4e91fbccad6b04384ba5792bce44f933b5a1c1ff tdreszer Tue Oct 4 11:56:27 2011 -0700 Further fixes to the cfgByType consistency logic, prompted by side by side comparisons on hg18 tracks. diff --git src/hg/hgTrackUi/hgTrackUi.c src/hg/hgTrackUi/hgTrackUi.c index 3916174..b860670 100644 --- src/hg/hgTrackUi/hgTrackUi.c +++ src/hg/hgTrackUi/hgTrackUi.c @@ -1699,63 +1699,30 @@ radioButton(logicTypeVar, logicTypeVal, "and"); radioButton(logicTypeVar, logicTypeVal, "or"); printf("<BR>\n"); /* List various fields you can filter on. */ printf("<table border=0 cellspacing=1 cellpadding=1 width=%d>\n", CONTROL_TABLE_WIDTH); cg = startControlGrid(4, NULL); for (fil = mud->filterList; fil != NULL; fil = fil->next) oneMrnaFilterUi(cg, fil->label, fil->key, cart); endControlGrid(&cg); baseColorDrawOptDropDown(cart, tdb); indelShowOptions(cart, tdb); } - -static void filterByChrom(struct trackDb *tdb) -{ -char *filterSetting; -char filterVar[256]; -char *filterVal = ""; - -printf("<p><b>Filter by chromosome (e.g. chr10):</b> "); -snprintf(filterVar, sizeof(filterVar), "%s.chromFilter", tdb->track); -filterSetting = cartUsualString(cart, filterVar, filterVal); -cgiMakeTextVar(filterVar, cartUsualString(cart, filterVar, ""), 15); -} - -void crossSpeciesUi(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("<p><b>Color track based on chromosome:</b> "); -snprintf(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("<br><br>"); -filterByChrom(tdb); -} - void transRegCodeUi(struct trackDb *tdb) /* Put up UI for transcriptional regulatory code - not * much more than score UI. */ { printf("%s", "<P>The scoring ranges from 0 to 1000 and is based on the number of lines " "of evidence that support the motif being active. Each of the two " "<I>sensu stricto</I> species in which the motif was conserved counts " "as a line of evidence. If the ChIP-chip data showed good (P ≤ 0.001) " "evidence of binding to the transcription factor associated with the " "motif, that counts as two lines of evidence. If the ChIP-chip data " "showed weaker (P ≤ 0.005) evidence of binding, that counts as just one line " "of evidence. The following table shows the relationship between lines " "of evidence and score:"); printf("<P>"); @@ -1847,31 +1814,31 @@ } } void chainColorUi(struct trackDb *tdb) /* UI for the chain tracks */ { boolean normScoreAvailable = chainDbNormScoreAvailable(tdb); boolean compositeTrack = tdbIsComposite(tdb); if (compositeTrack) return; // configuration taken care of by hCompositeUi() later else if (normScoreAvailable) chainCfgUi(database, cart, tdb, tdb->track, NULL, FALSE, chromosome); else - crossSpeciesUi(tdb); + crossSpeciesCfgUi(cart,tdb); } void chromGraphUi(struct trackDb *tdb) /* UI for the wiggle track */ { char varName[chromGraphVarNameMaxSize]; struct sqlConnection *conn = NULL; char *track = tdb->track; if (!isCustomTrack(track)) conn = hAllocConn(database); double minVal,maxVal; struct chromGraphSettings *cgs = chromGraphSettingsGet(track, conn, tdb, cart); printf("<b>Track height: </b>"); @@ -2355,30 +2322,39 @@ "&list_uids=%s&dopt=Abstract&tool=genome.ucsc.edu\" TARGET=_BLANK>%s</A>", pmId, ref); labelArr[refCount] = cloneString(label); valueArr[refCount++] = cloneString(pmId); if (! filterPmIdInCart) slNameAddHead(&checked, pmId); if (refCount >= MAX_DGV_REFS) errAbort("dgvUi: %s has too many references (max %d)", tdb->track, MAX_DGV_REFS); } sqlFreeResult(&sr); jsMakeCheckboxGroupSetClearButton(cartVarName, TRUE); jsMakeCheckboxGroupSetClearButton(cartVarName, FALSE); cgiMakeCheckboxGroupWithVals(cartVarName, labelArr, valueArr, refCount, checked, 4); hFreeConn(&conn); } +static void factorSourceUi(char *db,struct trackDb *tdb) +{ +printf("<BR><B>Cell Abbreviations:</B><BR>\n"); +char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable"); +struct sqlConnection *conn = hAllocConn(db); +hPrintAbbreviationTable(conn, sourceTable, "Cell Type"); +hFreeConn(&conn); +} + #ifdef UNUSED static boolean isInTrackList(struct trackDb *tdbList, struct trackDb *target) /* Return TRUE if target is in tdbList. */ { struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) if (tdb == target) return TRUE; return FALSE; } #endif /* UNUSED */ void superTrackUi(struct trackDb *superTdb, struct trackDb *tdbList) /* List tracks in this collection, with visibility controls and UI links */ { @@ -2435,31 +2411,38 @@ // TODO: use hTrackUiName() printf("<p><b>NOTE</b>: Early access to additional track data may be available on the <a target=_blank href='http://%s/cgi-bin/hgTrackUi?db=%s&g=%s'>Preview Browser</A>.", "genome-preview.ucsc.edu", db, tdb->track); } } } void specificUi(struct trackDb *tdb, struct trackDb *tdbList, struct customTrack *ct, boolean ajax) /* Draw track specific parts of UI. */ { char *track = tdb->track; // Ideally check cfgTypeFromTdb()/cfgByCfgType() first, but with all these special cases already in // place, lets be cautious at this time. // NOTE: Developer, please try to use cfgTypeFromTdb()/cfgByCfgType(). -if (sameString(track, "stsMap")) +// UI precedence: +// 1) supers to get them out of the way: they have no controls +// 2) special cases based upon track name (developer please avoid) +// 3) cfgTypeFromTdb()/cfgByCfgType() <== prefered method +// 4) special cases falling through the cracks but based upon type +if (tdbIsSuperTrack(tdb)) + superTrackUi(tdb, tdbList); +else if (sameString(track, "stsMap")) stsMapUi(tdb); else if (sameString(track, "affyTxnPhase2")) affyTxnPhase2Ui(tdb); else if (sameString(track, "cgapSage")) cgapSageUi(tdb); else if (sameString(track, "stsMapMouseNew")) stsMapMouseUi(tdb); else if (sameString(track, "stsMapRat")) stsMapRatUi(tdb); else if (sameString(track, "snpMap")) snpMapUi(tdb); else if (sameString(track, "snp")) snpUi(tdb); else if (snpVersion(track) >= 125) snp125Ui(tdb); @@ -2518,138 +2501,111 @@ rosettaUi(tdb); else if (startsWith("blastDm", track)) blastFBUi(tdb); else if (sameString(track, "blastSacCer1SG")) blastSGUi(tdb); else if (sameString(track, "blastHg17KG") || sameString(track, "blastHg16KG") || sameString(track, "blastCe3WB") || sameString(track, "blastHg18KG") || sameString(track, "blatzHg17KG") || startsWith("mrnaMap", track) || startsWith("mrnaXeno", track)) blastUi(tdb); else if (sameString(track, "hgPcrResult")) pcrResultUi(tdb); -else if (startsWith("chromGraph", tdb->type)) - chromGraphUi(tdb); else if (sameString(track, "ancientR")) ancientRUi(tdb); else if (sameString(track, "zoo") || sameString(track, "zooNew" )) zooWiggleUi(tdb); else if (sameString(track, "humMusL") || sameString( track, "musHumL") || sameString( track, "regpotent") || sameString( track, "mm3Rn2L" ) || sameString( track, "mm3Hg15L" ) || sameString( track, "hg15Mm3L" )) humMusUi(tdb,7); else if (startsWith("chain", track) || endsWith("chainSelf", track)) chainColorUi(tdb); else if (sameString(track, "orthoTop4") // still used ?? || sameString(track, "mouseOrtho") || sameString(track, "mouseSyn")) - // NOTE: type psl xeno <otherDb> tracks use crossSpeciesUi, so + // NOTE: type psl xeno <otherDb> tracks use crossSpeciesCfgUi, so // add explicitly here only if track has another type (bed, chain). - // For crossSpeciesUi, the + // For crossSpeciesCfgUi, the // default for chrom coloring is "on", unless track setting // colorChromDefault is set to "off" - crossSpeciesUi(tdb); + crossSpeciesCfgUi(cart,tdb); else if (sameString(track, "affyTranscriptome")) affyTranscriptomeUi(tdb); -else if (startsWith("sample", tdb->type)) - genericWiggleUi(tdb,7); else if (sameString(track, WIKI_TRACK_TABLE)) wikiTrackUi(tdb); else if (sameString(track, RULER_TRACK_NAME)) rulerUi(tdb); else if (sameString(track, OLIGO_MATCH_TRACK_NAME)) oligoMatchUi(tdb); else if (sameString(track, CUTTERS_TRACK_NAME)) cutterUi(tdb); else if(sameString(track, "affyTransfrags")) affyTransfragUi(tdb); else if (sameString(track, "gvPos")) gvUi(tdb); else if (sameString(track, "oreganno")) oregannoUi(tdb); else if (startsWith("retroposons", track)) retroposonsUi(tdb); else if (sameString(track, "tfbsConsSites")) tfbsConsSitesUi(tdb); else if (sameString(track, "CGHBreastCancerUCSF")) ucsfdemoUi(tdb); else if (startsWith("hapmapSnps", track)) hapmapSnpsUi(tdb); else if (sameString(track, "switchDbTss")) switchDbScoreUi(tdb); else if (sameString(track, "dgv") || (startsWith("dgvV", track) && isdigit(track[4]))) dgvUi(tdb); -else +else if (tdb->type != NULL) { // NOTE for developers: please avoid special cases and use cfgTypeFromTdb//cfgByCfgType() // When you do, then multi-view cfg and subtrack cfg will work. eCfgType cType = cfgTypeFromTdb(tdb,FALSE); if (cType != cfgNone) { boolean boxed = trackDbSettingClosestToHomeOn(tdb, "boxedCfg"); cfgByCfgType(cType,database, cart, tdb,tdb->track, NULL, boxed); } - else if (tdb->type != NULL) - { - /* handle all tracks with type genePred or bed or "psl xeno <otherDb>" */ - char *typeLine = cloneString(tdb->type); - char *words[8]; - int wordCount = 0; - wordCount = chopLine(typeLine, words); - if (wordCount > 0) - { - if (sameWord(words[0], "expRatio")) + // NOTE: these cases that fall through the cracks should probably get folded into cfgByCfgType() + else if (startsWithWord("expRatio", tdb->type)) expRatioUi(tdb); - else if (sameWord(words[0], "array")) /* not quite the same as an "expRatio" type (custom tracks) */ + else if (startsWith("chromGraph", tdb->type)) + chromGraphUi(tdb); + else if (startsWith("sample", tdb->type)) + genericWiggleUi(tdb,7); + else if (startsWithWord("array",tdb->type)) /* not quite the same as an "expRatio" type (custom tracks) */ expRatioCtUi(tdb); - else if (sameWord(words[0], "psl")) - { - if (wordCount == 3) - if (sameWord(words[1], "xeno")) - crossSpeciesUi(tdb); - baseColorDrawOptDropDown(cart, tdb); - indelShowOptions(cart, tdb); - } - else if (sameWord(words[0], "factorSource")) - { - printf("<BR><B>Cell Abbreviations:</B><BR>\n"); - char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable"); - struct sqlConnection *conn = hAllocConn(database); - hPrintAbbreviationTable(conn, sourceTable, "Cell Type"); - hFreeConn(&conn); - } - } - freeMem(typeLine); - } - } -if (tdbIsSuperTrack(tdb)) - { - superTrackUi(tdb, tdbList); + else if (startsWithWord("factorSource",tdb->type)) + factorSourceUi(database,tdb); } -else if (tdbIsComposite(tdb)) // for the moment generalizing this to include other containers... + +if (!ajax) // ajax asks for a simple cfg dialog for right-click popup or hgTrackUi subtrack cfg { + // Composites *might* have had their top level controls just printed, but almost certainly have additional controls + if (tdbIsComposite(tdb)) // for the moment generalizing this to include other containers... hCompositeUi(database, cart, tdb, NULL, NULL, MAIN_FORM, trackHash); - } -if (!ajax) - { + + // Additional special case navigation links may be added previewLinks(database, tdb); extraUiLinks(database,tdb, trackHash); } } #ifdef UNUSED static void findSuperChildrenAndSettings(struct trackDb *tdbList, struct trackDb *super) /* Find the tracks that have super as a parent and stuff references to them on * super's children list. Also do some visibility and parentName futzing. */ { struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { if (tdb->parent == super) {