0831c38af9c5724d398fbf12e56853d773b24cb5 angie Tue Jan 11 15:19:57 2011 -0800 Made several portions of the SNP controls page collapsible. diff --git src/hg/hgTrackUi/hgTrackUi.c src/hg/hgTrackUi/hgTrackUi.c index a2fb590..e796ca9 100644 --- src/hg/hgTrackUi/hgTrackUi.c +++ src/hg/hgTrackUi/hgTrackUi.c @@ -151,52 +151,55 @@ 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); + jsBeginCollapsibleSection(cart, tdb->track, "geneTracks", + "Use Gene Tracks for Functional Annotation", FALSE); 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 (!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); + jsEndCollapsibleSection(); } hFreeConn(&conn); } #define SNP125_FILTER_COLUMNS 4 #define SNP125_DEFAULTS "snp125Defaults" 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. */ { printf("<TR><TD><B>%s:</B> \n", attributeLabel); char cartVar[256]; safef(cartVar, sizeof(cartVar), "%s.include_%s", track, attributeVar); @@ -249,93 +252,101 @@ { char autoSubmit[2048]; char *orthoTable = snp125OrthoTable(tdb, NULL); int version = snpVersion(tdb->track); jsInit(); if (version < 130) 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"); + printf("<BR><BR>\n"); } +// Make wrapper table for collapsible sections: +puts("<TABLE border=0 cellspacing=0 cellpadding=0>"); + snp125OfferGeneTracksForFunction(tdb); //#*** 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> "); +printf("<TR><TD colspan=2><BR><B>Minimum <A HREF=\"#AvHet\">Average Heterozygosity</A>:</B> "); cgiMakeDoubleVar("snp125AvHetCutoff",snp125AvHetCutoff,6); +printf("</TD></TR>\n"); int snp125WeightCutoff = cartUsualInt(cart, "snp125WeightCutoff", SNP125_DEFAULT_MAX_WEIGHT); -printf("<BR><B>Maximum <A HREF=\"#Weight\">Weight</A>:</B> "); +printf("<TR><TD colspan=2><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(" <EM>Range: 1, 2 or 3; SNPs with higher weights are less reliable</EM><BR><BR>\n"); +printf("</TD></TR>\n"); -printf("<A name=\"filterControls\"><HR>\n" - "<B>Filter by Attribute</B><BR>\n" - "Check the boxes below to include SNPs with those attributes. " +printf("<TR><TD colspan=2><A name=\"filterControls\"></TD></TR>\n"); +jsBeginCollapsibleSection(cart, tdb->track, "filterByAttribute", "Filter by Attribute", FALSE); +printf("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"); if (version <= 127) 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"); +printf("</TABLE>\n"); +jsEndCollapsibleSection(); +puts("<TR><TD colspan=2><BR></TD></TR>"); 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) { 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"); +printf("<TR><TD colspan=2><A name=\"colorSpec\"></TD></TR>\n"); +jsBeginCollapsibleSection(cart, tdb->track, "colorByAttribute", "Color by Attribute", FALSE); +printf("<BR><B>SNP Feature for Color Specification:</B>\n"); char *snp125ColorSourceCart = cartUsualString(cart, snp125ColorSourceVarName, snp125ColorSourceDefault); if (version <= 127) cgiMakeDropListFull(snp125ColorSourceVarName, snp125ColorSourceLabels, snp125ColorSourceLabels, snp125ColorSourceArraySize, snp125ColorSourceCart, autoSubmit); else { if (stringArrayIx(snp125ColorSourceCart, snp128ColorSourceLabels, snp128ColorSourceArraySize) < 0) snp125ColorSourceCart = snp125ColorSourceDefault; cgiMakeDropListFull(snp125ColorSourceVarName, snp128ColorSourceLabels, snp128ColorSourceLabels, snp128ColorSourceArraySize, snp125ColorSourceCart, autoSubmit); } @@ -361,31 +372,33 @@ 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"); +jsEndCollapsibleSection(); +// End wrapper table for collapsible sections: +puts("</TABLE>"); } 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. * I'd also like to see 'submit' buttons at several places along the