b9f7469b125c83471a07002d953acbc50876a120 angie Mon Oct 24 17:07:27 2011 -0700 Code review advice from Tim about how to properly use ClosestToHome. diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c index 04d9c35..6416289 100644 --- src/hg/lib/vcfUi.c +++ src/hg/lib/vcfUi.c @@ -27,105 +27,103 @@ static void vcfCfgHaplotypeCenterHiddens(char *track, char *ctrName, char *ctrChrom, int ctrPos) /* Make hidden form inputs and button for setting the center variant for haplotype * clustering/sorting in hgTracks. */ { char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.centerVariantChrom", track); cgiMakeHiddenVar(cartVar, ctrChrom); safef(cartVar, sizeof(cartVar), "%s.centerVariantPos", track); char ctrPosStr[16]; safef(ctrPosStr, sizeof(ctrPosStr), "%d", ctrPos); cgiMakeHiddenVar(cartVar, ctrPosStr); safef(cartVar, sizeof(cartVar), "%s.centerVariantName", track); cgiMakeHiddenVar(cartVar, ctrName); } -void vcfCfgHaplotypeCenter(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, +void vcfCfgHaplotypeCenter(struct cart *cart, struct trackDb *tdb, char *track, + boolean compositeLevel, struct vcfFile *vcff, char *thisName, char *thisChrom, int thisPos, char *formName) /* If vcff has genotype data, show status and controls for choosing the center variant * for haplotype clustering/sorting in hgTracks. */ { if (vcff != NULL && vcff->genotypeCount > 1) { printf("\n"); if (isNotEmpty(thisChrom)) { // but we do have a candidate, so offer to make it the center: puts("\n"); } else printf("\n"); } else { // Describe the one specified in cart. - cgiMakeHiddenVar(cartVar, ""); - safef(cartVar, sizeof(cartVar), "%s.centerVariantPos", tdb->track); - int centerPos = cartInt(cart, cartVar); - safef(cartVar, sizeof(cartVar), "%s.centerVariantName", tdb->track); - char *centerName = cartString(cart, cartVar); + int centerPos = cartUsualIntClosestToHome(cart, tdb, compositeLevel, "centerVariantPos", + -1); + char *centerName = cartStringClosestToHome(cart, tdb, compositeLevel, "centerVariantName"); if (isNotEmpty(thisChrom)) { // These form inputs are for either "use me" or clear: - vcfCfgHaplotypeCenterHiddens(tdb->track, thisName, thisChrom, thisPos); + vcfCfgHaplotypeCenterHiddens(track, thisName, thisChrom, thisPos); // Is this variant the same as the center variant specified in cart? if (sameString(thisChrom, centerChrom) && sameString(thisName, centerName) && thisPos == centerPos) printf("this variant as anchor.\n"); else { // make a "use me" button printf("%s at %s:%d as anchor.\n\n"); } } else { // Form inputs (in case the clear button is clicked) - vcfCfgHaplotypeCenterHiddens(tdb->track, centerName, centerChrom, centerPos); + vcfCfgHaplotypeCenterHiddens(track, centerName, centerChrom, centerPos); printf("%s at %s:%d as anchor.\n", nameOrDefault(centerName, "variant"), centerChrom, centerPos+1); } // Make a clear button that modifies the hiddens using onClick puts("\n"); } puts("
" "Haplotype sorting order: using "); - char cartVar[1024]; - safef(cartVar, sizeof(cartVar), "%s.centerVariantChrom", tdb->track); - char *centerChrom = cartOptionalString(cart, cartVar); + char *centerChrom = cartOptionalStringClosestToHome(cart, tdb, compositeLevel, + "centerVariantChrom"); if (isEmpty(centerChrom)) { // Unspecified in cart -- describe the default action printf(VCF_HAPLOSORT_DEFAULT_DESC " as anchor.
"); - vcfCfgHaplotypeCenterHiddens(tdb->track, thisName, thisChrom, thisPos); + vcfCfgHaplotypeCenterHiddens(track, thisName, thisChrom, thisPos); char label[256]; safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant")); cgiMakeButton("submit", label); printf(" as anchor
To anchor the sorting to a particular variant, " "click on the variant in the genome browser, " "and then click on the 'Use this variant' button on the next page." "
\n", nameOrDefault(centerName, "variant"), centerChrom, centerPos+1); char label[256]; safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant")); cgiMakeButton("submit", label); printf(" as anchor
"); struct dyString *onClick = dyStringNew(0); dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantChrom', ''); ", - formName, tdb->track); + formName, track); dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantName', ''); ", - formName, tdb->track); + formName, track); dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantPos', 0);", - formName, tdb->track); + formName, track); dyStringPrintf(onClick, "document.%s.submit(); return false;", formName); cgiMakeButtonWithOnClick("submit", "Clear selection", NULL, onClick->string); printf(" (use " VCF_HAPLOSORT_DEFAULT_DESC ")
"); } } //TODO: share this code w/hgTracks, hgc in hg/lib/vcfFile.c static struct vcfFile *vcfHopefullyOpenHeader(struct cart *cart, struct trackDb *tdb) /* Defend against network errors and return the vcfFile object with header data, or NULL. */ { #if (defined USE_TABIX && defined KNETFILE_HOOKS) knetUdcInstall(); if (udcCacheTimeout() < 300) @@ -192,31 +190,31 @@ int cartHeight = cartUsualIntClosestToHome(cart, tdb, compositeLevel, VCF_HAP_HEIGHT_VAR, VCF_DEFAULT_HAP_HEIGHT); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_HAP_HEIGHT_VAR, name); cgiMakeIntVarInRange(varName, cartHeight, "Height (in pixels) of track", 5, "10", "2500"); puts("
"); } } static void vcfCfgHapCluster(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name, boolean compositeLevel) /* Show controls for haplotype-sorting display, which only makes sense to do when * the VCF file describes multiple genotypes. */ { vcfCfgHapClusterEnable(cart, tdb, name, compositeLevel); -vcfCfgHaplotypeCenter(cart, tdb, vcff, NULL, NULL, 0, "mainForm"); +vcfCfgHaplotypeCenter(cart, tdb, name, compositeLevel, vcff, NULL, NULL, 0, "mainForm"); vcfCfgHapClusterColor(cart, tdb, name, compositeLevel); vcfCfgHapClusterHeight(cart, tdb, vcff, name, compositeLevel); // thicken lines? // outline center variant? } static void vcfCfgMinQual(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name, boolean compositeLevel) /* If checkbox is checked, apply minimum value filter to QUAL column. */ { char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s." VCF_APPLY_MIN_QUAL_VAR, name); boolean applyFilter = cartUsualBooleanClosestToHome(cart, tdb, compositeLevel, VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL); cgiMakeCheckBox(cartVar, applyFilter); @@ -244,32 +242,32 @@ jsMakeCheckboxGroupSetClearButton(cartVar, FALSE); char *values[filterCount]; char *labels[filterCount]; int i; struct vcfInfoDef *filt; for (i=0, filt=vcff->filterDefs; filt != NULL; i++, filt = filt->next) { values[i] = filt->key; struct dyString *dy = dyStringNew(0); dyStringAppend(dy, filt->key); if (isNotEmpty(filt->description)) dyStringPrintf(dy, " (%s)", filt->description); labels[i] = dyStringCannibalize(&dy); } struct slName *selectedValues = NULL; -if (cartListVarExists(cart, cartVar)) - selectedValues = cartOptionalSlNameList(cart, cartVar); +if (cartListVarExistsAnyLevel(cart, tdb, FALSE, VCF_EXCLUDE_FILTER_VAR)) + selectedValues = cartOptionalSlNameListClosestToHome(cart, tdb, FALSE, VCF_EXCLUDE_FILTER_VAR); cgiMakeCheckboxGroupWithVals(cartVar, labels, values, filterCount, selectedValues, 1); } static void vcfCfgMinAlleleFreq(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name, boolean compositeLevel) /* Show input for minimum allele frequency, if we can extract it from the VCF INFO column. */ { printf("Minimum minor allele frequency (if INFO column includes AF or AC+AN):\n"); double cartMinFreq = cartUsualDoubleClosestToHome(cart, tdb, compositeLevel, VCF_MIN_ALLELE_FREQ_VAR, VCF_DEFAULT_MIN_ALLELE_FREQ); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_MIN_ALLELE_FREQ_VAR, name); cgiMakeDoubleVarInRange(varName, cartMinFreq, "minor allele frequency between 0.0 and 0.5", 5, "0.0", "0.5"); puts("
");