e0066b6bba1eea45452a32de72eaf4af8c331bbb angie Mon Aug 8 16:27:02 2011 -0700 Feature #2823 (VCF track handler): Added UI control over height of haplotype-sorting display. diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c index a4927cd..7e603fa 100644 --- src/hg/lib/vcfUi.c +++ src/hg/lib/vcfUi.c @@ -1,182 +1,207 @@ /* vcfUi - Variant Call Format user interface controls that are shared * between more than one CGI. */ #include "common.h" #include "cheapcgi.h" #include "errCatch.h" #include "hCommon.h" #include "hui.h" #include "vcf.h" #include "vcfUi.h" #if (defined USE_TABIX && defined KNETFILE_HOOKS) #include "knetUdc.h" #include "udc.h" #endif//def USE_TABIX && KNETFILE_HOOKS INLINE char *nameOrDefault(char *thisName, char *defaultVal) /* If thisName is not a placeholder value, return it; otherwise return default. */ { if (isNotEmpty(thisName) && !sameString(thisName, ".")) return thisName; return defaultVal; } #define VCF_HAPLOSORT_DEFAULT_DESC "middle variant in viewing window" 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, 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) { // cluster haplotypes or just show allele summary? // if clustering haplotypes: // track height? // thicken lines? // outline center variant? // choose center variant? [hgc option to make this variant's coords the center of viewed region?] // color haplotypes by red/blue or allele bases? 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); if (isNotEmpty(thisChrom)) { // These form inputs are for either "use me" or clear: vcfCfgHaplotypeCenterHiddens(tdb->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); 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: using "); char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.centerVariantChrom", tdb->track); char *centerChrom = cartOptionalString(cart, cartVar); if (isEmpty(centerChrom)) { // Unspecified in cart -- describe the default action printf(VCF_HAPLOSORT_DEFAULT_DESC " as anchor.
"); vcfCfgHaplotypeCenterHiddens(tdb->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); dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantName', ''); ", formName, tdb->track); dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantPos', 0);", formName, tdb->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) udcSetCacheTimeout(300); #endif//def USE_TABIX && KNETFILE_HOOKS char *db = cartString(cart, "db"); struct sqlConnection *conn = hAllocConnTrack(db, tdb); char *fileOrUrl = bbiNameFromSettingOrTable(tdb, conn, tdb->table); hFreeConn(&conn); int vcfMaxErr = 100; struct vcfFile *vcff = NULL; /* protect against temporary network error */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { vcff = vcfTabixFileMayOpen(fileOrUrl, NULL, 0, 0, vcfMaxErr); } errCatchEnd(errCatch); if (errCatch->gotError) { if (isNotEmpty(errCatch->message->string)) warn("unable to open %s: %s", fileOrUrl, errCatch->message->string); } errCatchFree(&errCatch); return vcff; } +void vcfCfgHapClusterHeight(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, + char *name) +/* Let the user specify a height for the track. */ +{ +if (vcff != NULL && vcff->genotypeCount > 1) + { + printf("Haplotype sorting display height: \n"); + boolean compositeLevel = isNameAtCompositeLevel(tdb, name); + 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"); + } +} + void vcfCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* VCF: Variant Call Format. redmine #3710 */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); printf("", boxed ? " width='100%'" : ""); struct vcfFile *vcff = vcfHopefullyOpenHeader(cart, tdb); +if (vcff != NULL) + { vcfCfgHaplotypeCenter(cart, tdb, vcff, NULL, NULL, 0, "mainForm"); + vcfCfgHapClusterHeight(cart, tdb, vcff, name); + } +else + { + printf("Sorry, couldn't access VCF file.
\n"); + } + // filter: // by qual column // by filter column // color bases like pgSnp or some better palette? printf(""); if (!boxed && fileExists(hHelpFile("hgVcfTrackHelp"))) printf("

VCF " "configuration help

"); cfgEndBox(boxed); }