d3f4b110a0c7befaff49a3bf40871ec7c88ca565 angie Mon Jan 10 16:56:55 2011 -0800 Track #1864 (SNPs 132 (dbSNP)): 1. Added new-in-snp132 columns (exceptions, submitters, alleles) to hgc. Wrapped an html table around several parts of the details page so that they could be made expandable/collapsible using utils.js's setTableRowVisibility. Also wrapped some SNP attributes in an html table for readability. 2. Changed attribute-filter cart variables in hg/lib/snp125Ui.c, hgTrackUi.c and hgTracks/variation.c to use one checkbox group per attribute, with the cart variable based on the track name, instead of one checkbox per attribute value with hardcoded cart var name that applies to all SNP tracks. Refactored to remove a lot of redundant extern global variables. Still need to make other SNP control cart vars based on track name. diff --git src/hg/hgTrackUi/hgTrackUi.c src/hg/hgTrackUi/hgTrackUi.c index 861a77c..508017d 100644 --- src/hg/hgTrackUi/hgTrackUi.c +++ src/hg/hgTrackUi/hgTrackUi.c @@ -131,317 +131,258 @@ snpMapSourceCart[snpMapSource] = cartUsualString(cart, snpMapSourceStrings[snpMapSource], snpMapSourceDefault[snpMapSource]); snpFilterButtons(snpMapSourceStrings[snpMapSource], snpMapSourceCart[snpMapSource]); printf(" - <B>%s</B><BR>\n", snpMapSourceLabels[snpMapSource]); } printf("<BR><B>Variant Types:</B><BR>\n"); for (snpMapType=0; snpMapType<snpMapTypeCartSize; snpMapType++) { snpMapTypeCart[snpMapType] = cartUsualString(cart, snpMapTypeStrings[snpMapType], snpMapTypeDefault[snpMapType]); snpMapTypeFilterButtons(snpMapTypeStrings[snpMapType], snpMapTypeCart[snpMapType]); printf(" - <B>%s</B><BR>\n", snpMapTypeLabels[snpMapType]); } } -/* A comment for the purposes of brancht-tag-move demo. */ - void snp125OfferGeneTracksForFunction(struct trackDb *tdb) { struct sqlConnection *conn = hAllocConn(database); struct slName *genePredTables = hTrackTablesOfType(conn, "genePred%%"), *gt; if (genePredTables != NULL) { struct trackDb *geneTdbList = NULL, *gTdb; for (gt = genePredTables; gt != NULL; gt = gt->next) { gTdb = hTrackDbForTrack(database, gt->name); if (gTdb && sameString(gTdb->grp, "genes")) { if (gTdb->parent) gTdb->priority = (gTdb->parent->priority + gTdb->priority/1000); slAddHead(&geneTdbList, gTdb); } } slSort(&geneTdbList, trackDbCmp); printf("<BR><B>On details page, show function and coding differences relative to: </B> "); char cartVar[256]; safef(cartVar, sizeof(cartVar), "%s_geneTrack", tdb->track); jsMakeCheckboxGroupSetClearButton(cartVar, TRUE); jsMakeCheckboxGroupSetClearButton(cartVar, FALSE); struct slName *selectedGeneTracks = cartOptionalSlNameList(cart, cartVar); - if (selectedGeneTracks == NULL) + if (!cartListVarExists(cart, cartVar)) { char *defaultGeneTracks = trackDbSetting(tdb, "defaultGeneTracks"); if (isNotEmpty(defaultGeneTracks)) selectedGeneTracks = slNameListFromComma(defaultGeneTracks); } int numCols = 4, i; 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; labels[i] = gTdb->shortLabel; } cgiMakeCheckboxGroupWithVals(cartVar, labels, values, menuSize, selectedGeneTracks, numCols); - cgiMakeHiddenVar(cartVar, "persistentShadow"); } hFreeConn(&conn); } #define SNP125_FILTER_COLUMNS 4 -#define SNP125_SET_ALL "snp125SetAll" -#define SNP125_CLEAR_ALL "snp125ClearAll" #define SNP125_DEFAULTS "snp125Defaults" -void snp125PrintFilterColGroup() -/* Print the fancy COLGROUP for the table enclosing all filter checkbox - * groups. */ -{ -int i; -/* Each colgroup has a skinny column for checkboxes followed by a proportional - * column for labels. */ -for (i = 0; i < SNP125_FILTER_COLUMNS; i++) - printf("<COLGROUP><COL><COL width=\"%d%%\"></COLGROUP>\n", - round(100 / SNP125_FILTER_COLUMNS)); -} - -void snp125PrintFilterControls(char *attributeName, - char *vars[], char *labels[], boolean checked[], - boolean defaults[], int varCount) +void snp125PrintFilterControls(char *track, char *attributeLabel, char *attributeVar, + char *labels[], char *values[], int menuSize) /* Print two or more rows (attribute name header and row(s) of checkboxes) * of a table displaying snp125 attribute filter checkboxes. */ { -struct slName *varList = slNameListFromStringArray(vars, varCount); -char buttonVar[1024]; -int i; -printf("<TR><TD colspan=%d><B>%s:</B> \n", - SNP125_FILTER_COLUMNS*2, attributeName); -safef(buttonVar, sizeof(buttonVar), "%s_%s", SNP125_SET_ALL, attributeName); -stripChar(buttonVar, ' '); -jsMakeSetClearButton(cart, MAIN_FORM, buttonVar, JS_SET_ALL_BUTTON_LABEL, "", - varList, NULL, TRUE, TRUE); -printf(" \n"); -safef(buttonVar, sizeof(buttonVar), "%s_%s", SNP125_CLEAR_ALL, attributeName); -stripChar(buttonVar, ' '); -jsMakeSetClearButton(cart, MAIN_FORM, buttonVar, JS_CLEAR_ALL_BUTTON_LABEL, "", - varList, NULL, TRUE, FALSE); +printf("<TR><TD><B>%s:</B> \n", attributeLabel); +char cartVar[256]; +safef(cartVar, sizeof(cartVar), "%s.include_%s", track, attributeVar); +jsMakeCheckboxGroupSetClearButton(cartVar, TRUE); +puts(" "); +jsMakeCheckboxGroupSetClearButton(cartVar, FALSE); +printf("</TD></TR>\n<TR><TD>\n"); +boolean foundInCart = FALSE; +struct slName *selectedAttributes = snp125FilterFromCart(cart, track, attributeVar, &foundInCart); +// Include all by default: +if (! foundInCart) + selectedAttributes = slNameListFromStringArray(values, menuSize); +cgiMakeCheckboxGroupWithVals(cartVar, labels, values, menuSize, selectedAttributes, + SNP125_FILTER_COLUMNS); printf("</TD></TR>\n"); -for (i=0; i < varCount; i++) - { - checked[i] = cartUsualBoolean(cart, vars[i], defaults[i]); - if (i % SNP125_FILTER_COLUMNS == 0) - { - if (i > 0) - printf("</TR>\n"); - printf("<TR>"); - } - printf("<TD>"); - cgiMakeCheckBox(vars[i], checked[i]); - printf("</TD><TD>%s</TD>\n", labels[i]); - } -printf("</TR>\n"); } -void snp125PrintColorSpec(char *vars[], char *labels[], char *selected[], - char *defaults[], int varCount) +void snp125PrintColorSpec(char *vars[], char *labels[], char *defaults[], int varCount) /* Print a table displaying snp125 attribute color selects. */ { int i; printf("<TABLE border=0 cellspacing=0 cellpadding=1>\n"); for (i=0; i < varCount; i++) { if (i % SNP125_FILTER_COLUMNS == 0) { if (i > 0) printf("</TR>\n"); printf("<TR>"); } printf("<TD align=right>%s</TD><TD>", labels[i]); - selected[i] = cartUsualString(cart, vars[i], defaults[i]); + char *selected = cartUsualString(cart, vars[i], defaults[i]); cgiMakeDropListWithVals(vars[i], snp125ColorLabel, snp125ColorLabel, - snp125ColorLabelSize, selected[i]); + snp125ColorArraySize, selected); printf("</TD><TD> </TD>"); } printf("</TABLE>\n"); } -void cartSetStringArray(struct cart *cart, char *vars[], char *defaults[], - int varCount) -/* Given parallel arrays of variable names and default values, set those - * cart variables to the default values. If a NULL is encountered in - * vars[], assume vars[] is NULL-terminated even if varCount has not - * been reached. */ +static void cartRemoveStringArray(struct cart *cart, char *vars[], int varCount) +/* Remove each variable in vars[]. */ { -if (vars == NULL) - return; int i; for (i = 0; i < varCount; i++) - { - if (vars[i] == NULL) - break; - cartSetString(cart, vars[i], defaults[i]); - } + cartRemove(cart, vars[i]); } void snp125Ui(struct trackDb *tdb) /* UI for dbSNP version 125 and later. */ { char autoSubmit[2048]; char *orthoTable = snp125OrthoTable(tdb, NULL); int version = snpVersion(tdb->track); +jsInit(); if (version < 130) - snp125ValidLabelsSize--; // no by-1000genomes + snp125ValidArraySize--; // no by-1000genomes if (isNotEmpty(orthoTable) && hTableExists(database, orthoTable)) { snp125ExtendedNames = cartUsualBoolean(cart, "snp125ExtendedNames", FALSE); printf("<BR><B>Include Chimp state and observed human alleles in name: </B> "); cgiMakeCheckBox("snp125ExtendedNames",snp125ExtendedNames); printf("<BR>(If enabled, chimp allele is displayed first, then '>', then human alleles). </B> "); printf("<BR>\n"); } snp125OfferGeneTracksForFunction(tdb); -snp125AvHetCutoff = atof(cartUsualString(cart, "snp125AvHetCutoff", "0")); +//#*** Need snp125Ui funcs for backwards compat with old cart vars when these have track-specific +//#*** settings as they should: +double snp125AvHetCutoff = cartUsualDouble(cart, "snp125AvHetCutoff", SNP125_DEFAULT_MIN_AVHET); printf("<BR><B>Minimum <A HREF=\"#AvHet\">Average Heterozygosity</A>:</B> "); cgiMakeDoubleVar("snp125AvHetCutoff",snp125AvHetCutoff,6); -snp125WeightCutoff = atoi(cartUsualString(cart, "snp125WeightCutoff", "3")); +int snp125WeightCutoff = cartUsualInt(cart, "snp125WeightCutoff", SNP125_DEFAULT_MAX_WEIGHT); printf("<BR><B>Maximum <A HREF=\"#Weight\">Weight</A>:</B> "); cgiMakeIntVar("snp125WeightCutoff",snp125WeightCutoff,4); printf(" <I>SNPs with higher weights are less reliable</I><BR><BR>\n"); printf("<A name=\"filterControls\"><HR>\n" "<B>Filter by Attribute</B><BR>\n" "Check the boxes below to include SNPs with those attributes. " "In order to be displayed, a SNP must pass the filter for each " "category. \n" "Some assemblies may not contain any SNPs that have some of the " "listed attributes.\n" "<BR><BR>\n"); printf("<TABLE border=0 cellspacing=0 cellpadding=0>\n"); -snp125PrintFilterColGroup(); if (version <= 127) - snp125PrintFilterControls("Location Type", snp125LocTypeIncludeStrings, - snp125LocTypeLabels, snp125LocTypeIncludeCart, - snp125LocTypeIncludeDefault, snp125LocTypeLabelsSize); -snp125PrintFilterControls("Class", snp125ClassIncludeStrings, - snp125ClassLabels, snp125ClassIncludeCart, - snp125ClassIncludeDefault, snp125ClassLabelsSize); -snp125PrintFilterControls("Validation", snp125ValidIncludeStrings, - snp125ValidLabels, snp125ValidIncludeCart, - snp125ValidIncludeDefault, snp125ValidLabelsSize); -int funcLabelsSize = (version < 130) ? snp125FuncLabelsSize : (snp125FuncLabelsSize - 1); -snp125PrintFilterControls("Function", snp125FuncIncludeStrings, - snp125FuncLabels, snp125FuncIncludeCart, - snp125FuncIncludeDefault, funcLabelsSize); -snp125PrintFilterControls("Molecule Type", snp125MolTypeIncludeStrings, - snp125MolTypeLabels, snp125MolTypeIncludeCart, - snp125MolTypeIncludeDefault, snp125MolTypeLabelsSize); + snp125PrintFilterControls(tdb->track, "Location Type", "locType", snp125LocTypeLabels, + snp125LocTypeDataName, snp125LocTypeArraySize); +snp125PrintFilterControls(tdb->track, "Class", "class", snp125ClassLabels, + snp125ClassDataName, snp125ClassArraySize); +snp125PrintFilterControls(tdb->track, "Validation", "valid", snp125ValidLabels, + snp125ValidDataName, snp125ValidArraySize); +int funcArraySize = (version < 130) ? snp125FuncArraySize : (snp125FuncArraySize - 1); +snp125PrintFilterControls(tdb->track, "Function", "func", snp125FuncLabels, + snp125FuncDataName, funcArraySize); +snp125PrintFilterControls(tdb->track, "Molecule Type", "molType", snp125MolTypeLabels, + snp125MolTypeDataName, snp125MolTypeArraySize); printf("</TABLE><BR>\n"); - -jsInit(); safef(autoSubmit, sizeof(autoSubmit), "onchange=\"" "document."MAIN_FORM".action = '%s'; %s" "document."MAIN_FORM".submit();\"", cgiScriptName(), jsSetVerticalPosition(MAIN_FORM)); cgiContinueHiddenVar("g"); cgiContinueHiddenVar("c"); /* The actual set defaults button is below, but we need to handle it here: */ char defaultButton[1024]; safef(defaultButton, sizeof(defaultButton), "%s_coloring", SNP125_DEFAULTS); stripChar(defaultButton, ' '); boolean defaultColoring = isNotEmpty(cgiOptionalString(defaultButton)); if (defaultColoring) { - cartSetString(cart, - snp125ColorSourceDataName[0], snp125ColorSourceDefault[0]); - cartSetStringArray(cart, snp125LocTypeStrings, snp125LocTypeDefault, - snp125LocTypeLabelsSize); - cartSetStringArray(cart, snp125ClassStrings, snp125ClassDefault, - snp125ClassLabelsSize); - cartSetStringArray(cart, snp125ValidStrings, snp125ValidDefault, - snp125ValidLabelsSize); - cartSetStringArray(cart, snp125FuncStrings, snp125FuncDefault, - funcLabelsSize); - cartSetStringArray(cart, snp125MolTypeStrings, snp125MolTypeDefault, - snp125MolTypeLabelsSize); + cartRemove(cart, snp125ColorSourceVarName); + cartRemoveStringArray(cart, snp125LocTypeStrings, snp125LocTypeArraySize); + cartRemoveStringArray(cart, snp125ClassStrings, snp125ClassArraySize); + cartRemoveStringArray(cart, snp125ValidStrings, snp125ValidArraySize); + cartRemoveStringArray(cart, snp125FuncStrings, funcArraySize); + cartRemoveStringArray(cart, snp125MolTypeStrings, snp125MolTypeArraySize); } printf("<A name=\"colorSpec\"><HR>\n"); printf("<B>SNP Feature for Color Specification:</B>\n"); -snp125ColorSourceCart[0] = cartUsualString(cart, snp125ColorSourceDataName[0], - snp125ColorSourceDefault[0]); +char *snp125ColorSourceCart = cartUsualString(cart, snp125ColorSourceVarName, + snp125ColorSourceDefault); if (version <= 127) - cgiMakeDropListFull(snp125ColorSourceDataName[0], snp125ColorSourceLabels, - snp125ColorSourceLabels, snp125ColorSourceLabelsSize, - snp125ColorSourceCart[0], autoSubmit); + cgiMakeDropListFull(snp125ColorSourceVarName, snp125ColorSourceLabels, + snp125ColorSourceLabels, snp125ColorSourceArraySize, + snp125ColorSourceCart, autoSubmit); else { - if (stringArrayIx(snp125ColorSourceCart[0], snp128ColorSourceLabels, - snp128ColorSourceLabelsSize) < 0) - snp125ColorSourceCart[0] = snp125ColorSourceDefault[0]; - cgiMakeDropListFull(snp125ColorSourceDataName[0], snp128ColorSourceLabels, - snp128ColorSourceLabels, snp128ColorSourceLabelsSize, - snp125ColorSourceCart[0], autoSubmit); + if (stringArrayIx(snp125ColorSourceCart, snp128ColorSourceLabels, + snp128ColorSourceArraySize) < 0) + snp125ColorSourceCart = snp125ColorSourceDefault; + cgiMakeDropListFull(snp125ColorSourceVarName, snp128ColorSourceLabels, + snp128ColorSourceLabels, snp128ColorSourceArraySize, + snp125ColorSourceCart, autoSubmit); } printf(" \n"); char javascript[2048]; safef(javascript, sizeof(javascript), "document."MAIN_FORM".action='%s'; %s document."MAIN_FORM".submit();", cgiScriptName(), jsSetVerticalPosition(MAIN_FORM)); cgiMakeOnClickSubmitButton(javascript, defaultButton, JS_DEFAULTS_BUTTON_LABEL); printf("<BR><BR>\n" "The selected "Feature for Color Specification" above has the\n" "selection of colors below for each attribute. Only the color\n" "options for the feature selected above will be used to color items;\n" "color options for other features will not be shown. If a SNP has more\n" "than one of these attributes, the stronger color will override the\n" "weaker color. The order of colors, from strongest to weakest, is red,\n" "green, blue, gray, and black.\n" "<BR><BR>\n"); -if (sameString(snp125ColorSourceCart[0], "Location Type")) +if (sameString(snp125ColorSourceCart, "Location Type")) { if (version <= 127) - snp125PrintColorSpec(snp125LocTypeStrings, snp125LocTypeLabels, - snp125LocTypeCart, snp125LocTypeDefault, - snp125LocTypeLabelsSize); - } -else if (sameString(snp125ColorSourceCart[0], "Class")) - snp125PrintColorSpec(snp125ClassStrings, snp125ClassLabels, - snp125ClassCart, snp125ClassDefault, - snp125ClassLabelsSize); -else if (sameString(snp125ColorSourceCart[0], "Validation")) - snp125PrintColorSpec(snp125ValidStrings, snp125ValidLabels, - snp125ValidCart, snp125ValidDefault, - snp125ValidLabelsSize); -else if (sameString(snp125ColorSourceCart[0], "Function")) - snp125PrintColorSpec(snp125FuncStrings, snp125FuncLabels, - snp125FuncCart, snp125FuncDefault, - funcLabelsSize); -else if (sameString(snp125ColorSourceCart[0], "Molecule Type")) - snp125PrintColorSpec(snp125MolTypeStrings, snp125MolTypeLabels, - snp125MolTypeCart, snp125MolTypeDefault, - snp125MolTypeLabelsSize); + snp125PrintColorSpec(snp125LocTypeStrings, snp125LocTypeLabels, snp125LocTypeDefault, + snp125LocTypeArraySize); + } +else if (sameString(snp125ColorSourceCart, "Class")) + snp125PrintColorSpec(snp125ClassStrings, snp125ClassLabels, snp125ClassDefault, + snp125ClassArraySize); +else if (sameString(snp125ColorSourceCart, "Validation")) + snp125PrintColorSpec(snp125ValidStrings, snp125ValidLabels, snp125ValidDefault, + snp125ValidArraySize); +else if (sameString(snp125ColorSourceCart, "Function")) + snp125PrintColorSpec(snp125FuncStrings, snp125FuncLabels, snp125FuncDefault, + funcArraySize); +else if (sameString(snp125ColorSourceCart, "Molecule Type")) + snp125PrintColorSpec(snp125MolTypeStrings, snp125MolTypeLabels, snp125MolTypeDefault, + snp125MolTypeArraySize); printf("<HR>\n"); } void snpUi(struct trackDb *tdb) /* Put up UI snp data. */ { int snpSource = 0; int snpMolType = 0; int snpClass = 0; int snpValid = 0; int snpFunc = 0; int snpLocType = 0; /* It would be nice to add a 'reset' button here to reset the snp * variables to their defaults.