%s", name, YLINEMARK ); cgiMakeDoubleVarInRange(option, yLineMark, "Indicator at Y", 0, NULL, NULL); safef(option, sizeof(option), "%s.%s", name, YLINEONOFF ); wiggleYLineMarkDropDown(option, yLineMarkOnOff); char *logoMaf = trackDbSetting(tdb, "logoMaf"); if (logoMaf) { printf("
Draw sequence logo when near base level:	"); safef(option, sizeof(option), "%s.%s", name, DOSEQUENCELOGOMODE ); cgiMakeCheckBox(option, doSequenceLogo); } } if (boxed) puts("

"); else { puts(""); if (!isLogo) printf("Graph configuration help",WIGGLE_HELP_PAGE); } // add a little javascript call to make sure we don't get whiskers with stacks in multiwigs if (didAggregate) jsInlineF("$(function () { multiWigSetupOnChange('%s'); });\n", name); cfgEndBox(boxed); } void filterButtons(char *filterTypeVar, char *filterTypeVal, boolean none) /* Put up some filter buttons. */ { printf("Filter: "); radioButton(filterTypeVar, filterTypeVal, "red"); radioButton(filterTypeVar, filterTypeVal, "green"); radioButton(filterTypeVar, filterTypeVal, "blue"); radioButton(filterTypeVar, filterTypeVal, "exclude"); radioButton(filterTypeVar, filterTypeVal, "include"); if (none) radioButton(filterTypeVar, filterTypeVal, "none"); } void radioButton(char *var, char *val, char *ourVal) /* Print one radio button */ { cgiMakeRadioButton(var, ourVal, sameString(ourVal, val)); printf("%s ", ourVal); } void oneMrnaFilterUi(struct controlGrid *cg, struct trackDb *tdb, char *text, char *var, char *suffix, struct cart *cart) /* Print out user interface for one type of mrna filter. */ { controlGridStartCell(cg); printf("%s:
", text); boolean parentLevel = isNameAtParentLevel(tdb,var); cgiMakeTextVar(var, cartUsualStringClosestToHome(cart, tdb, parentLevel,suffix, ""), 19); controlGridEndCell(cg); } void bedFiltCfgUi(struct cart *cart, struct trackDb *tdb, char *prefix, char *title, boolean boxed) /* Put up UI for an "bedFilter" tracks. */ { struct mrnaUiData *mud = newBedUiData(prefix); struct mrnaFilter *fil; struct controlGrid *cg = NULL; boolean parentLevel = isNameAtParentLevel(tdb,prefix); char *filterTypeVal = cartUsualStringClosestToHome(cart, tdb, parentLevel, mud->filterTypeSuffix, "red"); boxed = cfgBeginBoxAndTitle(tdb, boxed, title); /* Define type of filter. */ printf("

\n"); char buffer[256]; safef(buffer, sizeof buffer,"%s.%s",prefix,mud->filterTypeSuffix); filterButtons(buffer, filterTypeVal, FALSE); printf("
"); /* List various fields you can filter on. */ cg = startControlGrid(4, NULL); for (fil = mud->filterList; fil != NULL; fil = fil->next) { safef(buffer, sizeof buffer,"%s.%s",prefix,fil->suffix); oneMrnaFilterUi(cg, tdb, fil->label, buffer, fil->suffix, cart); } endControlGrid(&cg); cfgEndBox(boxed); } void genbankShowPatentControl(struct cart *cart, struct trackDb *tdb, char *prefix) /* controls for enabling display of GENBANK RNA patent sequences */ { char name[256]; safef(name, sizeof(name), "%s.%s", prefix, SHOW_PATENT_SEQUENCES_SUFFIX); printf("

Show patent sequences:"); cgiMakeCheckBox(name, cartUsualBoolean(cart, name, FALSE)); } void mrnaCfgUi(struct cart *cart, struct trackDb *tdb, char *prefix, char *title, boolean boxed) /* Put up UI for an mRNA (or EST) track. */ { boolean isXeno = (sameString(tdb->track, "xenoMrna") || sameString(tdb->track, "xenoEst")); struct mrnaUiData *mud = newMrnaUiData(prefix, isXeno); struct mrnaFilter *fil; struct controlGrid *cg = NULL; boolean parentLevel = isNameAtParentLevel(tdb,prefix); char *filterTypeVal = cartUsualStringClosestToHome(cart, tdb, parentLevel, mud->filterTypeSuffix,"red"); char *logicTypeVal = cartUsualStringClosestToHome(cart, tdb, parentLevel, mud->logicTypeSuffix, "and"); boxed = cfgBeginBoxAndTitle(tdb, boxed, title); /* Define type of filter. */ char buffer[256]; safef(buffer,sizeof buffer,"%s.%s",prefix,mud->filterTypeSuffix); filterButtons(buffer, filterTypeVal, FALSE); printf(" Combination Logic: "); safef(buffer,sizeof buffer,"%s.%s",prefix,mud->logicTypeSuffix); radioButton(buffer, logicTypeVal, "and"); radioButton(buffer, logicTypeVal, "or"); printf("
\n"); /* List various fields you can filter on. */ printf("\n"); cg = startControlGrid(4, NULL); for (fil = mud->filterList; fil != NULL; fil = fil->next) { safef(buffer,sizeof buffer,"%s.%s",prefix,fil->suffix); oneMrnaFilterUi(cg, tdb, fil->label, buffer, fil->suffix, cart); } endControlGrid(&cg); baseColorDrawOptDropDown(cart, tdb); indelShowOptions(cart, tdb); if (sameString(tdb->track, "mrna") || sameString(tdb->track, "xenoMrna")) genbankShowPatentControl(cart, tdb, prefix); wigOption(cart, prefix, title, tdb); cfgEndBox(boxed); } void scoreGrayLevelCfgUi(struct cart *cart, struct trackDb *tdb, char *prefix, int scoreMax) // If scoreMin has been set, let user select the shade of gray for that score, in case // the default is too light to see or darker than necessary. { boolean parentLevel = isNameAtParentLevel(tdb,prefix); char *scoreMinStr = trackDbSettingClosestToHome(tdb, GRAY_LEVEL_SCORE_MIN); if (scoreMinStr != NULL) { int scoreMin = atoi(scoreMinStr); // maxShade=9 taken from hgTracks/simpleTracks.c. Ignore the 10 in shadesOfGray[10+1] -- // maxShade is used to access the array. int maxShade = 9; int scoreMinGrayLevel = scoreMin * maxShade/scoreMax; if (scoreMinGrayLevel <= 0) scoreMinGrayLevel = 1; char *setting = trackDbSettingClosestToHome(tdb, MIN_GRAY_LEVEL); int minGrayLevel = cartUsualIntClosestToHome(cart, tdb, parentLevel, MIN_GRAY_LEVEL, setting ? atoi(setting) : scoreMinGrayLevel); if (minGrayLevel <= 0) minGrayLevel = 1; if (minGrayLevel > maxShade) minGrayLevel = maxShade; puts("\nShade of lowest-scoring items: "); // Add javascript to select so that its color is consistent with option colors: int level = 255 - (255*minGrayLevel / maxShade); printf("\n"); } } static boolean getScoreDefaultsFromTdb(struct trackDb *tdb, char *scoreName,char *defaults, char**min,char**max) // returns TRUE if defaults exist and sets the string pointer (because they may be float or int) // if min or max are set, then they should be freed { if (min) *min = NULL; // default these outs! if (max) *max = NULL; char *setting = trackDbSettingClosestToHome(tdb, scoreName); if (setting) { if (strchr(setting,':') != NULL) return colonPairToStrings(setting,min,max); else if (min) *min = cloneString(setting); return TRUE; } return FALSE; } static void setAsNewFilterType(struct trackDb *tdb, char *name, char *field) /* put the full name of the trackDb variable in a hash of field names if it's specified in the "new" way */ { struct hash *hash = tdb->isNewFilterHash; if (hash == NULL) hash = tdb->isNewFilterHash = newHash(5); hashAdd(hash, field, name); } static char *isNewFilterType(struct trackDb *tdb, char *name) /* check to see if a field name is in the "new" hash. If it is, return the full trackDb variable name */ { if ((tdb == NULL) || (tdb->isNewFilterHash == NULL)) return NULL; struct hashEl *hel = hashLookup(tdb->isNewFilterHash, name); if (hel == NULL) return NULL; return hel->val; } char *getScoreNameAdd(struct trackDb *tdb, char *scoreName, char *add) // Add a suffix to a filter for more information { char scoreLimitName[1024]; char *name = cloneString(scoreName); char *dot = strchr(name, '.'); if ((dot != NULL) && (isNewFilterType(tdb, dot+1) != NULL)) { *dot++ = 0; safef(scoreLimitName, sizeof(scoreLimitName), "%s%s.%s", name, add, dot); } else safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, add); return cloneString(scoreLimitName); } static boolean getScoreLimitsFromTdb(struct trackDb *tdb, char *scoreName,char *defaults, char**min,char**max) // returns TRUE if limits exist and sets the string pointer (because they may be float or int) // if min or max are set, then they should be freed { if (min) *min = NULL; // default these outs! if (max) *max = NULL; char *scoreLimitName = getScoreNameAdd(tdb, scoreName, _LIMITS); char *setting = trackDbSettingClosestToHome(tdb, scoreLimitName); if (setting) { return colonPairToStrings(setting,min,max); } else { if (min) { scoreLimitName = getScoreNameAdd(tdb, scoreName, _MIN); setting = trackDbSettingClosestToHome(tdb, scoreLimitName); if (setting) *min = cloneString(setting); } if (max) { scoreLimitName = getScoreNameAdd(tdb, scoreName, _MAX); setting = trackDbSettingClosestToHome(tdb, scoreLimitName); if (setting) *max = cloneString(setting); } return TRUE; } if (defaults != NULL && ((min && *min == NULL) || (max && *max == NULL))) { char *minLoc=NULL; char *maxLoc=NULL; if (colonPairToStrings(defaults,&minLoc,&maxLoc)) { if (min && *min == NULL && minLoc != NULL) *min=minLoc; else freeMem(minLoc); if (max && *max == NULL && maxLoc != NULL) *max=maxLoc; else freeMem(maxLoc); return TRUE; } } return FALSE; } void getScoreIntRangeFromCart(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *scoreName, int *limitMin, int *limitMax,int *min,int *max) // gets an integer score range from the cart, but the limits from trackDb // for any of the pointers provided, will return a value found, if found, else it's contents // are undisturbed (use NO_VALUE to recognize unavaliable values) { char scoreLimitName[128]; char *deMin=NULL,*deMax=NULL; if ((limitMin || limitMax) && getScoreLimitsFromTdb(tdb,scoreName,NULL,&deMin,&deMax)) { if (deMin != NULL && limitMin) *limitMin = atoi(deMin); if (deMax != NULL && limitMax) *limitMax = atoi(deMax); freeMem(deMin); freeMem(deMax); } if ((min || max) && getScoreDefaultsFromTdb(tdb,scoreName,NULL,&deMin,&deMax)) { if (deMin != NULL && min) *min = atoi(deMin); if (deMax != NULL && max) *max =atoi(deMax); freeMem(deMin); freeMem(deMax); } if (max) { safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, _MAX); deMax = cartOptionalStringClosestToHome(cart, tdb,parentLevel,scoreLimitName); if (deMax != NULL) *max = atoi(deMax); } if (min) { // Warning: name changes if max! safef(scoreLimitName, sizeof(scoreLimitName), "%s%s", scoreName, (max && deMax? _MIN:"")); deMin = cartOptionalStringClosestToHome(cart, tdb,parentLevel,scoreLimitName); if (deMin != NULL) *min = atoi(deMin); } // Defaulting min and max within limits. Sorry for the horizontal ifs, // but stacking the group makes them easier to follow if (min && limitMin && *limitMin != NO_VALUE && (*min == NO_VALUE || *min < *limitMin)) *min = *limitMin; if (min && limitMax && *limitMax != NO_VALUE && *min > *limitMax) *min = *limitMax; if (max && limitMax && *limitMax != NO_VALUE && (*max == NO_VALUE || *max > *limitMax)) *max = *limitMax; if (max && limitMin && *limitMin != NO_VALUE && *max < *limitMin) *max = *limitMin; } void getScoreFloatRangeFromCart(struct cart *cart, struct trackDb *tdb, boolean parentLevel, char *scoreName, double *limitMin,double *limitMax,double*min,double*max) // gets an double score range from the cart, but the limits from trackDb // for any of the pointers provided, will return a value found, if found, else it's contents // are undisturbed (use NO_VALUE to recognize unavaliable values) { char *deMin=NULL,*deMax=NULL; if ((limitMin || limitMax) && getScoreLimitsFromTdb(tdb,scoreName,NULL,&deMin,&deMax)) { if (deMin != NULL && limitMin) *limitMin = strtod(deMin,NULL); if (deMax != NULL && limitMax) *limitMax =strtod(deMax,NULL); freeMem(deMin); freeMem(deMax); } if ((min || max) && getScoreDefaultsFromTdb(tdb,scoreName,NULL,&deMin,&deMax)) { if (deMin != NULL && min) *min = strtod(deMin,NULL); if (deMax != NULL && max) *max =strtod(deMax,NULL); freeMem(deMin); freeMem(deMax); } if (max) { char *scoreLimitName = getScoreNameAdd(tdb, scoreName, _MAX); deMax = cartOptionalStringClosestToHome(cart, tdb,parentLevel,scoreLimitName); if (deMax != NULL) *max = strtod(deMax,NULL); } if (min) { // name is always {filterName}Min char *scoreLimitName = getScoreNameAdd(tdb, scoreName, _MIN); deMin = cartOptionalStringClosestToHome(cart, tdb,parentLevel,scoreLimitName); if (deMin == NULL) deMin = cartOptionalStringClosestToHome(cart, tdb,parentLevel,scoreName); if (deMin != NULL) *min = strtod(deMin,NULL); } // Defaulting min and max within limits. Sorry for the horizontal ifs, // but stacking the group makes them easier to follow if (min && limitMin && (int)(*limitMin) != NO_VALUE && ((int)(*min) == NO_VALUE || *min < *limitMin)) *min = *limitMin; if (min && limitMax && (int)(*limitMax) != NO_VALUE && *min > *limitMax) *min = *limitMax; if (max && limitMax && (int)(*limitMax) != NO_VALUE && ((int)(*max) == NO_VALUE || *max > *limitMax)) *max = *limitMax; if (max && limitMin && (int)(*limitMin) != NO_VALUE && *max < *limitMin) *max = *limitMin; } static boolean showScoreFilter(struct cart *cart, struct trackDb *tdb, boolean *opened, boolean boxed, boolean parentLevel,char *name, char *title, char *label, char *scoreName, boolean isHighlight) // Shows a score filter control with minimum value and optional range { char *setting = trackDbSetting(tdb, scoreName); if (setting) { if (*opened == FALSE) { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); puts("
"); *opened = TRUE; } printf("
%s: ",label); char varName[256]; char altLabel[256]; char *filterName = getScoreNameAdd(tdb, scoreName, _BY_RANGE); boolean filterByRange = trackDbSettingClosestToHomeOn(tdb, filterName); double minLimit=NO_VALUE,maxLimit=NO_VALUE; double minVal=minLimit,maxVal=maxLimit; colonPairToDoubles(setting,&minVal,&maxVal); getScoreFloatRangeFromCart(cart,tdb,parentLevel,scoreName,&minLimit,&maxLimit, &minVal, &maxVal); filterName = getScoreNameAdd(tdb, scoreName, filterByRange ? _MIN:""); safef(varName, sizeof(varName), "%s.%s", name, filterName); safef(altLabel, sizeof(altLabel), "%s%s", (filterByRange ? "Minimum " : ""), htmlEncode(htmlTextStripTags(label))); cgiMakeDoubleVarWithLimits(varName,minVal, altLabel, 0,minLimit, maxLimit); if (filterByRange) { printf(" to "); filterName = getScoreNameAdd(tdb, scoreName, _MAX); safef(varName, sizeof(varName), "%s.%s", name, filterName); safef(altLabel, sizeof(altLabel), "%s%s", (filterByRange?"Maximum ":""), label); cgiMakeDoubleVarWithLimits(varName,maxVal, altLabel, 0,minLimit, maxLimit); } safef(altLabel, sizeof(altLabel), "%s", (filterByRange?"": "colspan=3")); if (minLimit != NO_VALUE && maxLimit != NO_VALUE) printf(" (%s to %s)",altLabel,shorterDouble(minLimit), shorterDouble(maxLimit)); else if (minLimit != NO_VALUE) printf(" (minimum %s)",altLabel,shorterDouble(minLimit)); else if (maxLimit != NO_VALUE) printf(" (maximum %s)",altLabel,shorterDouble(maxLimit)); else printf(" "); return TRUE; } return FALSE; } static boolean isHighlightFilterPrefix(char *lowName) // Distinguish highlight filter passes from filter passes so we look up the right priority var. { return startsWith("highlight", lowName); } static double lookupFilterPriority(struct trackDb *tdb, char *fieldName, boolean isHighlight) // Find a filterPriority. / FilterPriority setting (or highlight equivalent) in tdb. // Returns TRACKDB_FILTER_DEFAULT_PRIORITY when no setting is found. { char setting[1024]; char *priorityLow = isHighlight ? HIGHLIGHT_PRIORITY_NAME_LOW : FILTER_PRIORITY_NAME_LOW; char *priorityCap = isHighlight ? HIGHLIGHT_PRIORITY_NAME_CAP : FILTER_PRIORITY_NAME_CAP; safef(setting, sizeof setting, "%s.%s", priorityLow, fieldName); char *val = trackDbSetting(tdb, setting); if (val == NULL) { safef(setting, sizeof setting, "%s%s", fieldName, priorityCap); val = trackDbSetting(tdb, setting); } if (val == NULL) return TRACKDB_FILTER_DEFAULT_PRIORITY; return atof(val); } static int trackDbFilterPriCmp(const void *va, const void *vb) // Sort trackDbFilters by priority ascending; tiebreak by name for determinism. { const struct trackDbFilter *a = *((struct trackDbFilter **)va); const struct trackDbFilter *b = *((struct trackDbFilter **)vb); if (a->priority < b->priority) return -1; if (a->priority > b->priority) return 1; return strcmp(a->name, b->name); } struct trackDbFilter *tdbGetTrackFilters( struct trackDb *tdb, char * lowWild, char * lowName, char * capWild, char * capName) // figure out which of the ways to specify trackDb filter variables we're using // and return the setting { struct trackDbFilter *trackDbFilterList = NULL; boolean isHighlight = isHighlightFilterPrefix(lowName); struct slName *filterSettings = trackDbSettingsWildMatch(tdb, lowWild); if (filterSettings) { struct trackDbFilter *tdbFilter; struct slName *filter = NULL; while ((filter = slPopHead(&filterSettings)) != NULL) { AllocVar(tdbFilter); slAddHead(&trackDbFilterList, tdbFilter); tdbFilter->name = cloneString(filter->name); tdbFilter->setting = trackDbSetting(tdb, filter->name); tdbFilter->fieldName = extractFieldNameNew(filter->name, lowName); tdbFilter->priority = lookupFilterPriority(tdb, tdbFilter->fieldName, isHighlight); setAsNewFilterType(tdb, tdbFilter->name, tdbFilter->fieldName); } } filterSettings = trackDbSettingsWildMatch(tdb, capWild); if (filterSettings) { struct trackDbFilter *tdbFilter; struct slName *filter = NULL; while ((filter = slPopHead(&filterSettings)) != NULL) { if (differentString(filter->name,NO_SCORE_FILTER)) { AllocVar(tdbFilter); slAddHead(&trackDbFilterList, tdbFilter); tdbFilter->name = cloneString(filter->name); tdbFilter->setting = trackDbSetting(tdb, filter->name); tdbFilter->fieldName = extractFieldNameOld(filter->name, capName); tdbFilter->priority = lookupFilterPriority(tdb, tdbFilter->fieldName, isHighlight); char *name; if ((name = isNewFilterType(tdb, tdbFilter->fieldName) ) != NULL) errAbort("error specifying a field's filters in both old (%s) and new format (%s).", tdbFilter->name, name); } } } slSort(&trackDbFilterList, trackDbFilterPriCmp); return trackDbFilterList; } struct trackDbFilter *tdbGetTrackNumFilters( struct trackDb *tdb) // get the number filters out of trackDb { return tdbGetTrackFilters( tdb, FILTER_NUMBER_WILDCARD_LOW, FILTER_NUMBER_NAME_LOW, FILTER_NUMBER_WILDCARD_CAP, FILTER_NUMBER_NAME_CAP); } struct trackDbFilter *tdbGetTrackTextFilters( struct trackDb *tdb) // get the text filters out of trackDb { return tdbGetTrackFilters( tdb, FILTER_TEXT_WILDCARD_LOW, FILTER_TEXT_NAME_LOW, FILTER_TEXT_WILDCARD_CAP, FILTER_TEXT_NAME_CAP); } struct trackDbFilter *tdbGetTrackFilterByFilters( struct trackDb *tdb) // get the values filters out of trackDb { return tdbGetTrackFilters( tdb, FILTER_VALUES_WILDCARD_LOW, FILTER_VALUES_NAME_LOW, FILTER_VALUES_WILDCARD_CAP, FILTER_VALUES_NAME_CAP); } struct trackDbFilter *tdbGetTrackNumHighlights( struct trackDb *tdb) // get the number filters out of trackDb { return tdbGetTrackFilters( tdb, HIGHLIGHT_NUMBER_WILDCARD_LOW, HIGHLIGHT_NUMBER_NAME_LOW, HIGHLIGHT_NUMBER_WILDCARD_CAP, HIGHLIGHT_NUMBER_NAME_CAP); } struct trackDbFilter *tdbGetTrackTextHighlights( struct trackDb *tdb) // get the text filters out of trackDb { return tdbGetTrackFilters( tdb, HIGHLIGHT_TEXT_WILDCARD_LOW, HIGHLIGHT_TEXT_NAME_LOW, HIGHLIGHT_TEXT_WILDCARD_CAP, HIGHLIGHT_TEXT_NAME_CAP); } struct trackDbFilter *tdbGetTrackHighlightByHighlights( struct trackDb *tdb) // get the values filters out of trackDb { return tdbGetTrackFilters( tdb, HIGHLIGHT_VALUES_WILDCARD_LOW, HIGHLIGHT_VALUES_NAME_LOW, HIGHLIGHT_VALUES_WILDCARD_CAP, HIGHLIGHT_VALUES_NAME_CAP); } char *prevHighlightColor(struct cart *cart, struct trackDb *tdb) /* Return the cart string for the highlight color if it has been changed else the default */ { return cartOrTdbString(cart, tdb, HIGHLIGHT_COLOR_CART_VAR, HIGHLIGHT_COLOR_DEFAULT); } static boolean didHighlightSelector = FALSE; void printHighlightColorPicker(struct cart *cart, struct trackDb *tdb) { if (didHighlightSelector) return; jsIncludeFile("ajax.js", NULL); jsIncludeFile("hui.js", NULL); puts("
"); char *text = "Note that multiple highlight selections use the same color, and are applied successively. So any item that meets at least one criteria will be highlighted."; printInfoIcon(text); puts("
"); puts("
"); jsInlineF("var cartHighlightColor = \"%s\"\n;", prevHighlightColor(cart, tdb)); jsInlineF("makeHighlightPicker(\"%s.highlightColor\", document.getElementById(\"hgTrackUiColorPicker\"), \"%s\");\n", tdb->track, tdb->track); } int defaultFieldLocation(char *field) /* Sometimes we get bigBed filters with field names that are not in the AS file. * Try to guess what the user means. */ { if (sameString("score", field)) return 4; if (sameString("signal", field)) return 6; if (sameString("signalValue", field)) return 6; if (sameString("pValue", field)) return 7; if (sameString("qValue", field)) return 8; return -1; } static int numericFiltersShowAll(char *db, struct cart *cart, struct trackDb *tdb, boolean *opened, boolean boxed, boolean parentLevel,char *name, char *title, boolean isHighlight) // Shows all *Filter style filters. Note that these are in random order and have no graceful title { int count = 0; struct trackDbFilter *trackDbFilters = NULL; if (isHighlight) trackDbFilters = tdbGetTrackNumHighlights(tdb); else trackDbFilters = tdbGetTrackNumFilters(tdb); if (trackDbFilters) { puts("
"); struct trackDbFilter *filter = NULL; struct sqlConnection *conn = NULL; if (!isHubTrack(db) && !isGenArk(db)) conn = hAllocConnTrack(db, tdb); struct asObject *as = asForTdb(conn, tdb); hFreeConn(&conn); while ((filter = slPopHead(&trackDbFilters)) != NULL) { char *field = filter->fieldName; char *scoreName = cloneString(filter->name); char *trackDbLabel = getLabelSetting(cart, tdb, field); if (as != NULL) { struct asColumn *asCol = asColumnFind(as, field); if (asCol != NULL) { // Found label so replace field; strip "|..." suffix used for detail page field = asCol->comment; char *pipe = strchr(field, '|'); if (pipe != NULL) field = cloneStringZ(field, pipe - field); } else if (defaultFieldLocation(field) < 0) errAbort("Building filter on field %s which is not in AS file.", field); } char labelBuf[1024]; char *label = labelBuf; char *filterName = getScoreNameAdd(tdb, scoreName, _BY_RANGE); boolean filterByRange = trackDbSettingClosestToHomeOn(tdb, filterName); if (trackDbLabel) label = trackDbLabel; else { if (isHighlight) safef(labelBuf, sizeof(labelBuf),"%s%s", filterByRange ? "": "Highlight items with Minimum ", field ); else safef(labelBuf, sizeof(labelBuf),"%s%s", filterByRange ? "": "Minimum ", field); } if (isHighlight && count == 0) printHighlightColorPicker(cart, tdb); showScoreFilter(cart,tdb,opened,boxed,parentLevel,name,title,label,scoreName,isHighlight); count++; } if (as != NULL) asObjectFree(&as); } if (count > 0) puts("
"); return count; } boolean bedHasFilters(struct trackDb *tdb) // Does track have filters { if (trackDbSettingClosestToHome(tdb, FILTER_BY)) return TRUE; if (trackDbSettingClosestToHome(tdb, GRAY_LEVEL_SCORE_MIN)) return TRUE; struct trackDbFilter *filterSettings = tdbGetTrackNumFilters( tdb); if (filterSettings != NULL) return TRUE; filterSettings = tdbGetTrackTextFilters( tdb); if (filterSettings != NULL) return TRUE; filterSettings = tdbGetTrackFilterByFilters( tdb); if (filterSettings != NULL) return TRUE; return FALSE; } boolean bedScoreHasCfgUi(struct trackDb *tdb) // Confirms that this track has a bedScore Cfg UI { // Assumes that cfgType == cfgBedScore if (trackDbSettingClosestToHome(tdb, FILTER_BY)) return TRUE; if (trackDbSettingClosestToHome(tdb, GRAY_LEVEL_SCORE_MIN)) return TRUE; boolean blocked = FALSE; struct trackDbFilter *filterSettings = tdbGetTrackNumFilters( tdb); if (filterSettings != NULL) { boolean one = FALSE; struct trackDbFilter *oneFilter = filterSettings; char *noScoreFilter = trackDbSetting(tdb, NO_SCORE_FILTER); if (noScoreFilter) blocked = TRUE; for (;oneFilter != NULL;oneFilter=oneFilter->next) { if (differentString(oneFilter->fieldName,"score")) // scoreFilter is implicit { // but could be blocked one = TRUE; break; } } if (one) return TRUE; } if (!blocked) // scoreFilter is implicit unless NO_SCORE_FILTER return TRUE; return FALSE; } char *getFilterType(struct cart *cart, struct trackDb *tdb, char *field, char *def) // figure out how the trackDb is specifying the FILTER_TYPE variable and return its setting { char settingString[4096]; safef(settingString, sizeof settingString, "%s.%s", FILTER_TYPE_NAME_LOW, field); char *setting = cartOrTdbString(cart, tdb, settingString, NULL); if (setting == NULL) { safef(settingString, sizeof settingString, "%s.%s", field, FILTER_TYPE_NAME_CAP); setting = cartOrTdbString(cart, tdb, settingString, NULL); } if (setting == NULL) { safef(settingString, sizeof settingString, "%s%s", field, FILTER_TYPE_NAME_CAP); setting = cartOrTdbString(cart, tdb, settingString, def); } return setting; } static int textFiltersShowAll(char *db, struct cart *cart, struct trackDb *tdb, boolean isHighlight) /* Show all the text filters for this track. */ { int count = 0; struct trackDbFilter *trackDbFilters = NULL; if (isHighlight) trackDbFilters = tdbGetTrackTextHighlights(tdb); else trackDbFilters = tdbGetTrackTextFilters(tdb); if (trackDbFilters) { puts("
"); struct trackDbFilter *filter = NULL; struct sqlConnection *conn = NULL; if (!isHubTrack(db) && !isGenArk(db)) conn = hAllocConnTrack(db, tdb); struct asObject *as = asForTdb(conn, tdb); hFreeConn(&conn); while ((filter = slPopHead(&trackDbFilters)) != NULL) { char *trackDbLabel = getLabelSetting(cart, tdb, filter->fieldName); char *value = cartUsualStringClosestToHome(cart, tdb, FALSE, filter->name, filter->setting); if (as != NULL) { struct asColumn *asCol = asColumnFind(as, filter->fieldName); if (asCol != NULL) { if (trackDbLabel == NULL) trackDbLabel = asCol->comment; } else if (defaultFieldLocation(filter->fieldName) < 0) errAbort("Building filter on field %s which is not in AS file.", filter->fieldName); } if (trackDbLabel == NULL) trackDbLabel = filter->fieldName; if (isHighlight && count == 0) printHighlightColorPicker(cart, tdb); count++; printf("

%s items in '%s' field: ", isHighlight ? "Highlight": "Filter", trackDbLabel); char cgiVar[128]; safef(cgiVar,sizeof(cgiVar),"%s.%s",tdb->track,filter->name); cgiMakeTextVar(cgiVar, value, 45); char *setting = getFilterType(cart, tdb, filter->fieldName, FILTERTEXT_WILDCARD); safef(cgiVar,sizeof(cgiVar),"%s.%s.%s",tdb->track,FILTER_TYPE_NAME_LOW, filter->fieldName); printf(" using "); printf(""); printf(" \n", tdb->track); printf("

"); } // using jquery id= syntax to make sure that selector works even if trackname has a dot in it jsInlineF("$('[class=\"buttonClear-%s\"]').click( function(ev) { \n" "$(ev.target).prevAll('input').val('*').trigger('change');\n" "$(ev.target).prevAll('select').val('%s');\n" "ev.preventDefault();\n" "});", tdb->track, FILTERTEXT_WILDCARD); } return count; } void scoreCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, int maxScore, boolean boxed) // Put up UI for filtering bed track based on a score { char option[256]; if (cartOptionalString(cart, "ajax") == NULL) { webIncludeResourceFile("ui.dropdownchecklist.css"); jsIncludeFile("ui.dropdownchecklist.js",NULL); jsIncludeFile("ddcl.js",NULL); } boolean parentLevel = isNameAtParentLevel(tdb,name); if (parentLevel) if (trackDbSettingOn(tdb->parent, "noParentConfig")) return; boolean skipScoreFilter = FALSE; // Numeric filters are first boolean isBoxOpened = FALSE; if (numericFiltersShowAll(db, cart, tdb, &isBoxOpened, boxed, parentLevel, name, title, FALSE) > 0) skipScoreFilter = TRUE; if (textFiltersShowAll(db, cart, tdb, FALSE)) skipScoreFilter = TRUE; // Add any multi-selects next filterBy_t *filterBySet = filterBySetGet(tdb,cart,name); if (filterBySet != NULL) { if (!tdbIsComposite(tdb) && cartOptionalString(cart, "ajax") == NULL) jsIncludeFile("hui.js",NULL); if (!isBoxOpened) // Note filterBy boxes are not double "boxed", printf("
"); // if there are no other filters filterBySetCfgUi(cart,tdb,filterBySet,TRUE, name); filterBySetFree(&filterBySet); skipScoreFilter = TRUE; } // add any highlights: // Numeric highlights are first if (numericFiltersShowAll(db, cart, tdb, &isBoxOpened, boxed, parentLevel, name, title, TRUE) > 0) { didHighlightSelector = TRUE; skipScoreFilter = TRUE; } if (textFiltersShowAll(db, cart, tdb, TRUE)) { didHighlightSelector = TRUE; skipScoreFilter = TRUE; } filterBy_t *highlightBySet = highlightBySetGet(tdb,cart,name); if (highlightBySet != NULL) { if (!tdbIsComposite(tdb) && cartOptionalString(cart, "ajax") == NULL) jsIncludeFile("hui.js",NULL); if (!didHighlightSelector) printHighlightColorPicker(cart, tdb); if (!isBoxOpened) // Note filterBy boxes are not double "boxed", printf("
"); // if there are no other filters highlightBySetCfgUi(cart,tdb,highlightBySet,TRUE, name, TRUE); filterBySetFree(&highlightBySet); skipScoreFilter = TRUE; } boolean scoreFilterOk = (trackDbSettingClosestToHome(tdb, NO_SCORE_FILTER) == NULL) && !skipScoreFilter; boolean glvlScoreMin = (trackDbSettingClosestToHome(tdb, GRAY_LEVEL_SCORE_MIN) != NULL); if (! (scoreFilterOk || glvlScoreMin)) { if (isBoxOpened) cfgEndBox(boxed); else printf("
"); return; } boxed = cfgBeginBoxAndTitle(tdb, boxed, title); if (scoreFilterOk) { int minLimit=0,maxLimit=maxScore,minVal=0,maxVal=maxScore; getScoreIntRangeFromCart(cart,tdb,parentLevel,SCORE_FILTER,&minLimit,&maxLimit, &minVal, &maxVal); boolean filterByRange = trackDbSettingClosestToHomeOn(tdb, SCORE_FILTER _BY_RANGE); if (filterByRange) { puts("Filter score range: min:"); safef(option, sizeof(option), "%s.%s", name,SCORE_FILTER _MIN); cgiMakeIntVarWithLimits(option, minVal, "Minimum score",0, minLimit,maxLimit); puts("max:"); safef(option, sizeof(option), "%s.%s", name,SCORE_FILTER _MAX); cgiMakeIntVarWithLimits(option, maxVal, "Maximum score",0,minLimit,maxLimit); printf("(%d to %d)\n",minLimit,maxLimit); } else { char* scoreLabel = trackDbSettingClosestToHomeOrDefault(tdb, SCORE_LABEL, "score"); printf("Show only items with %s at or above: ", scoreLabel); safef(option, sizeof(option), "%s.%s", name,SCORE_FILTER); cgiMakeIntVarWithLimits(option, minVal, "Minimum score",0, minLimit,maxLimit); printf(" (range: %d to %d)\n", minLimit, maxLimit); if (!boxed) printf("
\n"); } if (glvlScoreMin) printf("
"); } if (glvlScoreMin) scoreGrayLevelCfgUi(cart, tdb, name, maxScore); // filter top-scoring N items in track char *scoreCtString = trackDbSettingClosestToHome(tdb, "filterTopScorers"); if (scoreCtString != NULL) { // show only top-scoring items. This option only displayed if trackDb // setting exists. Format: filterTopScorers char *words[2]; char *scoreFilterCt = NULL; chopLine(cloneString(scoreCtString), words); safef(option, sizeof(option), "%s.filterTopScorersOn", name); bool doScoreCtFilter = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, "filterTopScorersOn", sameString(words[0], "on")); puts("

"); cgiMakeCheckBox(option, doScoreCtFilter); safef(option, sizeof(option), "%s.filterTopScorersCt", name); scoreFilterCt = cartUsualStringClosestToHome(cart, tdb, parentLevel, "filterTopScorersCt", words[1]); puts(" Show only items in top-scoring "); cgiMakeIntVarWithLimits(option,atoi(scoreFilterCt),"Top-scoring count",0,1,100000); //* Only check size of table if track does not have subtracks */ if ( !parentLevel && hTableExists(db, tdb->table)) printf(" (range: 1 to 100,000 total items: %d)\n",getTableSize(db, tdb->table)); else printf(" (range: 1 to 100,000)\n"); } cfgEndBox(boxed); } // Moved from hgTrackUi for consistency static void filterByChromCfgUi(struct cart *cart, struct trackDb *tdb) { char filterVar[256]; char *filterVal = ""; printf("

Filter by chromosome (e.g. chr10): "); safef(filterVar, sizeof(filterVar), "%s.chromFilter", tdb->track); (void) cartUsualString(cart, filterVar, filterVal); // ignore returned setting cgiMakeTextVar(filterVar, cartUsualString(cart, filterVar, ""), 15); } // Moved from hgTrackUi for consistency void crossSpeciesCfgUi(struct cart *cart, struct trackDb *tdb) // Put up UI for selecting rainbow chromosome color or intensity score. { char colorVar[256]; char *colorSetting; // initial value of chromosome coloring option is "on", unless // overridden by the colorChromDefault setting in the track char *colorDefault = trackDbSettingOrDefault(tdb, "colorChromDefault", "on"); printf("

Color track based on chromosome: "); safef(colorVar, sizeof(colorVar), "%s.color", tdb->track); colorSetting = cartUsualString(cart, colorVar, colorDefault); cgiMakeRadioButton(colorVar, "on", sameString(colorSetting, "on")); printf(" on "); cgiMakeRadioButton(colorVar, "off", sameString(colorSetting, "off")); printf(" off "); printf("

"); filterByChromCfgUi(cart,tdb); } struct slPair *buildFieldList(struct trackDb *tdb, char *trackDbVar, struct asObject *as) /* Build up a hash of a list of fields in an AS file. */ { char *fields = trackDbSettingClosestToHome(tdb, trackDbVar); if (fields == NULL) return NULL; if (sameString(fields, "none")) return slPairNew("none", NULL); struct slPair *list = NULL; struct slName *thisField, *fieldList = slNameListFromComma(fields); for(thisField = fieldList; thisField; thisField = thisField->next) { char *trimLabel = trimSpaces(thisField->name); unsigned colNum = asColumnFindIx(as->columnList, trimLabel); if (colNum == -1) errAbort("cannot find field named '%s' in AS file '%s'", trimLabel, as->name); slAddHead(&list, slPairNew(trimLabel, NULL + colNum)); } slReverse(&list); return list; } void labelCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *prefix) /* If there is a labelFields for a bigBed, this routine is called to put up the label options. */ { // composites can't label because they don't have an autoSql if (tdbIsComposite(tdb)) return; if (trackDbSettingClosestToHomeOn(tdb, "linkIdInName")) return; struct asObject *as = asForDb(tdb, db); if (as == NULL) return; struct slPair *labelList = buildFieldList(tdb, "labelFields", as); struct slPair *defaultLabelList = buildFieldList(tdb, "defaultLabelFields", as); char varName[1024]; if ((labelList == NULL) || sameString(labelList->name, "none")) return; struct slPair *thisLabel = labelList; if (thisLabel->next == NULL) // If there's only one option we either show the label or not. { printf("Show Label: "); safef(varName, sizeof(varName), "%s.label.%s", prefix, thisLabel->name); boolean option = cartUsualBoolean(cart, varName, TRUE); cgiMakeCheckBox(varName, option); } else { printf("Label: "); for(; thisLabel; thisLabel = thisLabel->next) { safef(varName, sizeof(varName), "%s.label.%s", prefix, thisLabel->name); boolean isDefault = FALSE; if (defaultLabelList == NULL) isDefault = (thisLabel == labelList); else if (sameString(defaultLabelList->name, "none")) isDefault = FALSE; else isDefault = (slPairFind(defaultLabelList, thisLabel->name) != NULL); boolean option = cartUsualBoolean(cart, varName, isDefault); cgiMakeCheckBox(varName, option); // find comment for the column listed struct asColumn *col = as->columnList; unsigned num = ptToInt(thisLabel->val); for(; col && num--; col = col->next) ; assert(col); // the comment comes from the autoSql inside the hub's bigBed, escape printf(" %s ", htmlEncode(col->comment)); } } } static char *colorFieldLabel(struct slPair *p) /* Derive a display label for one colorFields entry. * Uses the explicit ="label" if provided, otherwise strips a leading "colorBy" * prefix and replaces underscores with spaces. */ { if (isNotEmpty((char *)p->val)) return (char *)p->val; char *lbl = p->name; if (startsWith("colorBy", lbl)) lbl += strlen("colorBy"); char *derived = cloneString(lbl); subChar(derived, '_', ' '); return derived; } void colorFieldsCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *prefix) /* If trackDb declares colorFields, render a "Color by:" dropdown to choose among color schemes. * * colorFields is a space-separated list of fieldName[="Human Label"] pairs: * colorFields default="Evidence type" colorByHlaClass="HLA class" colorByKozak="Kozak strength" * * The special name "default" (with optional label) represents the standard itemRgb field * (col 9). When no default= entry is present, "Default" is added implicitly as the first * option. Any other name must be an extra bigBed field containing a pre-computed R,G,B string. * * Cart variable: .colorField — empty string means use field 9. */ { if (tdbIsComposite(tdb)) return; char *setting = trackDbSettingClosestToHome(tdb, "colorFields"); if (setting == NULL) return; struct slPair *pairs = slPairListFromString(setting, TRUE); if (pairs == NULL) return; /* Cart variable; empty string = use field 9. */ char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.colorField", prefix); char *current = cartUsualString(cart, cartVar, ""); /* Two-pass build of label/value arrays. * Pass 1: check whether the user supplied an explicit default= entry. * Pass 2: populate the arrays, putting the "use field 9" option first. */ char *defaultLabel = "Default"; struct slPair *p; int nAlternatives = 0; for (p = pairs; p != NULL; p = p->next) { if (sameString(p->name, "default")) defaultLabel = colorFieldLabel(p); else nAlternatives++; } int nOptions = 1 + nAlternatives; /* slot 0 = field-9 default + one per alternative */ char **labels = needMem(nOptions * sizeof(char *)); char **values = needMem(nOptions * sizeof(char *)); labels[0] = defaultLabel; values[0] = ""; int i = 1; for (p = pairs; p != NULL; p = p->next) { if (sameString(p->name, "default")) continue; values[i] = p->name; labels[i] = colorFieldLabel(p); i++; } printf("Color by: "); cgiMakeDropListFull(cartVar, labels, values, nOptions, current, NULL, NULL); printf("
\n"); } void mergeSpanCfgUi(struct cart *cart, struct trackDb *tdb, char *prefix) /* If this track offers a merge spanned items option, put up the cfg for it, which * is just a checkbox with a small explanation. Comparing tdb->track to prefix * ensures we don't offer this control at the composite level, as this is a * subtrack only config */ { if (trackDbSettingOn(tdb, MERGESPAN_TDB_SETTING) && sameString(tdb->track, prefix)) { boolean curOpt = trackDbSettingOn(tdb, "mergeSpannedItems"); char mergeSetting[256]; safef(mergeSetting, sizeof(mergeSetting), "%s.%s", tdb->track, MERGESPAN_CART_SETTING); if (cartVarExists(cart, mergeSetting)) curOpt = cartBoolean(cart, mergeSetting); printf("Merge items that span the current region:"); cgiMakeCheckBox(mergeSetting, curOpt); } } void pslCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* Put up UI for psl tracks */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); char *typeLine = cloneString(tdb->type); char *words[8]; int wordCount = wordCount = chopLine(typeLine, words); if (sameString(tdb->type, "bigPsl")) labelCfgUi(db, cart, tdb, name); if (wordCount == 3 && sameWord(words[1], "xeno")) crossSpeciesCfgUi(cart,tdb); baseColorDropLists(cart, tdb, name); indelShowOptionsWithName(cart, tdb, name); wigOption(cart, name, title, tdb); snakeOption(cart, name, title, tdb); cfgEndBox(boxed); } void netAlignCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *prefix, char *title, boolean boxed) /* Put up UI for net tracks */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); boolean parentLevel = isNameAtParentLevel(tdb,prefix); enum netColorEnum netColor = netFetchColorOption(cart, tdb, parentLevel); char optString[256]; /* our option strings here */ safef(optString, ArraySize(optString), "%s.%s", prefix, NET_COLOR ); printf("

Color nets by: "); netColorDropDown(optString, netColorEnumToString(netColor)); #ifdef NOT_YET enum netLevelEnum netLevel = netFetchLevelOption(cart, tdb, parentLevel); safef( optString, ArraySize(optString), "%s.%s", prefix, NET_LEVEL ); printf("

Limit display of nets to: "); netLevelDropDown(optString, netLevelEnumToString(netLevel)); #endif cfgEndBox(boxed); } void chainCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *prefix, char *title, boolean boxed, char *chromosome) /* Put up UI for chain tracks */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); boolean parentLevel = isNameAtParentLevel(tdb,prefix); enum chainColorEnum chainColor = chainFetchColorOption(cart, tdb, parentLevel); /* check if we have normalized scores available */ boolean normScoreAvailable = chainDbNormScoreAvailable(tdb); char optString[256]; if (normScoreAvailable) { safef(optString, ArraySize(optString), "%s.%s", prefix, OPT_CHROM_COLORS ); printf("

Color chains by: "); chainColorDropDown(optString, chainColorEnumToString(chainColor)); } else { printf("

Color track based on chromosome: "); char optString[256]; /* initial value of chromosome coloring option is "on", unless * overridden by the colorChromDefault setting in the track */ char *binaryColorDefault = trackDbSettingClosestToHomeOrDefault(tdb, "colorChromDefault", "on"); /* allow cart to override trackDb setting */ safef(optString, sizeof(optString), "%s.color", prefix); char * colorSetting = cartUsualStringClosestToHome(cart, tdb, parentLevel, "color", binaryColorDefault); cgiMakeRadioButton(optString, "on", sameString(colorSetting, "on")); printf(" on "); cgiMakeRadioButton(optString, "off", sameString(colorSetting, "off")); printf(" off "); printf("
\n"); } printf("

Filter by chromosome (e.g. chr10): "); safef(optString, ArraySize(optString), "%s.%s", prefix, OPT_CHROM_FILTER); cgiMakeTextVar(optString, cartUsualStringClosestToHome(cart, tdb, parentLevel, OPT_CHROM_FILTER, ""), 15); if (normScoreAvailable) scoreCfgUi(db, cart,tdb,prefix,NULL,CHAIN_SCORE_MAXIMUM,FALSE); wigOption(cart, prefix, title, tdb); snakeOption(cart, prefix, title, tdb); cfgEndBox(boxed); } struct dyString *dyAddFilterAsInt(struct cart *cart, struct trackDb *tdb, struct dyString *extraWhere,char *filter, char *defaultLimits, char*field, boolean *and) // creates the where clause condition to support numeric int filter range. // Filters are expected to follow // {fiterName}: trackDb min or min:max - default value(s); // {filterName}Min or {filterName}: min (user supplied) cart variable; // {filterName}Max: max (user supplied) cart variable; // {filterName}Limits: trackDb allowed range "0:1000" Optional // uses:{filterName}Min: old trackDb value if {filterName}Limits not found // {filterName}Max: old trackDb value if {filterName}Limits not found // defaultLimits: function param if no tdb limits settings found) // The 'and' param and dyString in/out allows stringing multiple where clauses together { char filterLimitName[64]; if (sameWord(filter,NO_SCORE_FILTER)) safef(filterLimitName, sizeof(filterLimitName), "%s", NO_SCORE_FILTER); else safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter,_NO); if (trackDbSettingClosestToHome(tdb, filterLimitName) != NULL) return extraWhere; char *setting = NULL; if (differentWord(filter,SCORE_FILTER)) setting = trackDbSettingClosestToHome(tdb, filter); else setting = trackDbSettingClosestToHomeOrDefault(tdb, filter,"0:1000"); if (setting || sameWord(filter,NO_SCORE_FILTER)) { boolean invalid = FALSE; int minValueTdb = 0,maxValueTdb = NO_VALUE; colonPairToInts(setting,&minValueTdb,&maxValueTdb); int minLimit=NO_VALUE,maxLimit=NO_VALUE,min=minValueTdb,max=maxValueTdb; colonPairToInts(defaultLimits,&minLimit,&maxLimit); getScoreIntRangeFromCart(cart,tdb,FALSE,filter,&minLimit,&maxLimit,&min,&max); if (minLimit != NO_VALUE || maxLimit != NO_VALUE) { // assume tdb default values within range! // (don't give user errors that have no consequence) if ((min != minValueTdb && ((minLimit != NO_VALUE && min < minLimit) || (maxLimit != NO_VALUE && min > maxLimit))) || (max != maxValueTdb && ((minLimit != NO_VALUE && max < minLimit) || (maxLimit != NO_VALUE && max > maxLimit)))) { invalid = TRUE; char value[64]; if (max == NO_VALUE) // min only is allowed, but max only is not safef(value, sizeof(value), "entered minimum (%d)", min); else safef(value, sizeof(value), "entered range (min:%d and max:%d)", min, max); char limits[64]; if (minLimit != NO_VALUE && maxLimit != NO_VALUE) safef(limits, sizeof(limits), "violates limits (%d to %d)", minLimit, maxLimit); else if (minLimit != NO_VALUE) safef(limits, sizeof(limits), "violates lower limit (%d)", minLimit); else //if (maxLimit != NO_VALUE) safef(limits, sizeof(limits), "violates uppper limit (%d)", maxLimit); warn("invalid filter by %s: %s %s for track %s", field, value, limits, tdb->track); } } // else no default limits! if (invalid) { safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, (max!=NO_VALUE?_MIN:"")); cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, _MAX); cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); } else if ((min != NO_VALUE && (minLimit == NO_VALUE || minLimit != min)) || (max != NO_VALUE && (maxLimit == NO_VALUE || maxLimit != max))) // Assumes min==NO_VALUE or min==minLimit is no filter // Assumes max==NO_VALUE or max==maxLimit is no filter! { if (max == NO_VALUE || (maxLimit != NO_VALUE && maxLimit == max)) { if (*and) sqlDyStringPrintf(extraWhere, " and "); sqlDyStringPrintf(extraWhere, "(%s >= %d)", field, min); // min only } else if (min == NO_VALUE || (minLimit != NO_VALUE && minLimit == min)) { if (*and) sqlDyStringPrintf(extraWhere, " and "); sqlDyStringPrintf(extraWhere, "(%s <= %d)", field, max); // max only } else { if (*and) sqlDyStringPrintf(extraWhere, " and "); sqlDyStringPrintf(extraWhere, "(%s BETWEEN %d and %d)", field, min, max); // both } *and=TRUE; } } //if (dyStringLen(extraWhere)) // warn("SELECT FROM %s WHERE %s",tdb->table,dyStringContents(extraWhere)); return extraWhere; } struct dyString *dyAddFilterAsDouble(struct cart *cart, struct trackDb *tdb, struct dyString *extraWhere,char *filter, char *defaultLimits, char*field, boolean *and) // creates the where clause condition to support numeric double filters. // Filters are expected to follow // {fiterName}: trackDb min or min:max - default value(s); // {filterName}Min or {filterName}: min (user supplied) cart variable; // {filterName}Max: max (user supplied) cart variable; // {filterName}Limits: trackDb allowed range "0.0:10.0" Optional // uses: defaultLimits: function param if no tdb limits settings found) // The 'and' param and dyString in/out allows stringing multiple where clauses together { char *setting = trackDbSettingClosestToHome(tdb, filter); if (setting) { boolean invalid = FALSE; double minValueTdb = 0,maxValueTdb = NO_VALUE; colonPairToDoubles(setting,&minValueTdb,&maxValueTdb); double minLimit=NO_VALUE,maxLimit=NO_VALUE,min=minValueTdb,max=maxValueTdb; colonPairToDoubles(defaultLimits,&minLimit,&maxLimit); getScoreFloatRangeFromCart(cart,tdb,FALSE,filter,&minLimit,&maxLimit,&min,&max); if ((int)minLimit != NO_VALUE || (int)maxLimit != NO_VALUE) { // assume tdb default values within range! // (don't give user errors that have no consequence) if ((min != minValueTdb && (((int)minLimit != NO_VALUE && min < minLimit) || ((int)maxLimit != NO_VALUE && min > maxLimit))) || (max != maxValueTdb && (((int)minLimit != NO_VALUE && max < minLimit) || ((int)maxLimit != NO_VALUE && max > maxLimit)))) { invalid = TRUE; char value[64]; if ((int)max == NO_VALUE) // min only is allowed, but max only is not safef(value, sizeof(value), "entered minimum (%g)", min); else safef(value, sizeof(value), "entered range (min:%g and max:%g)", min, max); char limits[64]; if ((int)minLimit != NO_VALUE && (int)maxLimit != NO_VALUE) safef(limits, sizeof(limits), "violates limits (%g to %g)", minLimit, maxLimit); else if ((int)minLimit != NO_VALUE) safef(limits, sizeof(limits), "violates lower limit (%g)", minLimit); else //if ((int)maxLimit != NO_VALUE) safef(limits, sizeof(limits), "violates uppper limit (%g)", maxLimit); warn("invalid filter by %s: %s %s for track %s", field, value, limits, tdb->track); } } if (invalid) { char filterLimitName[64]; safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, _MIN); cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); safef(filterLimitName, sizeof(filterLimitName), "%s%s", filter, _MAX); cartRemoveVariableClosestToHome(cart,tdb,FALSE,filterLimitName); } else if (((int)min != NO_VALUE && ((int)minLimit == NO_VALUE || minLimit != min)) || ((int)max != NO_VALUE && ((int)maxLimit == NO_VALUE || maxLimit != max))) // Assumes min==NO_VALUE or min==minLimit is no filter // Assumes max==NO_VALUE or max==maxLimit is no filter! { if ((int)max == NO_VALUE || ((int)maxLimit != NO_VALUE && maxLimit == max)) { if (*and) sqlDyStringPrintf(extraWhere, " and "); sqlDyStringPrintf(extraWhere, "(%s >= %g)", field, min); // min only } else if ((int)min == NO_VALUE || ((int)minLimit != NO_VALUE && minLimit == min)) { if (*and) sqlDyStringPrintf(extraWhere, " and "); sqlDyStringPrintf(extraWhere, "(%s <= %g)", field, max); // max only } else { if (*and) sqlDyStringPrintf(extraWhere, " and "); sqlDyStringPrintf(extraWhere, "(%s BETWEEN %g and %g)", field,min,max); // both } *and=TRUE; } } //if (dyStringLen(extraWhere)) // warn("SELECT FROM %s WHERE %s",tdb->table,dyStringContents(extraWhere)); return extraWhere; } struct dyString *dyAddAllScoreFilters(struct cart *cart, struct trackDb *tdb, struct dyString *extraWhere,boolean *and) // creates the where clause condition to gather together all random double filters // Filters are expected to follow // {fiterName}: trackDb min or min:max - default value(s); // {filterName}Min or {filterName}: min (user supplied) cart variable; // {filterName}Max: max (user supplied) cart variable; // {filterName}Limits: trackDb allowed range "0.0:10.0" Optional // uses: defaultLimits: function param if no tdb limits settings found) // The 'and' param and dyString in/out allows stringing multiple where clauses together { struct slName *filterSettings = trackDbSettingsWildMatch(tdb, FILTER_NUMBER_WILDCARD_CAP); if (filterSettings) { struct slName *filter = NULL; while ((filter = slPopHead(&filterSettings)) != NULL) { if (differentString(filter->name,"noScoreFilter") && differentString(filter->name,"scoreFilter")) // TODO: scoreFilter could be included { char *field = cloneString(filter->name); int ix = strlen(field) - strlen("filter"); assert(ix > 0); field[ix] = '\0'; char *setting = trackDbSetting(tdb, filter->name); // How to determine float or int ? // If actual tracDb setting has decimal places, then float! if (strchr(setting,'.') == NULL) extraWhere = dyAddFilterAsInt(cart,tdb,extraWhere,filter->name,"0:1000",field,and); else extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,filter->name,NULL,field,and); } slNameFree(&filter); } } return extraWhere; } boolean encodePeakHasCfgUi(struct trackDb *tdb) // Confirms that this track has encode Peak cfgUI { if (sameWord("narrowPeak",tdb->type) || sameWord("broadPeak", tdb->type) || sameWord("bigNarrowPeak", tdb->type) || sameWord("encodePeak",tdb->type) || sameWord("gappedPeak",tdb->type)) { return (trackDbSettingClosestToHome(tdb, SCORE_FILTER ) || trackDbSettingClosestToHome(tdb, SIGNAL_FILTER) || trackDbSettingClosestToHome(tdb, PVALUE_FILTER) || trackDbSettingClosestToHome(tdb, QVALUE_FILTER) || trackDbSettingClosestToHome(tdb, SCORE_FILTER )); } return FALSE; } void encodePeakCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) // Put up UI for filtering wgEnocde peaks based on score, Pval and Qval { boolean parentLevel = isNameAtParentLevel(tdb,name); boolean opened = FALSE; showScoreFilter(cart,tdb,&opened,boxed,parentLevel,name,title, "Minimum Signal value", SIGNAL_FILTER, FALSE); showScoreFilter(cart,tdb,&opened,boxed,parentLevel,name,title, "Minimum P-Value (-log₁₀)",PVALUE_FILTER, FALSE); showScoreFilter(cart,tdb,&opened,boxed,parentLevel,name,title, "Minimum Q-Value (-log₁₀)",QVALUE_FILTER, FALSE); char *setting = trackDbSettingClosestToHomeOrDefault(tdb, SCORE_FILTER,NULL);//"0:1000"); if (setting) { if (!opened) { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); puts("

"); opened = TRUE; } char varName[256]; int minLimit=0,maxLimit=1000,minVal=0,maxVal=NO_VALUE; colonPairToInts(setting,&minVal,&maxVal); getScoreIntRangeFromCart(cart,tdb,parentLevel,SCORE_FILTER,&minLimit,&maxLimit, &minVal, &maxVal); if (maxVal != NO_VALUE) puts(""); } } if (opened) { puts("

Score range: min:	"); else puts("
Minimum score:	"); safef(varName, sizeof(varName), "%s%s", SCORE_FILTER, _BY_RANGE); boolean filterByRange = trackDbSettingClosestToHomeOn(tdb, varName); safef(varName, sizeof(varName), "%s.%s%s", name, SCORE_FILTER, (filterByRange?_MIN:"")); cgiMakeIntVarWithLimits(varName, minVal, "Minimum score", 0, minLimit, maxLimit); if (filterByRange) { if (maxVal == NO_VALUE) maxVal = maxLimit; puts("	to	"); safef(varName, sizeof(varName), "%s.%s%s", name, SCORE_FILTER,_MAX); cgiMakeIntVarWithLimits(varName, maxVal, "Maximum score", 0, minLimit, maxLimit); } printf("	(%d to %d)",(filterByRange?"":" colspan=3"),minLimit, maxLimit); if (trackDbSettingClosestToHome(tdb, GRAY_LEVEL_SCORE_MIN) != NULL) { printf("
"); scoreGrayLevelCfgUi(cart, tdb, name, 1000); puts("

"); cfgEndBox(boxed); } } static void gencodeLabelControls(char *db, struct cart *cart, struct trackDb *tdb, char *name, boolean parentLevel) /* generate label checkboxes for GENCODE. */ { // See hgTracks/gencodeTracks.c:registerProductionTrackHandlers() // and hgTracks/gencodeTracks.c:assignConfiguredName() char *labelsNames[][2] = { {"gene name", "geneName"}, {"gene id", "geneId"}, {"transcript id", "transcriptId"}, {NULL, NULL} }; int i; for (i = 0; labelsNames[i][0] != NULL; i++) { char varName[64], varSuffix[64]; safef(varSuffix, sizeof(varSuffix), "label.%s", labelsNames[i][1]); safef(varName, sizeof(varName), "%s.%s", name, varSuffix); char *value = cartUsualStringClosestToHome(cart, tdb, parentLevel, varSuffix, NULL); boolean checked = (value != NULL) && !sameString(value, "0"); printf("%s%s: ", (i > 0) ? "  " : "", labelsNames[i][0]); cgiMakeCheckBoxMore(varName, checked, NULL); } } static void gencodeMaxTransControl(char *db, struct cart *cart, struct trackDb *tdb, char *name, boolean parentLevel) { static char *varSuffix = "maxTrans"; char varName[64]; safef(varName, sizeof(varName), "%s.%s", name, varSuffix); int maxTrans = cartUsualIntClosestToHome(cart, tdb, parentLevel, varSuffix, 0); printf("
Maximum number of transcripts to display: "); cgiMakeIntVar(varName, maxTrans, 5); printf(" (0 to display all)"); } static void gencodeDisplayControls(char *db, struct cart *cart, struct trackDb *tdb, char *name, boolean parentLevel) /* generate display controls */ { if (trackDbSettingClosestToHome(tdb, "maxTransEnabled")) gencodeMaxTransControl(db, cart, tdb, name, parentLevel); } static void newGencodeShowOptions(struct cart *cart, struct trackDb *tdb) /* Put up line of controls that describe what parts to show. */ { char varName[64]; printf("
Show: "); safef(varName, sizeof(varName), "%s.show.noncoding", tdb->track); boolean option = cartUsualBoolean(cart, varName, TRUE); cgiMakeCheckBox(varName, option); printf(" %s   ", "non-coding genes"); safef(varName, sizeof(varName), "%s.show.spliceVariants", tdb->track); option = cartUsualBoolean(cart, varName, TRUE); cgiMakeCheckBox(varName, option); printf(" %s   ", "splice variants"); safef(varName, sizeof(varName), "%s.show.pseudo", tdb->track); option = cartUsualBoolean(cart, varName, FALSE); cgiMakeCheckBox(varName, option); printf(" %s   ", "pseudogenes"); printf("
Tagged Sets: "); safef(varName, sizeof(varName), "%s.show.set", tdb->track); char *setString = cartUsualString(cart, varName, "basic"); cgiMakeRadioButton(varName, "MANE_Select", sameString(setString, "MANE_Select")); printf(" %s   ", "MANE only"); cgiMakeRadioButton(varName, "basic", sameString(setString, "basic")); printf(" %s   ", "BASIC only"); cgiMakeRadioButton(varName, "all", sameString(setString, "all")); printf(" %s   ", "All"); } void bedScoreCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* Put up bed-specific score controls */ { char *scoreMax = trackDbSettingClosestToHome(tdb, SCORE_FILTER _MAX); int maxScore = (scoreMax ? sqlUnsigned(scoreMax):1000); scoreCfgUi(db, cart,tdb,name,title,maxScore,boxed); if(tdbIsBigBed(tdb)) { labelCfgUi(db, cart, tdb, name); colorFieldsCfgUi(db, cart, tdb, name); mergeSpanCfgUi(cart, tdb, name); wigOption(cart, name, title, tdb); } } void genePredCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* Put up genePred-specific controls */ { char varName[64]; boolean parentLevel = isNameAtParentLevel(tdb,name); char *geneLabel = cartUsualStringClosestToHome(cart, tdb,parentLevel, "label", "gene"); boxed = cfgBeginBoxAndTitle(tdb, boxed, title); labelCfgUi(db, cart, tdb, name); colorFieldsCfgUi(db, cart, tdb, name); boolean isGencode3 = trackDbSettingOn(tdb, "isGencode3"); if (sameString(name, "acembly")) { char *acemblyClass = cartUsualStringClosestToHome(cart,tdb,parentLevel,"type", acemblyEnumToString(0)); printf("

Gene Class: "); acemblyDropDown("acembly.type", acemblyClass); printf(" "); } else if (isGencode3) { newGencodeShowOptions(cart, tdb); } else if (startsWith("wgEncodeGencode", name)) { // new GENCODEs gencodeLabelControls(db, cart, tdb, name, parentLevel); gencodeDisplayControls(db, cart, tdb, name, parentLevel); } else if (sameString("wgEncodeSangerGencode", name) || (startsWith("encodeGencode", name) && !sameString("encodeGencodeRaceFrags", name))) { // GENCODE pilot (see hgTracks/gencodeTracks.c:registerPilotTrackHandlers() // and hgTracks/simpleTracks.c:genePredAssignConfiguredName() printf("Label: "); safef(varName, sizeof(varName), "%s.label", name); cgiMakeRadioButton(varName, "gene", sameString("gene", geneLabel)); printf("%s ", "gene"); cgiMakeRadioButton(varName, "accession", sameString("accession", geneLabel)); printf("%s ", "accession"); cgiMakeRadioButton(varName, "both", sameString("both", geneLabel)); printf("%s ", "both"); cgiMakeRadioButton(varName, "none", sameString("none", geneLabel)); printf("%s ", "none"); } if (trackDbSettingClosestToHomeOn(tdb, "nmdFilter")) { boolean nmdDefault = FALSE; safef(varName, sizeof(varName), "hgt.%s.nmdFilter", name); nmdDefault = cartUsualBoolean(cart,varName, FALSE); // TODO: var name (hgt prefix) needs changing before ClosesToHome can be used printf("

Filter out NMD targets."); cgiMakeCheckBox(varName, nmdDefault); } if (!sameString(tdb->track, "tigrGeneIndex") && !sameString(tdb->track, "ensGeneNonCoding") && !sameString(tdb->track, "encodeGencodeRaceFrags")) baseColorDropLists(cart, tdb, name); // For bigGenePred, scoreCfgUi() (called below) renders the filterBy/highlightBy // controls itself. Rendering them here too produces two "); group = -1; lineBreakJustPrinted = FALSE; for (wmSpecies = wmSpeciesList, i = 0, j = 0; wmSpecies != NULL; wmSpecies = wmSpecies->next, i++) { char *label; prevGroup = group; group = wmSpecies->group; if (groupCt != 1 && group != prevGroup) { i = 0; j = 0; if (group != 0) puts("
\n"); /* replace underscores in group names */ subChar(groups[group], '_', ' '); printf("

%s", groups[group]); printf(" "); safef(option, sizeof(option), "plus_%s", groups[group]); PLUS_BUTTON( "id",option,"cb_maf_",groups[group]) safef(option, sizeof(option),"minus_%s", groups[group]); MINUS_BUTTON("id",option,"cb_maf_",groups[group]) puts("\n"); } numberPerRow = 5; /* new logic to decide if line break should be displayed here */ if ((j != 0 && (j % numberPerRow) == 0) && (lineBreakJustPrinted == FALSE)) { puts(""); lineBreakJustPrinted = TRUE; } char id[MAX_SP_SIZE]; if (defaultOffSpeciesCnt > 0) { if (stringArrayIx(wmSpecies->name,words,defaultOffSpeciesCnt) == -1) safef(id, sizeof(id), "cb_maf_%s_%s", groups[group], wmSpecies->name); else { safef(id, sizeof(id), "cb_maf_%s_%s_defOff", groups[group], wmSpecies->name); } } else safef(id, sizeof(id), "cb_maf_%s_%s", groups[group], wmSpecies->name); puts(""); lineBreakJustPrinted = FALSE; j++; } puts("
"); boolean defaultState = TRUE; if (offHash != NULL) defaultState = (hashLookup(offHash, wmSpecies->name) == NULL); safecpy(option, sizeof(option), name); wmSpecies->on = isSpeciesOn(cart, tdb, wmSpecies->name, option, sizeof option, defaultState ); cgiMakeCheckBoxWithId(option, wmSpecies->on,id); char *remapName = NULL; if ((labelHash != NULL) && (remapName = hashFindVal(labelHash,wmSpecies->name))) label = remapName; else { label = hOrganism(wmSpecies->name); if (label == NULL) label = wmSpecies->name; if (lowerFirstChar) *label = tolower(*label); } printf("%s
", label); puts("

\n"); freez(&words); return wmSpeciesList; } void wigMafCfgUi(struct cart *cart, struct trackDb *tdb,char *name, char *title, boolean boxed, char *db) /* UI for maf/wiggle track * NOTE: calls wigCfgUi */ { int i; char option[MAX_SP_SIZE]; boolean parentLevel = isNameAtParentLevel(tdb,name); boxed = cfgBeginBoxAndTitle(tdb, boxed, title); char *defaultCodonSpecies = trackDbSetting(tdb, SPECIES_CODON_DEFAULT); char *framesTable = trackDbSetting(tdb, "frames"); char *snpTable = trackDbSetting(tdb, "snpTable"); char *treeImage = NULL; struct consWiggle *consWig, *consWiggles = wigMafWiggles(db, tdb); boolean isWigMafProt = FALSE; if (strstr(tdb->type, "wigMafProt")) isWigMafProt = TRUE; puts("
"); if (consWiggles && consWiggles->next) { /* check for alternate conservation wiggles -- create checkboxes */ puts("
Conservation:" ); boolean first = TRUE; for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { char *wigVarSuffix = NULL; char *wigVar = wigMafWiggleVar(name, consWig, &wigVarSuffix); cgiMakeCheckBox(wigVar, cartUsualBooleanClosestToHome(cart,tdb,parentLevel,wigVarSuffix,first)); freeMem(wigVar); first = FALSE; subChar(consWig->uiLabel, '_', ' '); printf ("%s ", consWig->uiLabel); } } struct wigMafSpecies *wmSpeciesList = wigMafSpeciesTable(cart, tdb, name, db); struct wigMafSpecies *wmSpecies; if (isWigMafProt) puts("Multiple alignment amino acid-level:
" ); else puts("Multiple alignment base-level:
" ); boolean mafDotIsOn = trackDbSettingClosestToHomeOn(tdb, MAF_DOT_VAR); safef(option, sizeof option, "%s.%s", name, MAF_DOT_VAR); cgiMakeCheckBox(option, cartUsualBooleanClosestToHome(cart, tdb, parentLevel,MAF_DOT_VAR, mafDotIsOn)); if (isWigMafProt) puts("Display amino acids identical to reference as dots
" ); else puts("Display bases identical to reference as dots
" ); safef(option, sizeof option, "%s.%s", name, MAF_CHAIN_VAR); cgiMakeCheckBox(option, cartUsualBooleanClosestToHome(cart,tdb,parentLevel,MAF_CHAIN_VAR,TRUE)); char *irowStr = trackDbSetting(tdb, "irows"); boolean doIrows = (irowStr == NULL) || !sameString(irowStr, "off"); if (isCustomTrack(tdb->track) || doIrows) puts("Display chains between alignments
"); else { if (isWigMafProt) puts("Display unaligned amino acids with spanning chain as 'o's
"); else puts("Display unaligned bases with spanning chain as 'o's
"); } safef(option, sizeof option, "%s.%s", name, MAF_SHOW_SNP); if (snpTable) { printf("
Codon Changes:
"); cgiMakeCheckBox(option, cartOrTdbBoolean(cart, tdb, MAF_SHOW_SNP,FALSE)); puts("Display synonymous and non-synonymous changes in coding exons.
"); } safef(option, sizeof option, "%s.%s", name, "codons"); if (framesTable) { int nodeCount = slCount(wmSpeciesList) + 1; /* +1 for reference db */ char **nodeNames; char buffer[128]; AllocArray(nodeNames, nodeCount); printf("
Codon Translation:
"); printf("Default species to establish reading frame: "); nodeNames[0] = db; for (wmSpecies = wmSpeciesList, i = 1; wmSpecies != NULL; wmSpecies = wmSpecies->next, i++) { nodeNames[i] = wmSpecies->name; } cgiMakeDropList(SPECIES_CODON_DEFAULT, nodeNames, nodeCount, // tdb independent var cartUsualString(cart, SPECIES_CODON_DEFAULT, defaultCodonSpecies)); puts("
"); char *cartVal = cartUsualStringClosestToHome(cart, tdb, parentLevel, "codons","codonDefault"); safef(buffer, sizeof(buffer), "%s.codons",name); cgiMakeRadioButton(buffer,"codonNone", sameWord(cartVal,"codonNone")); printf("No codon translation
"); cgiMakeRadioButton(buffer,"codonDefault", sameWord(cartVal,"codonDefault")); printf("Use default species reading frames for translation
"); cgiMakeRadioButton(buffer,"codonFrameNone",sameWord(cartVal,"codonFrameNone")); printf("Use reading frames for species if available, otherwise no translation
"); cgiMakeRadioButton(buffer,"codonFrameDef", sameWord(cartVal,"codonFrameDef")); printf("Use reading frames for species if available, otherwise use default species
"); freeMem(nodeNames); } else { /* Codon highlighting does not apply to wigMafProt type */ if (!strstr(tdb->type, "wigMafProt")) { puts("
Codon highlighting:
" ); #ifdef GENE_FRAMING safef(option, sizeof(option), "%s.%s", name, MAF_FRAME_VAR); char *currentCodonMode = cartCgiUsualString(cart, option, MAF_FRAME_GENE); /* Disable codon highlighting */ cgiMakeRadioButton(option, MAF_FRAME_NONE, sameString(MAF_FRAME_NONE, currentCodonMode)); puts("None "); /* Use gene pred */ cgiMakeRadioButton(option, MAF_FRAME_GENE, sameString(MAF_FRAME_GENE, currentCodonMode)); puts("CDS-annotated frame based on"); safef(option, sizeof(option), "%s.%s", name, MAF_GENEPRED_VAR); genePredDropDown(cart, makeTrackHash(db, chromosome), NULL, option); #else safef(option, sizeof(option), "%s.%s", name, BASE_COLORS_VAR); puts(" Alternate colors every"); cgiMakeIntVar(option, cartCgiUsualInt(cart, option, 0), 1); puts("bases
"); safef(option, sizeof(option), "%s.%s", name, BASE_COLORS_OFFSET_VAR); puts(" Offset alternate colors by"); cgiMakeIntVar(option, cartCgiUsualInt(cart, option, 0), 1); puts("bases
"); #endif } } treeImage = trackDbSetting(tdb, "treeImage"); if (treeImage) printf("
", treeImage); else puts("

"); if (trackDbSetting(tdb, CONS_WIGGLE) != NULL) { wigCfgUi(cart,tdb,name,"Conservation graph:",FALSE); } cfgEndBox(boxed); } static char *grayLabels[] = { "alignment quality", "base qualities", "unpaired ends", }; static char *grayValues[] = { BAM_GRAY_MODE_ALI_QUAL, BAM_GRAY_MODE_BASE_QUAL, BAM_GRAY_MODE_UNPAIRED, }; // When a child input of a radio set is changed, click its radio button: #define UPDATE_RADIO_FORMAT_JS "\ var inputs = document.getElementsByName('%s'); \ if (inputs) { \ for (var i=0; i < inputs.length; i++) { \ if (inputs[i].type == 'radio') { \ inputs[i].checked = (inputs[i].value == '%s'); \ } \ } \ }" void bamCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* BAM: short-read-oriented alignment file format. */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); char cartVarName[1024]; printf("",boxed?" width='100%'":""); bamAddBaseAndIndelSettings(tdb); // Deal with tdb being from a subtrack when a view is being configured, ugh: if (differentString(tdb->track, name) && tdb->parent != NULL && sameString(tdb->parent->type, "bam")) bamAddBaseAndIndelSettings(tdb->parent); #ifdef NOTNOW // temporarily (?) remove this check box because code doesn't allow for setting wiggle options char *showWig = cartOrTdbString(cart, tdb, BAMWIG_MODE, "0"); safef(cartVarName, sizeof(cartVarName), "%s.%s", name, BAMWIG_MODE); cgiMakeCheckBox(cartVarName, SETTING_IS_ON(showWig)); printf("Only show coverage of reads"); #endif printf("\n"); printf("\n"); char *showNames = cartOrTdbString(cart, tdb, BAM_SHOW_NAMES, "0"); safef(cartVarName, sizeof(cartVarName), "%s.%s", name, BAM_SHOW_NAMES); cgiMakeCheckBox(cartVarName, SETTING_IS_ON(showNames)); printf("Display read names"); if (boxed && fileExists(hHelpFile("hgBamTrackHelp"))) printf("BAM configuration help"); printf("\n"); boolean canPair = (cartOrTdbString(cart, tdb, BAM_PAIR_ENDS_BY_NAME, NULL) != NULL); if (canPair) { char *doPairing = cartOrTdbString(cart, tdb, BAM_PAIR_ENDS_BY_NAME, "0"); printf(""); safef(cartVarName, sizeof(cartVarName), "%s." BAM_PAIR_ENDS_BY_NAME, name); cgiMakeCheckBox(cartVarName, SETTING_IS_ON(doPairing)); printf("Attempt to join paired end reads by name\n"); } printf("Minimum alignment quality:\n"); safef(cartVarName, sizeof(cartVarName), "%s." BAM_MIN_ALI_QUAL, name); cgiMakeIntVar(cartVarName, atoi(cartOrTdbString(cart, tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT)), 4); printf(""); baseColorDropLists(cart, tdb, name); puts("
"); indelShowOptionsWithName(cart, tdb, name); printf("
\n"); printf("Additional coloring modes:
\n"); safef(cartVarName, sizeof(cartVarName), "%s." BAM_COLOR_MODE, name); char *selected = cartOrTdbString(cart, tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT); cgiMakeRadioButton(cartVarName, BAM_COLOR_MODE_STRAND, sameString(selected, BAM_COLOR_MODE_STRAND)); printf("Color by strand (blue for +, red for -)
\n"); cgiMakeRadioButton(cartVarName, BAM_COLOR_MODE_GRAY, sameString(selected, BAM_COLOR_MODE_GRAY)); printf("Use gray for\n"); char cartVarName2[1024]; safef(cartVarName2, sizeof(cartVarName2), "%s." BAM_GRAY_MODE, name); int grayMenuSize = canPair ? ArraySize(grayLabels) : ArraySize(grayLabels)-1; char *sel2 = cartOrTdbString(cart, tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT); char onChange[2048]; safef(onChange, sizeof(onChange), UPDATE_RADIO_FORMAT_JS, cartVarName, BAM_COLOR_MODE_GRAY); cgiMakeDropListFull(cartVarName2, grayLabels, grayValues, grayMenuSize, sel2, "change", onChange); printf("
\n"); if (trackDbSettingClosestToHome(tdb, "noColorTag") == NULL) { cgiMakeRadioButton(cartVarName, BAM_COLOR_MODE_TAG, sameString(selected, BAM_COLOR_MODE_TAG)); printf("Use R,G,B colors specified in user-defined tag "); safef(cartVarName2, sizeof(cartVarName2), "%s." BAM_COLOR_TAG, name); sel2 = cartOrTdbString(cart, tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT); safef(onChange, sizeof(onChange), UPDATE_RADIO_FORMAT_JS, cartVarName, BAM_COLOR_MODE_TAG); cgiMakeTextVarWithJs(cartVarName2, sel2, 30, "keypress", onChange); printf("
\n"); } cgiMakeRadioButton(cartVarName, BAM_COLOR_MODE_OFF, sameString(selected, BAM_COLOR_MODE_OFF)); printf("No additional coloring"); // let the user choose to see the track in wiggle mode wigOption(cart, name, title, tdb); //TODO: include / exclude flags if (!boxed && fileExists(hHelpFile("hgBamTrackHelp"))) printf("

BAM " "configuration help

"); cfgEndBox(boxed); } void lrgCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* LRG: Locus Reference Genomic sequences mapped to assembly. */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); printf("",boxed?" width='100%'":""); baseColorDrawOptDropDown(cart, tdb); indelShowOptionsWithNameExt(cart, tdb, name, "LRG sequence", FALSE, FALSE); cfgEndBox(boxed); } void lrgTranscriptAliCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* LRG Transcripts: Locus Reference Genomic transcript sequences mapped to assembly. */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); printf("",boxed?" width='100%'":""); baseColorDrawOptDropDown(cart, tdb); indelShowOptionsWithNameExt(cart, tdb, name, "LRG transcript sequence", FALSE, FALSE); cfgEndBox(boxed); } struct trackDb *rFindView(struct trackDb *forest, char *view) // Return the trackDb on the list that matches the view tag. Prefers ancestors before decendents { struct trackDb *tdb; for (tdb = forest; tdb != NULL; tdb = tdb->next) { char *viewSetting = trackDbSetting(tdb, "view"); if (sameOk(viewSetting, view) || sameOk(tagEncode(viewSetting), view)) return tdb; } for (tdb = forest; tdb != NULL; tdb = tdb->next) { struct trackDb *viewTdb = rFindView(tdb->subtracks, view); if (viewTdb != NULL) return viewTdb; } return NULL; } static boolean compositeViewCfgExpandedByDefault(struct trackDb *parentTdb,char *view, char **retVisibility) // returns true if the view cfg is expanded by default. Optionally allocates string of view // setting (eg 'dense') { boolean expanded = FALSE; if ( retVisibility != NULL ) *retVisibility = cloneString(hStringFromTv(parentTdb->visibility)); struct trackDb *viewTdb = rFindView(parentTdb->subtracks, view); if (viewTdb == NULL) return FALSE; if (retVisibility != NULL) *retVisibility = cloneString(hStringFromTv(viewTdb->visibility)); if (trackDbSetting(viewTdb, "viewUi")) expanded = TRUE; return expanded; } enum trackVisibility visCompositeViewDefault(struct trackDb *parentTdb,char *view) // returns the default track visibility of particular view within a composite track { char *visibility = NULL; compositeViewCfgExpandedByDefault(parentTdb,view,&visibility); enum trackVisibility vis = hTvFromString(visibility); freeMem(visibility); return vis; } static boolean hCompositeDisplayViewDropDowns(char *db, struct cart *cart, struct trackDb *parentTdb) // UI for composite view drop down selections. { int ix; char classes[SMALLBUF]; char javascript[JBUFSIZE]; char id[256]; #define CFG_LINK "%s ▾" #define CFG_LINK_JS "return (showConfigControls('%s') == false);" #define MAKE_CFG_LINK(name,title,viewTrack,open) \ safef(id, sizeof id, "%s_link", (name)); \ printf(CFG_LINK, (name),id,(title),(title),(viewTrack),((open)?"on":"off")); \ safef(javascript, sizeof javascript, CFG_LINK_JS, (name)); \ jsOnEventById("click", id, javascript); // membersForAll is generated once per track, then cached membersForAll_t *membersForAll = membersForAllSubGroupsGet(parentTdb, cart); members_t *membersOfView = membersForAll->members[dimV]; if (membersOfView == NULL) return FALSE; char configurable[membersOfView->count]; memset(configurable,cfgNone,sizeof(configurable)); int firstOpened = -1; boolean makeCfgRows = FALSE; struct trackDb **matchedViewTracks = needMem(sizeof(struct trackDb *) * membersOfView->count); for (ix = 0; ix < membersOfView->count; ix++) { if (membersOfView->subtrackList != NULL && membersOfView->subtrackList[ix] != NULL) { struct trackDb *subtrack = membersOfView->subtrackList[ix]->val; matchedViewTracks[ix] = subtrack->parent; configurable[ix] = (char)cfgTypeFromTdb(subtrack, TRUE); if (configurable[ix] != cfgNone && trackDbSettingBlocksConfiguration(subtrack,FALSE)) configurable[ix] = cfgNone; if (configurable[ix] != cfgNone) { if (firstOpened == -1) { if (cartOrTdbBoolean(cart, matchedViewTracks[ix], "showCfg", FALSE)) firstOpened = ix; } makeCfgRows = TRUE; } } } toLowerN(membersOfView->groupTitle, 1); printf("Select %s (Help):\n", membersOfView->groupTitle); printf("\n"); // Make row of vis drop downs for (ix = 0; ix < membersOfView->count; ix++) { char *viewName = membersOfView->tags[ix]; if (matchedViewTracks[ix] != NULL) { printf(""); char varName[SMALLBUF]; safef(varName, sizeof(varName), "%s", matchedViewTracks[ix]->track); enum trackVisibility tv = hTvFromString(cartUsualString(cart,varName, hStringFromTv(visCompositeViewDefault(parentTdb,viewName)))); struct slPair *events = NULL; safef(javascript, sizeof(javascript), "matSelectViewForSubTracks(this,'%s');", viewName); slPairAdd(&events, "change", cloneString(javascript)); safef(javascript, sizeof(javascript), "this.lastIndex=this.selectedIndex;"); slPairAdd(&events, "focus", cloneString(javascript)); printf(""); } } puts(""); // Make row of cfg boxes if needed if (makeCfgRows) { puts("

"); if (configurable[ix] != cfgNone) { MAKE_CFG_LINK(membersOfView->tags[ix],membersOfView->titles[ix], matchedViewTracks[ix]->track,(firstOpened == ix)) } else printf("%s",membersOfView->titles[ix]); puts("

"); safef(classes, sizeof(classes), "viewDD normalText %s", membersOfView->tags[ix]); hTvDropDownClassWithJavascript(varName, NULL, tv, parentTdb->canPack, classes, events); puts("

"); for (ix = 0; ix < membersOfView->count; ix++) { struct trackDb *view = matchedViewTracks[ix]; if (view != NULL) { char *viewName = membersOfView->tags[ix]; printf("tags[ix],NULL)) || (firstOpened != -1 && firstOpened != ix)) printf(" style=\"display:none\""); printf(">"); int ix2=ix; while (0 < ix2--) printf(""); printf(""); } } } puts("

",membersOfView->count+1); if (configurable[ix] != cfgNone) { // Hint: subtrack is model but named for view cfgByCfgType(configurable[ix],db,cart,view->subtracks,view->track, membersOfView->titles[ix],TRUE); } printf("

"); freeMem(matchedViewTracks); return TRUE; } char *compositeLabelWithVocabLink(char *db,struct trackDb *parentTdb, struct trackDb *childTdb, char *vocabType, char *label) // If the parentTdb has a controlledVocabulary setting and the vocabType is found, // then label will be wrapped with the link to display it. Return string is cloned. { char *vocab = trackDbSetting(parentTdb, "controlledVocabulary"); // WARNING: this is needed to cache metadata in trackDb object (accessed by metadataFindValue) (void)metadataForTable(db,childTdb,NULL); if (vocab == NULL) return cloneString(label); // No wrapping! // Currently implemented just for ENCODE style vocab if (!vocabSettingIsEncode(vocab)) return cloneString(label); char *words[SMALLBUF]; int count; if ((count = chopByWhite(cloneString(vocab), words, SMALLBUF)) <= 1) return cloneString(label); char *suffix = NULL; char *rootLabel = labelRoot(label, &suffix); boolean found = FALSE; int ix; for (ix=1;ix" #define PM_BUTTON_UC_JS "return (matSetMatrixCheckBoxes(%s%sCSS.escape(\"%s\")%s%s%s) == false);" #define PM_MAKE_BUTTON_UC(s1,s2,s3,s4,s5,s6,name,img) \ safef(id, sizeof id, "btn_%s", (name)); \ printf(PM_BUTTON_UC, htmlEncode(id), (img)); \ safef(javascript, sizeof javascript, PM_BUTTON_UC_JS, (s1),(s2),(s3),(s4),(s5),(s6)); \ jsOnEventById("click", id, javascript); #define MATRIX_RIGHT_BUTTONS_AFTER 8 #define MATRIX_BOTTOM_BUTTONS_AFTER 20 static void buttonsForAll(boolean left, boolean top) { char id[256]; char javascript[1024]; char fullname[256]; safef(fullname, sizeof fullname, "plus_all_%s_%s", left ? "left" : "right", top ? "top" : "bottom"); PM_MAKE_BUTTON_UC("true", ",", "", "", "", "", fullname, "add_sm.gif") safef(fullname, sizeof fullname, "minus_all_%s_%s", left ? "left" : "right", top ? "top" : "bottom"); PM_MAKE_BUTTON_UC("false",",", "", "", "", "", fullname, "remove_sm.gif") } static void buttonsForOne(char *class, boolean vertical, boolean left, boolean top) { char id[256]; char javascript[1024]; char fullname[256]; safef(fullname, sizeof fullname, "plus_%s_all_%s_%s" , class, left ? "left" : "right", top ? "top" : "bottom"); PM_MAKE_BUTTON_UC("true", ",", class, "", "", "", fullname, "add_sm.gif") if (vertical) puts("
"); safef(fullname, sizeof fullname, "minus_%s_all_%s_%s", class, left ? "left" : "right", top ? "top" : "bottom"); PM_MAKE_BUTTON_UC("false", ",", class, "", "", "", fullname, "remove_sm.gif") } #define MATRIX_SQUEEZE 10 static boolean matrixSqueeze(membersForAll_t* membersForAll) // Returns non-zero if the matrix will be squeezed. Non-zero is actually squeezedLabelHeight { char *browserVersion; if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '9') return 0; members_t *dimensionX = membersForAll->members[dimX]; members_t *dimensionY = membersForAll->members[dimY]; if (dimensionX && dimensionY) { if (dimensionX->count>MATRIX_SQUEEZE) { int ixX,cntX=0; for (ixX = 0; ixX < dimensionX->count; ixX++) { if (dimensionX->subtrackList && dimensionX->subtrackList[ixX] && dimensionX->subtrackList[ixX]->val) cntX++; } if (cntX>MATRIX_SQUEEZE) return TRUE; } } return FALSE; } static void matrixXheadingsRow1(char *db, struct trackDb *parentTdb, boolean squeeze, membersForAll_t* membersForAll, boolean top) // prints the top row of a matrix: 'All' buttons; X titles; buttons 'All' { members_t *dimensionX = membersForAll->members[dimX]; members_t *dimensionY = membersForAll->members[dimY]; printf("\n",top?"BOTTOM":"TOP"); if (dimensionX && dimensionY) { printf("",top?"TOP":"BOTTOM"); //printf("",(top == squeeze)?"BOTTOM":"TOP");//"TOP":"BOTTOM"); buttonsForAll(TRUE, top); puts(" All"); } // If there is an X dimension, then titles go across the top if (dimensionX) { int ixX,cntX=0; if (dimensionY) { if (squeeze) printf("

", (top?"up45":"dn45"), dimensionX->groupTitle); else printf("%s", dimensionX->groupTitle); } else printf(" %s", (top ? "TOP" : "BOTTOM"), dimensionX->groupTitle); for (ixX = 0; ixX < dimensionX->count; ixX++) { if (dimensionX->subtrackList && dimensionX->subtrackList[ixX] && dimensionX->subtrackList[ixX]->val) { if (dimensionY && squeeze) { // Breaks must be removed! strSwapStrs(dimensionX->titles[ixX],strlen(dimensionX->titles[ixX]),"
"," "); printf("

\n", dimensionX->tags[ixX],(top?"up45":"dn45"), compositeLabelWithVocabLink(db,parentTdb,dimensionX->subtrackList[ixX]->val, dimensionX->groupTag,dimensionX->titles[ixX])); } else { char *label =replaceChars(dimensionX->titles[ixX]," (","
("); printf(" %s ", dimensionX->tags[ixX], compositeLabelWithVocabLink(db,parentTdb,dimensionX->subtrackList[ixX]->val, dimensionX->groupTag,label)); freeMem(label); } cntX++; } } // If dimension is big enough, then add Y buttons to right as well if (cntX>MATRIX_RIGHT_BUTTONS_AFTER) { if (dimensionY) { if (squeeze) printf("

", (top?"up45":"dn45"), dimensionX->groupTitle); else printf("%s", dimensionX->groupTitle); printf("All ",top?"TOP":"BOTTOM"); buttonsForAll(FALSE, top); puts(""); } else printf("%s ", top ? "TOP" : "BOTTOM", dimensionX->groupTitle); } } else if (dimensionY) { printf(""); printf("%s", dimensionY->groupTitle); printf(""); buttonsForAll(FALSE, top); puts(""); } puts("\n"); } static void matrixXheadingsRow2(struct trackDb *parentTdb, boolean squeeze, membersForAll_t* membersForAll, boolean top) // prints the 2nd row of a matrix: Y title; X buttons; title Y { members_t *dimensionX = membersForAll->members[dimX]; members_t *dimensionY = membersForAll->members[dimY]; // If there are both X and Y dimensions, then there is a row of buttons in X if (dimensionX && dimensionY) { int ixX,cntX=0; printf("%s", dimensionY->groupTitle); for (ixX = 0; ixX < dimensionX->count; ixX++) // Special row of +- +- +- { if (dimensionX->subtrackList && dimensionX->subtrackList[ixX] && dimensionX->subtrackList[ixX]->val) { printf("\n",dimensionX->tags[ixX]); buttonsForOne(dimensionX->tags[ixX], squeeze, TRUE, top); puts(""); cntX++; } } // If dimension is big enough, then add Y buttons to right as well if (cntX>MATRIX_RIGHT_BUTTONS_AFTER) printf("%s", dimensionY->groupTitle); puts("\n"); } } static boolean matrixXheadings(char *db,struct trackDb *parentTdb, membersForAll_t* membersForAll, boolean top) // UI for X headings in matrix { boolean squeeze = matrixSqueeze(membersForAll); if (top) matrixXheadingsRow1(db, parentTdb, squeeze, membersForAll, top); matrixXheadingsRow2(parentTdb, squeeze, membersForAll, top); if (!top) matrixXheadingsRow1(db, parentTdb, squeeze, membersForAll, top); return squeeze; } static void matrixYheadings(char *db,struct trackDb *parentTdb, membersForAll_t* membersForAll, int ixY, boolean left) // prints the column of Y labels and buttons { members_t *dimensionX = membersForAll->members[dimX]; members_t *dimensionY = membersForAll->members[dimY]; struct trackDb *childTdb = NULL; if (dimensionY && dimensionY->subtrackList && dimensionY->subtrackList[ixY] && dimensionY->subtrackList[ixY]->val) childTdb = dimensionY->subtrackList[ixY]->val; if (dimensionX && dimensionY && childTdb != NULL) // Both X and Y, then column of buttons { printf("", htmlEncode(dimensionY->tags[ixY]),left?"RIGHT":"LEFT"); if (left) printf("%s ",compositeLabelWithVocabLink(db,parentTdb,childTdb,dimensionY->groupTag, dimensionY->titles[ixY])); buttonsForOne(dimensionY->tags[ixY], FALSE, left, FALSE); if (!left) printf(" %s",compositeLabelWithVocabLink(db,parentTdb,childTdb,dimensionY->groupTag, dimensionY->titles[ixY])); puts(""); } else if (dimensionX) { printf("",left?"RIGHT":"LEFT"); buttonsForAll(TRUE, TRUE); puts(""); } else if (left && dimensionY && childTdb != NULL) printf("%s\n",htmlEncode(dimensionY->tags[ixY]), compositeLabelWithVocabLink(db,parentTdb,childTdb,dimensionY->groupTag, dimensionY->titles[ixY])); } static int displayABCdimensions(char *db,struct cart *cart, struct trackDb *parentTdb, struct slRef *subtrackRefList, membersForAll_t* membersForAll) // This will walk through all declared nonX&Y dimensions (X and Y is the 2D matrix of CBs. // NOTE: ABC dims are only supported if there are X & Y both. // Also expected number should be passed in { int count=0,ix; for (ix=dimA;ixdimMax;ix++) { if (membersForAll->members[ix]==NULL) continue; if (membersForAll->members[ix]->count<1) continue; count++; if (count==1) // First time set up a table puts("
"); printf("", membersForAll->members[ix]->groupTitle); int aIx; for (aIx=0;aIxmembers[ix]->count;aIx++) { if (membersForAll->members[ix]->tags[aIx] != NULL) { assert(membersForAll->members[ix]->subtrackList[aIx]->val != NULL); printf(""); } } puts(""); } if (count>0) puts("

%s:

"); char objName[SMALLBUF]; char other[JBUFSIZE]; boolean alreadySet=FALSE; if (membersForAll->members[ix]->selected != NULL) alreadySet = membersForAll->members[ix]->selected[aIx]; safef(objName, sizeof(objName), "%s.mat_%s_dim%c_cb",parentTdb->track, membersForAll->members[ix]->tags[aIx],membersForAll->letters[ix]); safef(other, sizeof other, "class='matCB abc %s'", membersForAll->members[ix]->tags[aIx]); cgiMakeCheckBoxIdAndMore(objName,alreadySet,objName,other); jsOnEventById("click", objName, "matCbClick(this);"); printf("%s",compositeLabelWithVocabLink(db,parentTdb, membersForAll->members[ix]->subtrackList[aIx]->val, membersForAll->members[ix]->groupTag, membersForAll->members[ix]->titles[aIx])); puts("

"); return count; } #ifdef DEBUG static void dumpDimension(members_t *dimension, char *name, FILE *f) /* Dump out information on dimension. */ { int count = dimension->count; fprintf(f, "%s: count=%d tag=%s title=%s setting=%s
\n", name, count, dimension->tag, dimension->title, dimension->setting); int i; for (i=0; inames[i], dimension->values[i]); fprintf(f, "
\n"); } #endif /* DEBUG */ static char *labelWithVocabLinkForMultiples(char *db,struct trackDb *parentTdb, members_t* members) // If the parentTdb has a controlledVocabulary setting and the vocabType is found, // then label will be wrapped with the link to all relevent terms. Return string is cloned. { assert(members->subtrackList != NULL); char *vocab = cloneString(trackDbSetting(parentTdb, "controlledVocabulary")); if (vocab == NULL) return cloneString(members->groupTitle); // No link wrapping! char *words[15]; int count,ix; boolean found=FALSE; if ((count = chopByWhite(vocab, words,15)) <= 1) // vocab now contains just the file name return cloneString(members->groupTitle); char *mdbVar = NULL; // Find mdb var to look up based upon the groupTag and cv setting for (ix=1;ixgroupTag,words[ix])) // controlledVocabulary setting matches tag { // so all labels are linked mdbVar = members->groupTag; break; } else if (startsWithWordByDelimiter(members->groupTag,'=',words[ix])) { mdbVar = words[ix] + strlen(members->groupTag) + 1; break; } } if (mdbVar == NULL) { freeMem(vocab); return cloneString(members->groupTitle); } #define VOCAB_MULTILINK_BEG "%s" struct dyString *dyLink = dyStringCreate(VOCAB_MULTILINK_BEG, (sameWord(mdbVar,"antibody")?"target":"term")); // Now build the comma delimited string of mdb vals (all have same mdb var) boolean first = TRUE; for (ix=0;ixcount;ix++) { if (members->subtrackList[ix] != NULL && members->subtrackList[ix]->val != NULL) { struct trackDb *childTdb = members->subtrackList[ix]->val; (void)metadataForTable(db,childTdb,NULL); // Makes sure this has been populated const char * mdbVal = metadataFindValue(childTdb,mdbVar); // one for each is enough if (mdbVal != NULL) { if (!first) dyStringAppendC(dyLink,','); dyStringAppend(dyLink,(char *)mdbVal); first = FALSE; } } } dyStringPrintf(dyLink,VOCAB_MULTILINK_END,members->groupTitle,members->groupTitle); freeMem(vocab); return dyStringCannibalize(&dyLink); } static boolean compositeUiByFilter(char *db, struct cart *cart, struct trackDb *parentTdb, char *formName) // UI for composite tracks: filter subgroups by multiselects to select subtracks. { membersForAll_t* membersForAll = membersForAllSubGroupsGet(parentTdb,cart); if (membersForAll == NULL || membersForAll->filters == FALSE) // Not Matrix or filters return FALSE; if (cartOptionalString(cart, "ajax") == NULL) { webIncludeResourceFile("ui.dropdownchecklist.css"); jsIncludeFile("ui.dropdownchecklist.js",NULL); jsIncludeFile("ddcl.js",NULL); } cgiDown(0.7); printf("Select subtracks %sby: (select multiple %sitems - %s)
\n", (membersForAll->members[dimX] != NULL || membersForAll->members[dimY] != NULL ? "further ":""), (membersForAll->dimMax == dimA?"":"categories and "),FILTERBY_HELP_LINK); printf("\n"); char id[256]; char javascript[1024]; // Do All [+][-] buttons if (membersForAll->members[dimX] == NULL && membersForAll->members[dimY] == NULL) // No matrix { printf("\n"); } // Now make a filterComp box for each ABC dimension int dimIx=dimA; for (dimIx=dimA;dimIxdimMax;dimIx++) { printf("\n"); } printf("

All:
"); // TODO: Test when a real world case actually calls this. Currently no trackDb.ra cases exist #define PM_BUTTON_FILTER_COMP "" #define PM_BUTTON_FILTER_COMP_JS "waitOnFunction(filterCompositeSet,this,%s);return false;" #define MAKE_PM_BUTTON_FILTER_COMP(tf,fc,plmi) \ safef(id, sizeof id, "btn_%s", (fc)); \ printf(PM_BUTTON_FILTER_COMP, id, (plmi)); \ safef(javascript, sizeof javascript, PM_BUTTON_FILTER_COMP_JS, (tf)); \ jsOnEventById("click", id, javascript); MAKE_PM_BUTTON_FILTER_COMP("true", "plus_fc",'+') MAKE_PM_BUTTON_FILTER_COMP("false","minus_fc",'-') printf("

%s:
\n", labelWithVocabLinkForMultiples(db,parentTdb,membersForAll->members[dimIx])); safef(id, sizeof id, "fc%d",dimIx); printf( ""); if (membersForAll->members[dimIx]->fcType == fctOneOnly) printf(" (select only one)"); printf("

\n"); puts("
\n"); return TRUE; } void fastMatixToSubtrackMap() // prints out the "common" globals json hash // This hash is the one utils.js and therefore all CGIs know about { struct dyString *dy = dyStringNew(1024); dyStringPrintf(dy, "var mtxSubMap = {};\n" "$( document ).ready(function()\n" "{\n" "matCB = $('input.matCB:first');\n" "if (!matCB)\n" " return;\n" "var matClassList = $( matCB ).attr('class').split(' ');\n" "matClassList = aryRemove(matClassList,['matCB','changed','disabled','abc']);\n" "if (matClassList.length === 0 )\n" " return;\n" "subCBs = $('input.subCB');\n" "$( subCBs ).each( function (i) { \n" " // class='subCB BS-Seq Mantle_Cell_Lymphoma venous_blood A007MCL CNAG CPG_methylation_cov signal' \n" " var classList = $( this ).attr('class').split(' ');\n" " if (matClassList.length === 1) {\n" " var classes = '.' + classList[1]; // dimX or dimY \n" " } else {\n" " var classes = '.' + classList[1] + '.' + classList[2]; // dimX and dimY \n" " }\n" " if (mtxSubMap[classes] === undefined) {\n" " mtxSubMap[classes] = [this];\n" " } else {\n" " mtxSubMap[classes].push(this);\n" " }\n" "});\n" "});\n" ); jsInline(dy->string); dyStringFree(&dy); } static boolean compositeUiByMatrix(char *db, struct cart *cart, struct trackDb *parentTdb, char *formName) // UI for composite tracks: matrix of checkboxes. { //int ix; char objName[SMALLBUF]; membersForAll_t* membersForAll = membersForAllSubGroupsGet(parentTdb,cart); if (membersForAll == NULL || membersForAll->dimensions == NULL) // Not Matrix! return FALSE; int ixX,ixY; members_t *dimensionX = membersForAll->members[dimX]; members_t *dimensionY = membersForAll->members[dimY]; // use array of char determine all the cells (in X,Y,Z dimensions) that are actually populated char *value; int sizeOfX = dimensionX?dimensionX->count:1; int sizeOfY = dimensionY?dimensionY->count:1; int cells[sizeOfX][sizeOfY]; // There needs to be atleast one element in dimension int chked[sizeOfX][sizeOfY]; // How many subCBs are checked per matCB? int enabd[sizeOfX][sizeOfY]; // How many subCBs are enabled per matCB? memset(cells, 0, sizeof(cells)); memset(chked, 0, sizeof(chked)); memset(enabd, 0, sizeof(chked)); struct slRef *subtrackRef, *subtrackRefList = trackDbListGetRefsToDescendantLeaves(parentTdb->subtracks); struct trackDb *subtrack; if (dimensionX || dimensionY) // Must be an X or Y dimension { // Fill the cells based upon subtrack membership for (subtrackRef = subtrackRefList; subtrackRef != NULL; subtrackRef = subtrackRef->next) { subtrack = subtrackRef->val; ixX = (dimensionX ? -1 : 0 ); ixY = (dimensionY ? -1 : 0 ); if (dimensionX && subgroupFind(subtrack,dimensionX->groupTag,&value)) { ixX = stringArrayIx(value,dimensionX->tags,dimensionX->count); subgroupFree(&value); } if (dimensionY && subgroupFind(subtrack,dimensionY->groupTag,&value)) { ixY = stringArrayIx(value,dimensionY->tags,dimensionY->count); subgroupFree(&value); } if (ixX > -1 && ixY > -1) { cells[ixX][ixY]++; int fourState = subtrackFourStateChecked(subtrack,cart); // hidden views are handled by 4-way CBs: only count enabled if (fourStateEnabled(fourState)) { // Only bother if the subtrack is found in all ABC dims checked if (subtrackInAllCurrentABCs(subtrack,membersForAll)) { enabd[ixX][ixY]++; if (fourStateChecked(fourState) == 1) chked[ixX][ixY]++; } } } } } // If there is no matrix and if there is a filterComposite, then were are done. if (dimensionX == NULL && dimensionY == NULL) { if (compositeUiByFilter(db, cart, parentTdb, formName)) return FALSE; } // Tell the user what to do: char javascript[JBUFSIZE]; //puts("Select subtracks by characterization:
"); printf("Select subtracks by "); if (dimensionX && !dimensionY) safef(javascript, sizeof(javascript), "%s:",dimensionX->groupTitle); else if (!dimensionX && dimensionY) safef(javascript, sizeof(javascript), "%s:",dimensionY->groupTitle); else if (dimensionX && dimensionY) safef(javascript, sizeof(javascript), "%s and %s:", dimensionX->groupTitle,dimensionY->groupTitle); else safef(javascript, sizeof(javascript), "multiple variables:"); puts(strLower(javascript)); if (!subgroupingExists(parentTdb,"view")) puts("(help)\n"); puts("
\n"); if (membersForAll->abcCount > 0 && membersForAll->filters == FALSE) { displayABCdimensions(db,cart,parentTdb,subtrackRefList,membersForAll); } // Could have been just filterComposite. Must be an X or Y dimension if (dimensionX == NULL && dimensionY == NULL) return FALSE; // if there is a treeimage, put it beside the matrix in the green box char *treeImage = trackDbSetting(parentTdb, "treeImage"); if (treeImage != NULL) { printf("

"); printf("\n", COLOR_BG_ALTDEFAULT); } else printf("

\n", COLOR_BG_ALTDEFAULT); (void)matrixXheadings(db,parentTdb,membersForAll,TRUE); // Now the Y by X matrix int cntX=0,cntY=0; for (ixY = 0; ixY < sizeOfY; ixY++) { if (dimensionY == NULL || (dimensionY->tags[ixY])) { cntY++; assert(!dimensionY || ixY < dimensionY->count); printf(""); matrixYheadings(db,parentTdb, membersForAll,ixY,TRUE); #define MAT_CB_SETUP "" #define MAT_CB(name,js) printf(MAT_CB_SETUP,(htmlEncode(name)),(htmlEncode(name)),(js)); for (ixX = 0; ixX < sizeOfX; ixX++) { if (dimensionX == NULL || (dimensionX->tags[ixX])) { assert(!dimensionX || ixX < dimensionX->count); if (cntY==1) // Only do this on the first good Y cntX++; if (dimensionX && ixX == dimensionX->count) break; char *ttlX = NULL; char *ttlY = NULL; if (dimensionX) { ttlX = cloneString(dimensionX->titles[ixX]); stripString(ttlX,""); stripString(ttlX,""); } if (dimensionY != NULL) { ttlY = cloneString(dimensionY->titles[ixY]); stripString(ttlY,""); stripString(ttlY,""); } if (cells[ixX][ixY] > 0) { boolean halfChecked = ( chked[ixX][ixY] > 0 && chked[ixX][ixY] < enabd[ixX][ixY]); struct dyString *dySettings = dyStringNew(256); if (dimensionX && dimensionY) { safef(objName, sizeof(objName), "mat_%s_%s_cb", dimensionX->tags[ixX],dimensionY->tags[ixY]); } else { safef(objName, sizeof(objName), "mat_%s_cb", (dimensionX ? dimensionX->tags[ixX] : dimensionY->tags[ixY])); } if (ttlX && ttlY) printf(""); } else { if (ttlX && ttlY) printf("\n", dimensionX->tags[ixX],dimensionY->tags[ixY]); else printf("\n", (dimensionX ? dimensionX->tags[ixX] : dimensionY->tags[ixY])); } } } if (dimensionX && cntX>MATRIX_RIGHT_BUTTONS_AFTER) matrixYheadings(db,parentTdb, membersForAll,ixY,FALSE); puts("\n"); } } if (dimensionY && cntY>MATRIX_BOTTOM_BUTTONS_AFTER) matrixXheadings(db,parentTdb,membersForAll,FALSE); puts("

\n", htmlEncode(dimensionX->tags[ixX]),htmlEncode(dimensionY->tags[ixY])); else printf("

\n", htmlEncode(dimensionX ? dimensionX->tags[ixX] : dimensionY->tags[ixY])); dyStringPrintf(dySettings, " class=\"matCB"); if (halfChecked) dyStringPrintf(dySettings, " disabled"); // appears disabled but still clickable! if (dimensionX) dyStringPrintf(dySettings, " %s",dimensionX->tags[ixX]); if (dimensionY) dyStringPrintf(dySettings, " %s",dimensionY->tags[ixY]); dyStringAppendC(dySettings,'"'); if (chked[ixX][ixY] > 0) dyStringAppend(dySettings," CHECKED"); if (halfChecked) dyStringAppend(dySettings," title='Not all associated subtracks have been selected'"); MAT_CB(objName,dyStringCannibalize(&dySettings)); jsOnEventById("click", objName, "matCbClick(this);"); // X&Y are set by javascript puts("

"); // if there is a treeImage, put it beside the matrix if (treeImage != NULL) printf("

", treeImage); // If any filter additional filter composites, they can be added at the end. compositeUiByFilter(db, cart, parentTdb, formName); fastMatixToSubtrackMap(); return TRUE; } static boolean compositeUiAllButtons(char *db, struct cart *cart, struct trackDb *parentTdb, char *formName) // UI for composite tracks: all/none buttons only (as opposed to matrix or lots of buttons { if (trackDbCountDescendantLeaves(parentTdb) <= 1) return FALSE; if (dimensionsExist(parentTdb)) return FALSE; #define PM_BUTTON_GLOBAL "

" #define PM_BUTTON_GLOBAL_JS "matSubCBsCheck(%s);" char id[256]; safef(id, sizeof id, "btn_plus_all"); printf(PM_BUTTON_GLOBAL, id, "add_sm.gif"); jsOnEventByIdF("click", id, PM_BUTTON_GLOBAL_JS, "true"); safef(id, sizeof id, "btn_minus_all"); printf(PM_BUTTON_GLOBAL, id, "remove_sm.gif"); jsOnEventByIdF("click", id, PM_BUTTON_GLOBAL_JS, "false"); puts(" Select all subtracks
"); return TRUE; } static boolean compositeUiNoMatrix(char *db, struct cart *cart, struct trackDb *parentTdb, char *formName) // UI for composite tracks: subtrack selection. This is the default UI // without matrix controls. { int i, j, k; char *words[SMALLBUF]; char option[SMALLBUF]; int wordCnt; char *name, *value; char buttonVar[1024]; char setting[] = "subGroupN"; char *button; struct trackDb *subtrack; bool hasSubgroups = (trackDbSetting(parentTdb, "subGroup1") != NULL); if (dimensionsExist(parentTdb)) return FALSE; puts(""); if (hasSubgroups) { puts("Select subtracks:"); puts(""); puts("

*All* " "	"); } else { puts("
All subtracks:	"); } safef(buttonVar, sizeof buttonVar, "%s", "button_all"); if (formName) { makeAddClearButtonPair("cpmUiNoMtx_but_all", NULL,"	"); // NULL means all } else { cgiMakeButton(buttonVar, ADD_BUTTON_LABEL); puts("	"); cgiMakeButton(buttonVar, CLEAR_BUTTON_LABEL); } button = cgiOptionalString(buttonVar); if (isNotEmpty(button)) { struct slRef tdbRefList = trackDbListGetRefsToDescendantLeaves(parentTdb->subtracks); struct slRef tdbRef; for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { subtrack = tdbRef->val; boolean newVal = FALSE; safef(option, sizeof(option), "%s_sel", subtrack->track); newVal = sameString(button, ADD_BUTTON_LABEL); cartSetBoolean(cart, option, newVal); } } puts("

"); // generate set & clear buttons for subgroups for (i = 0; i < MAX_SUBGROUP; i++) { char *subGroup; safef(setting, sizeof setting, "subGroup%d", i+1); if (trackDbSetting(parentTdb, setting) == NULL) break; wordCnt = chopLine(cloneString(trackDbSetting(parentTdb, setting)), words); if (wordCnt < 2) continue; subGroup = cloneString(words[0]); if (sameWord(subGroup,"view")) continue; // Multi-view should have taken care of "view" subgroup already puts(""); printf("", words[1]); for (j = 2; j < wordCnt; j++) { if (!parseAssignment(words[j], &name, &value)) continue; printf(""); button = cgiOptionalString(buttonVar); if (isEmpty(button)) continue; struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(parentTdb->subtracks); struct slRef *tdbRef; for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { subtrack = tdbRef->val; char *p; int n; if ((p = trackDbSetting(subtrack, "subGroups")) == NULL) continue; n = chopLine(cloneString(p), words); for (k = 0; k < n; k++) { char *subName, *subValue; if (!parseAssignment(words[k], &subName, &subValue)) continue; if (sameString(subName, subGroup) && sameString(subValue, name)) { boolean newVal = FALSE; safef(option, sizeof(option),"%s_sel", subtrack->track); newVal = sameString(button, ADD_BUTTON_LABEL); cartSetBoolean(cart, option, newVal); } } } } puts("

%s
%s	", value); safef(buttonVar, sizeof buttonVar, "%s_%s", subGroup, name); if (formName) { char id[256]; safef(id, sizeof id, "cpmUiNoMtx_but_%d_%d", i, j); makeAddClearButtonPair(id, name,"	"); } else { cgiMakeButton(buttonVar, ADD_BUTTON_LABEL); puts("	"); cgiMakeButton(buttonVar, CLEAR_BUTTON_LABEL); } puts("

"); } return TRUE; } static bool mouseOverJsDone = FALSE; void printInfoIconSvg(char *color) /* Print just info icon (i) as svg tag to stdout, default color is #1C274C */ { puts(""); } void printInfoIconColor(char *mouseover, char *color) /* Print info icon (i) with explanatory text on mouseover, with color */ { printf("", mouseover); printInfoIconSvg(color); puts(""); if (!mouseOverJsDone) { jsInline("document.addEventListener('DOMContentLoaded', function() {\n" " convertTitleTagsToMouseovers();\n" " });\n"); mouseOverJsDone = TRUE; } } void printInfoIcon(char *mouseover) /* Print info icon (i) with explanatory text on mouseover */ { // see https://www.svgrepo.com/svg/524660/info-circle printf("", mouseover); printInfoIconSvg("#1C274C"); puts(""); if (!mouseOverJsDone) { jsInline("document.addEventListener('DOMContentLoaded', function() {\n" " convertTitleTagsToMouseovers();\n" " });\n"); mouseOverJsDone = TRUE; } } void hCompositeUi(char *db, struct cart *cart, struct trackDb *tdb, char *primarySubtrack, char *fakeSubmit, char *formName) // UI for composite tracks: subtrack selection. If primarySubtrack is // non-NULL, don't allow it to be cleared and only offer subtracks // that have the same type. If fakeSubmit is non-NULL, add a hidden // var with that name so it looks like it was pressed. { bool hasSubgroups = (trackDbSetting(tdb, "subGroup1") != NULL); boolean isMatrix = dimensionsExist(tdb); boolean viewsOnly = FALSE; if (primarySubtrack == NULL && !cartVarExists(cart, "ajax")) { if (trackDbSetting(tdb, "dragAndDrop") != NULL) jsIncludeFile("jquery.tablednd.js", NULL); jsIncludeFile("ajax.js",NULL); jsIncludeFile("hui.js",NULL); jsIncludeFile("subCfg.js",NULL); jsIncludeFile("ddcl.js", NULL); webIncludeResourceFile("ui.dropdownchecklist.css"); jsIncludeFile("ui.dropdownchecklist.js",NULL); } cgiDown(0.3); compositeHideEmptySubtracksUi(cart, tdb); if (trackDbCountDescendantLeaves(tdb) < MANY_SUBTRACKS && !hasSubgroups) { if (primarySubtrack) compositeUiSubtracksMatchingPrimary(db, cart, tdb,primarySubtrack); else compositeUiSubtracks(db, cart, tdb); return; } if (fakeSubmit) cgiMakeHiddenVar(fakeSubmit, "submit"); if (primarySubtrack == NULL) { if (subgroupingExists(tdb,"view")) { hCompositeDisplayViewDropDowns(db, cart,tdb); if (subgroupCount(tdb) <= 1) viewsOnly = TRUE; } if (!viewsOnly) { cgiDown(0.7); if (trackDbSettingOn(tdb, "allButtonPair")) { compositeUiAllButtons(db, cart, tdb, formName); } else if (!hasSubgroups || !isMatrix) { compositeUiNoMatrix(db, cart, tdb, formName); } else { compositeUiByMatrix(db, cart, tdb, formName); } } } cartSaveSession(cart); cgiContinueHiddenVar("g"); if (primarySubtrack) compositeUiSubtracksMatchingPrimary(db, cart, tdb,primarySubtrack); else compositeUiSubtracks(db, cart, tdb); if (primarySubtrack == NULL) // primarySubtrack is set for tableBrowser but not hgTrackUi { if (trackDbCountDescendantLeaves(tdb) > 5) { cgiDown(0.7); cgiMakeButton("Submit", "Submit"); } } } boolean superTrackDropDownWithExtra(struct cart *cart, struct trackDb *tdb, int visibleChild, struct slPair *events) // Displays hide/show dropdown for supertrack. // Set visibleChild to indicate whether 'show' should be grayed // out to indicate that no supertrack members are visible: // 0 to gray out (no visible children) // 1 don't gray out (there are visible children) // -1 don't know (this function should determine) // If -1,i the subtracks field must be populated with the child trackDbs. // Returns false if not a supertrack { if (!tdbIsSuperTrack(tdb)) return FALSE; // determine if supertrack is show/hide boolean show = FALSE; char *setting = cartUsualString(cart, tdb->track, tdb->isShow ? "show" : "hide"); if (sameString("show", setting)) show = TRUE; // Determine if any tracks in supertrack are visible; if not, the 'show' is grayed out if (show && (visibleChild == -1)) { visibleChild = 0; struct slRef *childRef; for ( childRef = tdb->children; childRef != NULL; childRef = childRef->next) { struct trackDb *cTdb = childRef->val; cTdb->visibility = hTvFromString(cartUsualString(cart, cTdb->track, hStringFromTv(cTdb->visibility))); if (cTdb->visibility != tvHide) visibleChild = 1; } } hideShowDropDownWithClassExtraAndLabel(tdb->track, NULL, show, (show && visibleChild) ? "superDropdown normalText visDD" : "superDropdown hiddenText visDD", events, tdb->shortLabel); return TRUE; } int tvConvertToNumericOrder(enum trackVisibility v) { return ((v) == tvShow ? 5 : \ (v) == tvFull ? 4 : \ (v) == tvPack ? 3 : \ (v) == tvSquish ? 2 : \ (v) == tvDense ? 1 : 0); } int tvCompare(enum trackVisibility a, enum trackVisibility b) /* enum trackVis isn't in numeric order by visibility, so compare * symbolically: */ { return (tvConvertToNumericOrder(b) - tvConvertToNumericOrder(a)); } enum trackVisibility tvMin(enum trackVisibility a, enum trackVisibility b) /* Return the less visible of a and b. */ { if (tvCompare(a, b) >= 0) return a; else return b; } enum trackVisibility tdbLocalVisibility(struct cart *cart, struct trackDb *tdb, boolean *subtrackOverride) // returns visibility NOT limited by ancestry. // Fills optional boolean if subtrack specific vis is found // If not NULL cart will be examined without ClosestToHome. // Folders/supertracks resolve to hide/full { if (subtrackOverride != NULL) *subtrackOverride = FALSE; // default // tdb->visibility should reflect local trackDb setting enum trackVisibility vis = tdb->visibility; if (tdbIsSuperTrack(tdb)) vis = (tdb->isShow ? tvFull : tvHide); if (cart != NULL) // cart is optional { char *cartVis = cartOptionalString(cart, tdb->track); boolean cgiVar = FALSE; // check hub tracks for visibility settings without the hub prefix if (startsWith("hub_", tdb->track) && (cartVis == NULL)) { cartVis = cgiOptionalString( trackHubSkipHubName(tdb->track)); cgiVar = TRUE; } if (cartVis != NULL) { vis = hTvFromString(cartVis); if (subtrackOverride != NULL && tdbIsContainerChild(tdb)) *subtrackOverride = TRUE; if (cgiVar) { cartSetString(cart, tdb->track, cartVis); // add the decorated visibility to the cart cartRemove(cart, trackHubSkipHubName(tdb->track)); // remove the undecorated version } } } return vis; } enum trackVisibility tdbVisLimitedByAncestors(struct cart *cart, struct trackDb *tdb, boolean checkBoxToo, boolean foldersToo) // returns visibility limited by ancestry. // This includes subtrack vis override and parents limit maximum. // cart may be null, in which case, only trackDb settings (default state) are examined // checkBoxToo means ensure subtrack checkbox state is visible // foldersToo means limit by folders (aka superTracks) as well. { boolean subtrackOverride = FALSE; enum trackVisibility vis = tdbLocalVisibility(cart,tdb,&subtrackOverride); // Children of a faceted composite are heterogeneous enough that one inherited vis won't // do, so they keep a display mode of their own and the parent's vis is only a ceiling. boolean facetedChild = (tdbIsContainerChild(tdb) && tdbIsFacetedComposite(tdb->parent)); char *onlyVis = (facetedChild ? trackDbLocalSetting(tdb, "onlyVisibility") : NULL); if (tdbIsContainerChild(tdb)) { if (facetedChild) { // A child of a faceted composite holds a display mode of its own rather than // inheriting the parent's. NOTE: tdb->visibility can't tell "asked for something" // from "inherited a default", since trackDbFieldsFromSettings() fills it through // the inheriting trackDbSetting() - hence trackDbLocalSetting here. boolean hasOwnVis = (subtrackOverride || trackDbLocalSetting(tdb, "visibility") != NULL); if (onlyVis != NULL) { // onlyVisibility pins the child to a single mode, but asking to hide still hides if (!(hasOwnVis && vis == tvHide)) vis = tvFromVisOnlySetting(onlyVis); } else if (!hasOwnVis) vis = tvFull; // No mode of its own, so take whatever the parent allows } // subtracks without explicit (cart) vis but are selected, should get inherited vis else if (!subtrackOverride) vis = tvFull; // subtracks with checkbox that says no, are stopped cold if (checkBoxToo && !fourStateVisible(subtrackFourStateChecked(tdb,cart))) vis = tvHide; // Checkbox says no } if (facetedChild) { // Note this skips the subtrackOverride shortcut below on purpose: escaping the // parent's limit is exactly the behavior a faceted composite doesn't want. if (vis == tvHide) return tvHide; enum trackVisibility maxVis = tdbVisLimitedByAncestors(cart,tdb->parent,checkBoxToo, foldersToo); - if (onlyVis != NULL) // A pinned child either fits under the maximum or doesn't draw - return (tvCompare(vis,maxVis) >= 0 ? vis : tvHide); + // The container's vis is a ceiling, so it limits a pinned child the same way it + // limits any other one. It must not drop the child instead: a container sitting at + // pack over children pinned to full then draws nothing at all, with nothing on the + // page to say why. return tvMin(vis,maxVis); } if (subtrackOverride) return vis; // aka superTrack if (vis == tvHide || tdb->parent == NULL || (!foldersToo && tdbIsFolder(tdb->parent))) return vis; // end of line return tvMin(vis,tdbVisLimitedByAncestors(cart,tdb->parent,checkBoxToo,foldersToo)); } char *compositeViewControlNameFromTdb(struct trackDb *tdb) // Returns a string with the composite view control name if one exists { char *stView = NULL; char *name = NULL; char *rootName = NULL; // This routine should give these results: compositeName.viewName or else subtrackName.viewName // or else compositeName or else subtrackName if (tdbIsCompositeChild(tdb) == TRUE && trackDbLocalSetting(tdb, "parent") != NULL) { if (trackDbSettingClosestToHomeOn(tdb, "configurable")) rootName = tdb->track; // subtrackName else rootName = firstWordInLine(cloneString(trackDbLocalSetting(tdb, "parent"))); } if (rootName != NULL) { if (subgroupFind(tdb,"view",&stView)) { int len = strlen(rootName) + strlen(stView) + 3; name = needMem(len); safef(name,len,"%s.%s",rootName,stView); subgroupFree(&stView); } else name = cloneString(rootName); } else name = cloneString(tdb->track); return name; } void compositeViewControlNameFree(char **name) // frees a string allocated by compositeViewControlNameFromTdb { if (name && *name) freez(name); } boolean isNameAtParentLevel(struct trackDb *tdb,char *name) // cfgUi controls are passed a prefix name that may be at the composite, view or subtrack level // returns TRUE if name at view or composite level { struct trackDb *parent; for (parent = tdb->parent; parent != NULL; parent = parent->parent) if (startsWithWordByDelimiter(parent->track, '.', name)) return TRUE; return FALSE; } boolean chainDbNormScoreAvailable(struct trackDb *tdb) /* check if normScore column is specified in trackDb as available */ { boolean normScoreAvailable = FALSE; char * normScoreTest = trackDbSettingClosestToHomeOrDefault(tdb, "chainNormScoreAvailable", "no"); if (differentWord(normScoreTest, "no")) normScoreAvailable = TRUE; return normScoreAvailable; } void hPrintAbbreviationTable(struct sqlConnection *conn, char *sourceTable, char *label) /* Print out table of abbreviations. */ { char query[256]; sqlSafef(query, sizeof(query), "select name,description from %s order by name", sourceTable); struct sqlResult *sr = sqlGetResult(conn, query); webPrintLinkTableStart(); webPrintLabelCell("Symbol"); webPrintLabelCell(label); char **row; while ((row = sqlNextRow(sr)) != NULL) { printf("\n"); char *name = row[0]; char *description = row[1]; webPrintLinkCell(name); webPrintLinkCell(description); } sqlFreeResult(&sr); webPrintLinkTableEnd(); } /* Special info (cell type abbreviations) for factorSource tracks */ struct factorSourceInfo /* Cell type and description */ { struct factorSourceInfo *next; char *name; char *description; }; static int factorSourceInfoCmp(const void *va, const void *vb) /* Compare two factorSourceInfo's, sorting on name and then description fields */ { static char bufA[64], bufB[64]; const struct factorSourceInfo *a = *((struct factorSourceInfo **)va); const struct factorSourceInfo *b = *((struct factorSourceInfo **)vb); safef(bufA, 64, "%s+%s", a->name, a->description); safef(bufB, 64, "%s+%s", b->name, b->description); return strcmp(bufA, bufB); } void hPrintFactorSourceAbbrevTable(struct sqlConnection *conn, struct trackDb *tdb) /* Print out table of abbreviations. With 'pack' setting, * show cell name only (before '+') and uniqify */ { char *label = "Cell Type"; char *sourceTable = trackDbRequiredSetting(tdb, SOURCE_TABLE); char query[256]; sqlSafef(query, sizeof(query), "select name,description from %s order by name", sourceTable); struct sqlResult *sr = sqlGetResult(conn, query); webPrintLinkTableStart(); webPrintLabelCell("Symbol"); webPrintLabelCell(label); char **row; char *plus; struct factorSourceInfo *source = NULL, *sources = NULL; while ((row = sqlNextRow(sr)) != NULL) { char *name = row[0]; char *description = row[1]; // truncate description to just the cell type if ((plus = strchr(description, '+')) != NULL) *plus = 0; AllocVar(source); source->name = cloneString(name); source->description = cloneString(description); slAddHead(&sources, source); } slUniqify(&sources, factorSourceInfoCmp, NULL); int count = 0; while ((source = slPopHead(&sources)) != NULL) { printf("\n"); webPrintLinkCell(source->name); webPrintLinkCellStart(); fputs(source->description, stdout); count++; while (sources && sameString(sources->name, source->name)) { source = slPopHead(&sources); fputs(", ", stdout); fputs(source->description, stdout); count++; } webPrintLinkCellEnd(); } sqlFreeResult(&sr); webPrintLinkTableEnd(); printf("Total: %d\n", count); } static char *makeOnePennantIcon(char *setting, char **hintRet) // Builds a string with pennantIcon HTML and returns it. Also returns hint. */ { setting = cloneString(setting); char *icon = nextWord(&setting); char buffer[4096]; char *src = NULL; char *url = NULL, *hint = NULL, *color = NULL; boolean isTextIcon = FALSE; if (!(endsWith(icon, ".jpg") || endsWith(icon, ".png"))) { isTextIcon = TRUE; color = nextWord(&setting); src = strLower(icon); } else if (startsWith("http://", icon) || startsWith("https://", icon) || startsWith("ftp://", icon)) src = htmlEncode(icon); else { safef(buffer, sizeof buffer, "../images/%s", icon); src = htmlEncode(buffer); } if (setting) { url = nextWord(&setting); if (setting) { hint = htmlEncode(stripEnclosingDoubleQuotes(setting)); } } struct dyString *ds = dyStringNew(0); // generate markup if (url) dyStringPrintf(ds, ""); // add text or image if (isTextIcon) dyStringPrintf(ds, "%s", src); else dyStringPrintf(ds, "

", src); // close tags if (url) dyStringAppend(ds, ""); else if (isTextIcon) dyStringAppend(ds, ""); dyStringAppend(ds, "\n"); if (hint && hintRet) *hintRet = cloneString(hint); return dyStringCannibalize(&ds); } static struct slPair *makePennantIcons(struct trackDb *tdb) /* Return a list of pairs of pennantIcon HTML and note strings. */ { char *setting = trackDbSetting(tdb, "pennantIcon"); if (setting == NULL || sameString(setting, "none")) return NULL; struct slPair *list = NULL; int maxPennants = 3; char *pennants[maxPennants]; int numPennants = chopByChar(setting, ';', pennants, ArraySize(pennants)); int i; for (i = 0; i < numPennants; i++) { char *hint = NULL; char *html = makeOnePennantIcon(pennants[i], &hint); slPairAdd(&list, html, hint); freeMem(html); } slReverse(&list); return list; } void hPrintIcons(struct trackDb *tdb) /* prints optional folder and pennants icons and a space, if any icons were printed */ { bool hasIcon = hPrintPennantIcon(tdb); if (tdbIsSuper(tdb) || tdbIsComposite(tdb)) { // this is the folder.svg icon from the font-awesome collection. // the icon collection also contains a "fa fa-folder-o" icon, which is the outlined version // It was decided to use only the filled out icon for now and use the same icon for super // and composite tracks. Adding the SVG removes a dependency and makes the icons show up instantly, // instead of the short delay when using fonts. Github uses icons like this. hPrintf("" ""); hasIcon = TRUE; } if (hasIcon) hPrintf(" "); } boolean hPrintPennantIcon(struct trackDb *tdb) // Returns TRUE and prints out the "pennantIcon" when found. // Example: ENCODE tracks in hgTracks config list. { if (trackDbSetting(tdb, "wgEncode") != NULL) { hPrintf("\n"); } struct slPair *list = makePennantIcons(tdb), *el; boolean gotPennant = (list != NULL); for (el = list; el != NULL; el = el->next) hPrintf("%s\n", el->name); slPairFreeValsAndList(&list); return gotPennant; } boolean printPennantIconNote(struct trackDb *tdb) // Returns TRUE and prints out the "pennantIcon" and note when found. //This is used by hgTrackUi and hgc before printing out trackDb "html" { struct slPair *list = makePennantIcons(tdb), *el; boolean gotPennant = (list != NULL); for (el = list; el != NULL; el = el->next) { printf("
%s\n", el->name); char *hint = el->val; if (hint) printf("Note: %s\n", hint); } slPairFreeValsAndList(&list); return gotPennant; } void printUpdateTime(char *database, struct trackDb *tdb, struct customTrack *ct) /* display table update time */ { if (trackHubDatabase(database)) return; /* synthetic tracks have no data file or table to check */ if (trackDbSetting(tdb, "syntheticTrack") != NULL) return; /* have not decided what to do for a composite container */ if (tdbIsComposite(tdb) || tdbIsSuper(tdb)) return; struct sqlConnection *conn = NULL; char *tableName = NULL; if (isCustomTrack(tdb->track)) { if (ct) { conn = hAllocConn(CUSTOM_TRASH); tableName = ct->dbTableName; } } else if (startsWith("big", tdb->type)) { char *tableName = hTableForTrack(database, tdb->table); struct sqlConnection *conn = hAllocConnTrack(database, tdb); char *bbiFileName = bbiNameFromSettingOrTable(tdb, conn, tableName); hFreeConn(&conn); struct bbiFile *bbi = NULL; if (startsWith("bigWig", tdb->type)) bbi = bigWigFileOpen(bbiFileName); else bbi = bigBedFileOpen(bbiFileName); time_t timep = 0; if (bbi) { timep = bbiUpdateTime(bbi); bbiFileClose(&bbi); } printBbiUpdateTime(&timep); } else { tableName = hTableForTrack(database, tdb->table); conn = hAllocConnTrack(database, tdb); } if (tableName) { char *date = firstWordInLine(sqlTableUpdate(conn, tableName)); if (date != NULL) printf("Data last updated at UCSC: %s
\n", date); } hFreeConn(&conn); } char *getTrackHtml(char *db, char *trackName) /* Grab HTML from trackDb in native database for quickLift tracks. */ { char *html = NULL; if (trackHubDatabase(db) || isGenArk(db)) { struct trackHub *hub = NULL; struct trackHubGenome *hubGenome = trackHubGetGenome(db); if (hubGenome != NULL) hub = hubGenome->trackHub; else if (isGenArk(db)) { char *hubUrl = genarkUrl(db); if (hubUrl != NULL) { hub = trackHubOpen(hubUrl, ""); if (hub != NULL) hubGenome = trackHubFindGenome(hub, db); } } if (hubGenome != NULL) { struct trackDb *tdbList = trackHubAddTracksGenome(hubGenome); struct trackDb *tdb = findTdbByBareName(tdbList, trackHubSkipHubName(trackName)); if (tdb != NULL) { trackHubAddDescription(hubGenome->trackDbFile, tdb); html = tdb->html; } } } else { char query[4096]; sqlSafef(query, sizeof query, "tableName = '%s'", trackHubSkipHubName(trackName)); struct trackDb *loadTrackDb(char *db, char *where); struct trackDb *tdb = loadTrackDb(db, query); html = tdb->html; //char *html = tdb->html; if (isEmpty(tdb->html)) { char *parent = trackDbSetting(tdb, "parent"); char *words[10]; chopLine(parent,words); sqlSafef(query, sizeof query, "tableName = '%s'", trackHubSkipHubName(words[0])); struct trackDb *tdb = loadTrackDb(db, query); html = tdb->html; } } return html; } void printBbiUpdateTime(time_t *timep) /* for bbi files, print out the timep value */ { printf("Data last updated at UCSC: %s
\n", sqlUnixTimeToDate(timep, FALSE)); } static boolean tableDescriptionsExists(struct sqlConnection *conn) /* Cache flag for whether tableDescriptions exists in conn, in case we will need to * fetch a lot of descriptions from tableDescriptions. */ { static struct hash *hash = NULL; if (hash == NULL) hash = hashNew(0); char *db = sqlGetDatabase(conn); int exists = hashIntValDefault(hash, db, -1); if (exists < 0) { exists = sqlTableExists(conn, "tableDescriptions"); hashAddInt(hash, db, exists); } return (boolean)exists; } struct asObject *asFromTableDescriptions(struct sqlConnection *conn, char *table) // If there is a tableDescriptions table and it has an entry for table, return // a parsed autoSql object; otherwise return NULL. { struct asObject *asObj = NULL; // Callers occasionally invoke asForTdb with conn=NULL (e.g. superTrack filter // rendering that isn't tied to a data table). Nothing to look up in that case. if (conn == NULL) return NULL; if (tableDescriptionsExists(conn)) { char query[PATH_LEN*2]; // Try unsplit table first. sqlSafef(query, sizeof(query), "select autoSqlDef from tableDescriptions where tableName='%s'", table); char *asText = sqlQuickString(conn, query); // If no result try split table. if (asText == NULL) { sqlSafef(query, sizeof(query), "select autoSqlDef from tableDescriptions where tableName='chrN_%s'", table); asText = sqlQuickString(conn, query); } if (isNotEmpty(asText)) asObj = asParseText(asText); freez(&asText); } return asObj; } static struct asObject *asForTdbOrDie(struct sqlConnection *conn, struct trackDb *tdb) // Get autoSQL description if any associated with tdb. // Abort if there's a problem { struct asObject *asObj = NULL; if (tdbIsBigBed(tdb)) { char *fileName = hReplaceGbdb(tdbBigFileName(conn, tdb)); if (fileName == NULL) return NULL; asObj = bigBedFileAsObjOrDefault(fileName); freeMem(fileName); } // TODO: standardize to a wig as //else if (tdbIsBigWig(tdb)) // asObj = asObjFrombigBed(conn,tdb); else if (tdbIsLongTabix(tdb)) asObj = longTabixAsObj(); else if (tdbIsBam(tdb)) asObj = bamAsObj(); else if (tdbIsVcf(tdb)) asObj = vcfAsObj(); else if (isMyVariantsType(tdb->type)) asObj = myVariantsAsObj(); else if (sameWord("bedDetail", tdb->type)) asObj = bedDetailAsObj(); else if (sameWord("pgSnp", tdb->type)) asObj = pgSnpAsObj(); else if (sameWord("barChart", tdb->type)) asObj = asParseText(barChartAutoSqlString); else if (sameWord("interact", tdb->type)) asObj = interactAsObj(); else if (sameWord("hic", tdb->type)) // HI-C data are stored in .hic files, but parsed into interact objects asObj = interactAsObj(); else if (sameWord("bedMethyl", tdb->type)) asObj = bedMethylAsObj(); else asObj = asFromTableDescriptions(conn, tdb->table); return asObj; } struct asObject *asForTdb(struct sqlConnection *conn, struct trackDb *tdb) // Get autoSQL description if any associated with table, ignoring errAborts if any. { struct errCatch *errCatch = errCatchNew(); struct asObject *asObj = NULL; // Wrap some error catching around asForTdbOrDie. if (errCatchStart(errCatch)) { asObj = asForTdbOrDie(conn, tdb); } errCatchEnd(errCatch); errCatchFree(&errCatch); return asObj; } struct asObject *asForDb(struct trackDb *tdb, char* database) /* return asObject given the database. NULL if not found */ { struct sqlConnection *conn = NULL ; // database can be a quickLift track's source assembly, which for a GenArk arrives // here as a bare accession with no MySQL database behind it. if (!trackHubDatabase(database) && !isGenArk(database)) conn = hAllocConnTrack(database, tdb); struct asObject *as = asForTdb(conn, tdb); hFreeConn(&conn); return as; } #ifdef OLD /* This got moved to main library . */ struct asColumn *asColumnFind(struct asObject *asObj, char *name) // Return named column. { struct asColumn *asCol = NULL; if (asObj!= NULL) { for (asCol = asObj->columnList; asCol != NULL; asCol = asCol->next) if (sameString(asCol->name, name)) break; } return asCol; } #endif /* OLD */ struct slName *asColNames(struct asObject *as) // Get list of column names. { struct slName *list = NULL, *el; struct asColumn *col; for (col = as->columnList; col != NULL; col = col->next) { el = slNameNew(col->name); slAddHead(&list, el); } slReverse(&list); return list; } static struct dyString *subMulti(char *orig, int subCount, char *in[], char *out[]) /* Perform multiple substitions on orig. */ { int i; struct dyString *s = dyStringNew(256), *d = NULL; dyStringAppend(s, orig); for (i=0; istring, in[i], out[i]); dyStringFree(&s); s = d; d = NULL; } return s; } char *replaceInUrl(char *url, char *idInUrl, struct cart *cart, char *db, char *seqName, int winStart, int winEnd, char *track, boolean encode, struct slPair *fields) /* replace $$ in url with idInUrl. Supports many other wildchards, and custom fields $ * XX Do we have readable docs for these parameters somewhere? * Look at http://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html */ { struct dyString *uUrl = NULL; struct dyString *eUrl = NULL; char startString[64], endString[64],oneBasedStart[64]; char *ins[14], *outs[14]; char *eItem = (encode ? cgiEncode(idInUrl) : cloneString(idInUrl)); char *scName = NULL; // try to avoid the mysql query it not necessary if (stringIn("$n", url)) { char *tmp = hScientificName(db); scName = replaceChars(tmp, " ", "_"); freeMem(tmp); } char *taxId = NULL; // try to avoid the mysql query it not necessary if (stringIn("$taxId", url)) { char query[256]; struct sqlConnection *centralConn = hConnectCentral(); sqlSafef(query, sizeof(query), "select taxId from %s " "where name='%s'", dbDbTable(), db); taxId = sqlQuickString(centralConn, query); hDisconnectCentral(¢ralConn); } safef(startString, sizeof startString, "%d", winStart); safef(endString, sizeof endString, "%d", winEnd); ins[0] = "$$"; outs[0] = idInUrl; ins[1] = "$T"; outs[1] = track; ins[2] = "$S"; outs[2] = seqName; ins[3] = "$["; outs[3] = startString; ins[4] = "$]"; outs[4] = endString; ins[5] = "$s"; outs[5] = skipChr(seqName); ins[6] = "$D"; outs[6] = trackHubSkipHubName(db); ins[7] = "$P"; /* for an item name of the form: prefix:suffix */ ins[8] = "$p"; /* the P is the prefix, the p is the suffix */ if (idInUrl && stringIn(":", idInUrl)) { char *itemClone = cloneString(idInUrl); char *suffix = stringIn(":", itemClone); char *suffixClone = cloneString(suffix+1); /* +1 skip the : */ char *nextColon = stringIn(":", suffixClone+1); if (nextColon) /* terminate suffixClone suffix */ *nextColon = '\0'; /* when next colon is present */ *suffix = '\0'; /* terminate itemClone prefix */ outs[7] = itemClone; outs[8] = suffixClone; /* small memory leak here for these cloned strings */ /* not important for a one-time operation in a CGI that will exit */ } else { outs[7] = idInUrl; /* otherwise, these are not expected */ outs[8] = idInUrl; /* to be used */ } // URL may now contain item boundaries ins[9] = "${"; ins[10] = "$}"; ins[13] = "$#"; if (cart!=NULL && cartOptionalString(cart, "o") && cartOptionalString(cart, "t")) { char *itemBeg = cartString(cart, "o"); // unexpected commas? char *itemEnd = cartString(cart, "t"); outs[9] = itemBeg; outs[10] = itemEnd; safef(oneBasedStart, sizeof(oneBasedStart), "%d", cartInt(cart, "o") + 1); outs[13] = oneBasedStart; } else // should never be but I am unwilling to bet the farm { outs[9] = startString; outs[10] = endString; safef(oneBasedStart, sizeof(oneBasedStart), "%d", winStart + 1); outs[13] = oneBasedStart; } ins[11] = "$n"; outs[11] = scName; ins[12] = "$taxId"; outs[12] = taxId; uUrl = subMulti(url, ArraySize(ins), ins, outs); outs[0] = eItem; eUrl = subMulti(url, ArraySize(ins), ins, outs); dyStringFree(&uUrl); freeMem(eItem); freeMem(scName); // substitute $ variables if (!fields) return eUrl->string; int fieldCount = slCount(fields); char **fieldNames = NULL, **fieldVals = NULL; AllocArray(fieldNames, fieldCount); AllocArray(fieldVals, fieldCount); int i; struct slPair *field; for (i=0, field=fields; inext) { char buf[64]; safef(buf, sizeof buf, "$<%s>", field->name); fieldNames[i] = cloneString(buf); fieldVals[i] = (char *)field->val; } struct dyString *fUrl = subMulti(eUrl->string, fieldCount, fieldNames, fieldVals); return fUrl->string; } static boolean isPublicDataPath(char *path) /* Return TRUE if path names a file in the /gbdb tree. Only a plain path counts, a ".." * component makes the name mean something outside that tree, so it is not accepted. */ { if (!startsWith("/gbdb/", path)) return FALSE; char *s = path + strlen("/gbdb/"); while (s != NULL && s[0] != '\0') { if (s[0] == '.' && s[1] == '.' && (s[2] == '/' || s[2] == '\0')) return FALSE; s = strchr(s, '/'); if (s != NULL) s += 1; } return TRUE; } char *checkDataVersion(char *database, struct trackDb *tdb) /* see if trackDb has a dataVersion setting and check that file for version */ { // try the metadata metadataForTable(database, tdb, NULL); char *version = (char *)metadataFindValue(tdb, "dataVersion"); // try trackDb itself, this automatically will go up the hierarchy if (version == NULL) version = trackDbSetting(tdb, "dataVersion"); if (version != NULL && startsWith("/", version)) { // dataVersion can also be the path to a local file, for otto tracks. // For quickLifted tracks the file lives on the source assembly, so // substitute $D using quickLiftDb rather than the destination database. char *liftDb = trackDbSetting(tdb, "quickLiftDb"); char *resolveDb = trackHubSkipHubName(liftDb ? liftDb : database); char *path = replaceInUrl(version, "", NULL, resolveDb, "", 0, 0, tdb->track, FALSE, NULL); // A hub is user-supplied, so a hub track may not name just any local file. Paths under // /gbdb are the exception: that tree is public data, mirrored on hgdownload, so reading // one discloses nothing. Curated-hub assemblies need this - hs1 and friends are served // to the browser as a hub, which makes their otto tracks hub tracks, and without it // hgTrackUi prints the raw path where the version should be. quickLifted tracks land // here too, their dataVersion file is under /gbdb on the source assembly. $D is // substituted before the test, since on a quickLifted track it comes from the hub. if (isPublicDataPath(path) || (!trackHubDatabase(database) && !isHubTrack(tdb->table))) { struct lineFile* lf = lineFileMayOpen(path, TRUE); if (lf) version = lineFileReadAll(lf); else version = NULL; lineFileClose(&lf); } } return version; } void printDataVersion(char *database, struct trackDb *tdb) /* If this annotation has a dataVersion setting, print it. * check hgFixed.trackVersion, meta data and trackDb 'dataVersion'. */ { char *version = checkDataVersion(database, tdb); if (version == NULL) { // try the hgFixed.trackVersion table struct trackVersion *trackVersion = getTrackVersion(database, tdb->track); // try trackVersion table with parent, for composites/superTracks if (trackVersion == NULL && tdb->parent != NULL) trackVersion = getTrackVersion(database, tdb->parent->track); if (trackVersion != NULL) version = trackVersion->version; } if (isNotEmpty(version)) // dataVersion can come from a track hub, escape printf("Version: %s
\n", htmlEncode(version)); } void printRelatedTracks(char *database, struct hash *trackHash, struct trackDb *tdb, struct cart *cart) /* Maybe print a "related track" section */ { if (trackHubDatabase(database)) return; char *relatedTrackTable = cfgOptionDefault("db.relatedTrack","relatedTrack"); struct sqlConnection *conn = hAllocConn(database); if (!sqlTableExists(conn, relatedTrackTable)) { hFreeConn(&conn); return; } char query[256]; sqlSafef(query, sizeof(query), "select track2, why from %s where track1='%s'", relatedTrackTable, tdb->track); char **row; struct sqlResult *sr; sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { puts("Related tracks\n"); puts("

"); printf("%s", hTrackUiForTrack(otherTdb->track), database, otherTdb->track, cartSidUrlString(cart), otherTdb->shortLabel); puts(": "); puts(why); } } puts("

\n"); } sqlFreeResult(&sr); hFreeConn(&conn); } char *gcOnFlyWinSize(struct cart *cart) /* Return window size for GC on the fly track calculation */ { char *returnSize = NULL; char *s = cartOptionalString(cart, gcOnFlyWindowSize); if (s != NULL) returnSize = cloneString(s); else returnSize = cloneString(gcOnFlyDefaultSize); return returnSize; }

%s
shortLabel:	%s
%s:	",mdbVar->var); struct slName fileSet = slNameListFromComma(mdbVar->val); while (fileSet != NULL) { struct slName file = slPopHead(&fileSet); dyStringAppend(dyTable,htmlStringForDownloadsLink(db, tdb, file->name, TRUE)); if (fileSet != NULL) dyStringAppend(dyTable," "); slNameFree(&file); } dyStringAppend(dyTable,"
" "%s:	%s
" "%s:	%s
%s:	%s

Alignment Gap/Insertion Display Options"); printf(" Help on display options
", INDEL_HELP_PAGE); if (includeDoubleInsert) { safef(var, sizeof(var), "%s.%s", name, INDEL_DOUBLE_INSERT); cgiMakeCheckBox(var, showDoubleInsert); printf("	Draw double horizontal lines when both genome and %s have " "an insertion
", queryTerm); } safef(var, sizeof(var), "%s.%s", name, INDEL_QUERY_INSERT); cgiMakeCheckBox(var, showQueryInsert); printf("	Draw a vertical purple line for an insertion at the beginning or " "end of the %s, orange for insertion in the middle of the %s
", queryTerm, queryTerm); if (includePolyA) { safef(var, sizeof(var), "%s.%s", name, INDEL_POLY_A); /* We can highlight valid polyA's only if we have query sequence -- * so indelPolyA code piggiebacks on baseColor code: */ if (baseColorGotSequence(tdb)) { cgiMakeCheckBox(var, showPolyA); printf("	Draw a vertical green line where %s has a polyA tail " "insertion