dbb7cbfd254794919a8e491cc3d3eb7c6009ba15 angie Tue Jan 25 14:58:05 2011 -0800 Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart var names to use track name, keeping backwards compat with old sessions. Lots of refactoring -- got rid of snp125Extended business (mostly so I wouldn't have to make a snp132Extended); color is stored in snp->weight now, and extraName stuff overwrites name. Added new color-sorting in squish mode so the most interesting SNPs appear at the top. Also added new trackDb var defaultMaxWeight for the NonUnique subset (so its items aren't invisible by default). diff --git src/hg/hgTrackUi/hgTrackUi.c src/hg/hgTrackUi/hgTrackUi.c index d6d9865..5bab68d 100644 --- src/hg/hgTrackUi/hgTrackUi.c +++ src/hg/hgTrackUi/hgTrackUi.c @@ -210,198 +210,294 @@ 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"); } -void snp125PrintColorSpec(char *vars[], char *labels[], char *defaults[], int varCount) +static void snp125PrintColorSpec(char *track, char *attribute, char *vars[], boolean varsAreOld, + 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]); - char *selected = cartUsualString(cart, vars[i], defaults[i]); - cgiMakeDropListWithVals(vars[i], snp125ColorLabel, snp125ColorLabel, + char cartVar[512]; + safef(cartVar, sizeof(cartVar), "%s.%s%s", track, attribute, + (varsAreOld ? snp125OldColorVarToNew(vars[i], attribute) : vars[i])); + char *defaultCol = defaults[i]; + if (varsAreOld) + defaultCol = cartUsualString(cart, vars[i], defaultCol); + char *selected = cartUsualString(cart, cartVar, defaultCol); + cgiMakeDropListWithVals(cartVar, snp125ColorLabel, snp125ColorLabel, snp125ColorArraySize, selected); printf("</TD><TD> </TD>"); } printf("</TABLE>\n"); } -static void cartRemoveStringArray(struct cart *cart, char *vars[], int varCount) -/* Remove each variable in vars[]. */ +static void snp125RemoveColorVars(struct cart *cart, char *vars[], boolean varsAreOld, + int varCount, char *track, char *attribute) +/* Remove each cart variable in vars[], as well as the new cart vars that begin with + * the track name if varsAreOld. */ { int i; for (i = 0; i < varCount; i++) + { + if (varsAreOld) cartRemove(cart, vars[i]); + char cartVar[512]; + safef(cartVar, sizeof(cartVar), "%s.%s%s", track, attribute, + (varsAreOld ? snp125OldColorVarToNew(vars[i], attribute) : vars[i])); + cartRemove(cart, cartVar); + } +} + +static void snp125ResetColorVarsIfNecessary(struct trackDb *tdb, char *buttonVar, int version) +/* If the 'Set defaults' button has been clicked, remove all color-control cart variables. */ +{ +// Note we use CGI, not cart, to detect a click: +if (isNotEmpty(cgiOptionalString(buttonVar))) + { + char cartVar[512]; + safef(cartVar, sizeof(cartVar), "%s.colorSource", tdb->track); + cartRemove(cart, cartVar); + cartRemove(cart, snp125ColorSourceOldVar); + snp125RemoveColorVars(cart, snp125LocTypeOldColorVars, TRUE, snp125LocTypeArraySize, + tdb->track, "locType"); + snp125RemoveColorVars(cart, snp125ClassOldColorVars, TRUE, snp125ClassArraySize, + tdb->track, "class"); + snp125RemoveColorVars(cart, snp125ValidOldColorVars, TRUE, snp125ValidArraySize, + tdb->track, "valid"); + int funcArraySize = (version < 130) ? snp125FuncArraySize : (snp125FuncArraySize - 1); + snp125RemoveColorVars(cart, snp125FuncOldColorVars, TRUE, funcArraySize, + tdb->track, "func"); + snp125RemoveColorVars(cart, snp125MolTypeOldColorVars, TRUE, snp125MolTypeArraySize, + tdb->track, "molType"); + snp125RemoveColorVars(cart, snp132ExceptionVarName, FALSE, snp132ExceptionArraySize, + tdb->track, "exceptions"); + snp125RemoveColorVars(cart, snp132BitfieldVarName, FALSE, snp132BitfieldArraySize, + tdb->track, "bitfields"); + } +} + +void snp125PrintColorControlSection(struct trackDb *tdb, int version) +/* Print a collapsible section of color controls: user selects an attribute to color by, + * and then a color for each possible value of the selected attribute. */ +{ +printf("<TR><TD colspan=2><A name=\"colorSpec\"></TD></TR>\n"); +jsBeginCollapsibleSection(cart, tdb->track, "colorByAttribute", "Color by Attribute", FALSE); + +char defaultButtonVar[512]; +safef(defaultButtonVar, sizeof(defaultButtonVar), "%s_coloring", SNP125_DEFAULTS); +stripChar(defaultButtonVar, ' '); +snp125ResetColorVarsIfNecessary(tdb, defaultButtonVar, version); + +printf("<BR><B>SNP Feature for Color Specification:</B>\n"); +char cartVar[512]; +safef(cartVar, sizeof(cartVar), "%s.colorSource", tdb->track); +char *snp125ColorSourceDefault = snp125ColorSourceLabels[SNP125_DEFAULT_COLOR_SOURCE]; +char *colorSourceCart = cartUsualString(cart, cartVar, + cartUsualString(cart, snp125ColorSourceOldVar, + snp125ColorSourceDefault)); +char **labels = snp132ColorSourceLabels; +int arraySize = snp132ColorSourceArraySize; +if (version <= 127) + { + labels = snp125ColorSourceLabels; + arraySize = snp125ColorSourceArraySize; + } +else if (version <= 131) + { + labels = snp128ColorSourceLabels; + arraySize = snp128ColorSourceArraySize; + } +if (stringArrayIx(colorSourceCart, labels, arraySize) < 0) + colorSourceCart = snp125ColorSourceDefault; + +// It would be preferable for Javascript to handle changing the color selection +// menus when the color source selection changes, but for now we do a submit that +// returns to the current vertical position: +char autoSubmit[2048]; +safef(autoSubmit, sizeof(autoSubmit), "onchange=\"" + "document."MAIN_FORM".action = '%s'; %s" + "document."MAIN_FORM".submit();\"", + cgiScriptName(), jsSetVerticalPosition(MAIN_FORM)); +cgiContinueHiddenVar("g"); +cgiContinueHiddenVar("c"); + +cgiMakeDropListFull(cartVar, labels, labels, arraySize, colorSourceCart, 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, defaultButtonVar, 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(colorSourceCart, "Location Type")) + { + if (version <= 127) + snp125PrintColorSpec(tdb->track, "locType", snp125LocTypeOldColorVars, TRUE, + snp125LocTypeLabels, snp125LocTypeDefault, snp125LocTypeArraySize); + } +else if (sameString(colorSourceCart, "Class")) + snp125PrintColorSpec(tdb->track, "class", snp125ClassOldColorVars, TRUE, + snp125ClassLabels, snp125ClassDefault, snp125ClassArraySize); +else if (sameString(colorSourceCart, "Validation")) + snp125PrintColorSpec(tdb->track, "valid", snp125ValidOldColorVars, TRUE, + snp125ValidLabels, snp125ValidDefault, snp125ValidArraySize); +else if (sameString(colorSourceCart, "Function")) + { + int funcArraySize = (version < 130) ? snp125FuncArraySize : (snp125FuncArraySize - 1); + snp125PrintColorSpec(tdb->track, "func", snp125FuncOldColorVars, TRUE, + snp125FuncLabels, snp125FuncDefault, funcArraySize); + } +else if (sameString(colorSourceCart, "Molecule Type")) + snp125PrintColorSpec(tdb->track, "molType", snp125MolTypeOldColorVars, TRUE, + snp125MolTypeLabels, snp125MolTypeDefault, snp125MolTypeArraySize); +else if (sameString(colorSourceCart, "Unusual Conditions (UCSC)")) + snp125PrintColorSpec(tdb->track, "exceptions", snp132ExceptionVarName, FALSE, + snp132ExceptionLabels, snp132ExceptionDefault, snp132ExceptionArraySize); +else if (sameString(colorSourceCart, "Miscellaneous Attributes (dbSNP)")) + snp125PrintColorSpec(tdb->track, "bitfields", snp132BitfieldVarName, FALSE, + snp132BitfieldLabels, snp132BitfieldDefault, snp132BitfieldArraySize); +jsEndCollapsibleSection(); } 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); +char cartVar[512]; 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> "); + safef(cartVar, sizeof(cartVar), "%s.extendedNames", tdb->track); + snp125ExtendedNames = cartUsualBoolean(cart, cartVar, + // Check old cart var name for backwards compatibility w/ old sessions: + cartUsualBoolean(cart, "snp125ExtendedNames", FALSE)); + cgiMakeCheckBox(cartVar, snp125ExtendedNames); + printf("<BR>(If enabled, chimp allele is displayed first, then '>', then human alleles)."); printf("<BR><BR>\n"); } +else + puts("<BR>"); // 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("<TR><TD colspan=2><BR><B>Minimum <A HREF=\"#AvHet\">Average Heterozygosity</A>:</B> "); -cgiMakeDoubleVar("snp125AvHetCutoff",snp125AvHetCutoff,6); +printf("<TR><TD colspan=2><BR></TD></TR>\n"); +printf("<TR><TD colspan=2><A name=\"filterControls\"></TD></TR>\n"); + +safef(cartVar, sizeof(cartVar), "%s.minAvHet", tdb->track); +double minAvHet = cartUsualDouble(cart, cartVar, + // Check old cart var name: + cartUsualDouble(cart, "snp125AvHetCutoff", SNP125_DEFAULT_MIN_AVHET)); +printf("<TR><TD colspan=2><B>Minimum <A HREF=\"#AvHet\">Average Heterozygosity</A>:</B> "); +cgiMakeDoubleVar(cartVar, minAvHet, 6); printf("</TD></TR>\n"); -int snp125WeightCutoff = cartUsualInt(cart, "snp125WeightCutoff", SNP125_DEFAULT_MAX_WEIGHT); +safef(cartVar, sizeof(cartVar), "%s.maxWeight", tdb->track); +int defaultMaxWeight = SNP125_DEFAULT_MAX_WEIGHT; +char *setting = trackDbSetting(tdb, "defaultMaxWeight"); +if (isNotEmpty(setting)) + defaultMaxWeight = atoi(setting); +int maxWeight = cartUsualInt(cart, cartVar, + // Check old cart var name: + cartUsualInt(cart, "snp125WeightCutoff", defaultMaxWeight)); printf("<TR><TD colspan=2><B>Maximum <A HREF=\"#Weight\">Weight</A>:</B> "); -cgiMakeIntVar("snp125WeightCutoff",snp125WeightCutoff,4); -printf(" <EM>Range: 1, 2 or 3; SNPs with higher weights are less reliable</EM><BR><BR>\n"); +cgiMakeIntVar(cartVar, maxWeight, 4); +printf(" <EM>Range: 1, 2 or 3; SNPs with higher weights are less reliable</EM><BR>\n"); printf("</TD></TR>\n"); -printf("<TR><TD colspan=2><A name=\"filterControls\"></TD></TR>\n"); +if (version >= 132) + { + printf("<TR><TD colspan=2><B>Minimum number of distinct " + "<A HREF=\"#Submitters\">Submitters</A>:</B> "); + safef(cartVar, sizeof(cartVar), "%s.minSubmitters", tdb->track); + cgiMakeIntVar(cartVar, cartUsualInt(cart, cartVar, SNP132_DEFAULT_MIN_SUBMITTERS), 4); + printf("</TD></TR>\n"); + } + +printf("<TR><TD colspan=2><BR></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); +if (version >= 132) + { + snp125PrintFilterControls(tdb->track, "Unusual Conditions (UCSC)", "exceptions", + snp132ExceptionLabels, snp132ExceptionVarName, snp132ExceptionArraySize); + snp125PrintFilterControls(tdb->track, "Miscellaneous Attributes (dbSNP)", "bitfields", + snp132BitfieldLabels, snp132BitfieldDataName, snp132BitfieldArraySize); + } 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("<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); - } -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, "Location Type")) - { - if (version <= 127) - 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); -jsEndCollapsibleSection(); +snp125PrintColorControlSection(tdb, version); // 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