5fe6a3b2ce5a7099de38022ab8875d5651797780 tdreszer Fri Dec 16 11:41:01 2011 -0800 Just a changed name tree wide. The 'compositeLevel' paramter to closestToHome cart functions was confusing. What it means is the request is for a setting one step above the tdb passed in. It is used for view level controls where the model tdb is a subtrack. This checkin has NO functional affect. diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c index 859455b..209dc7c 100644 --- src/hg/lib/vcfUi.c +++ src/hg/lib/vcfUi.c @@ -1,335 +1,335 @@ /* 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 "jsHelper.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, char *track, - boolean compositeLevel, struct vcfFile *vcff, + boolean parentLevel, 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. - int centerPos = cartUsualIntClosestToHome(cart, tdb, compositeLevel, "centerVariantPos", + int centerPos = cartUsualIntClosestToHome(cart, tdb, parentLevel, "centerVariantPos", -1); - char *centerName = cartStringClosestToHome(cart, tdb, compositeLevel, "centerVariantName"); + char *centerName = cartStringClosestToHome(cart, tdb, parentLevel, "centerVariantName"); if (isNotEmpty(thisChrom)) { // These form inputs are for either "use me" or clear: 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(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 *centerChrom = cartOptionalStringClosestToHome(cart, tdb, compositeLevel, + char *centerChrom = cartOptionalStringClosestToHome(cart, tdb, parentLevel, "centerVariantChrom"); if (isEmpty(centerChrom)) { // Unspecified in cart -- describe the default action printf(VCF_HAPLOSORT_DEFAULT_DESC " as anchor.
"); 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, track); dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantName', ''); ", formName, track); dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantPos', 0);", 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) 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, -1); } errCatchEnd(errCatch); if (errCatch->gotError) { if (isNotEmpty(errCatch->message->string)) warn("unable to open %s: %s", fileOrUrl, errCatch->message->string); } errCatchFree(&errCatch); return vcff; } static void vcfCfgHapClusterEnable(struct cart *cart, struct trackDb *tdb, char *name, - boolean compositeLevel) + boolean parentLevel) /* Let the user enable/disable haplotype sorting display. */ { -boolean hapClustEnabled = cartUsualBooleanClosestToHome(cart, tdb, compositeLevel, +boolean hapClustEnabled = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, VCF_HAP_ENABLED_VAR, TRUE); char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s." VCF_HAP_ENABLED_VAR, name); cgiMakeCheckBox(cartVar, hapClustEnabled); printf("Enable Haplotype sorting display
\n"); } static void vcfCfgHapClusterColor(struct cart *cart, struct trackDb *tdb, char *name, - boolean compositeLevel) + boolean parentLevel) /* Let the user choose how to color the sorted haplotypes. */ { printf("Haplotype coloring scheme:
\n"); -char *colorBy = cartUsualStringClosestToHome(cart, tdb, compositeLevel, +char *colorBy = cartUsualStringClosestToHome(cart, tdb, parentLevel, VCF_HAP_COLORBY_VAR, VCF_DEFAULT_HAP_COLORBY); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_HAP_COLORBY_VAR, name); cgiMakeRadioButton(varName, VCF_HAP_COLORBY_ALTONLY, sameString(colorBy, VCF_HAP_COLORBY_ALTONLY)); printf("reference alleles invisible, alternate alleles in black
\n"); cgiMakeRadioButton(varName, VCF_HAP_COLORBY_REFALT, sameString(colorBy, VCF_HAP_COLORBY_REFALT)); printf("reference alleles in blue, alternate alleles in red
\n"); cgiMakeRadioButton(varName, VCF_HAP_COLORBY_BASE, sameString(colorBy, VCF_HAP_COLORBY_BASE)); printf("first base of allele (A = red, C = blue, G = green, T = magenta)
\n"); } static void vcfCfgHapClusterTreeAngle(struct cart *cart, struct trackDb *tdb, char *name, - boolean compositeLevel) + boolean parentLevel) /* Let the user choose branch shape. */ { printf("Haplotype clustering tree leaf shape:
\n"); -char *treeAngle = cartUsualStringClosestToHome(cart, tdb, compositeLevel, +char *treeAngle = cartUsualStringClosestToHome(cart, tdb, parentLevel, VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE); char varName[1024]; safef(varName, sizeof(varName), "%s." VCF_HAP_TREEANGLE_VAR, name); cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_TRIANGLE, sameString(treeAngle, VCF_HAP_TREEANGLE_TRIANGLE)); printf("draw leaf clusters as <
\n"); cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_RECTANGLE, sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE)); printf("draw leaf clusters as [
\n"); } static void vcfCfgHapClusterHeight(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, - char *name, boolean compositeLevel) + char *name, boolean parentLevel) /* Let the user specify a height for the track. */ { if (vcff != NULL && vcff->genotypeCount > 1) { printf("Haplotype sorting display height: \n"); - int cartHeight = cartUsualIntClosestToHome(cart, tdb, compositeLevel, + int cartHeight = cartUsualIntClosestToHome(cart, tdb, parentLevel, 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, "4", "2500"); puts("
"); } } static void vcfCfgHapCluster(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, - char *name, boolean compositeLevel) + char *name, boolean parentLevel) /* 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, name, compositeLevel, vcff, NULL, NULL, 0, "mainForm"); -vcfCfgHapClusterColor(cart, tdb, name, compositeLevel); -vcfCfgHapClusterTreeAngle(cart, tdb, name, compositeLevel); -vcfCfgHapClusterHeight(cart, tdb, vcff, name, compositeLevel); +vcfCfgHapClusterEnable(cart, tdb, name, parentLevel); +vcfCfgHaplotypeCenter(cart, tdb, name, parentLevel, vcff, NULL, NULL, 0, "mainForm"); +vcfCfgHapClusterColor(cart, tdb, name, parentLevel); +vcfCfgHapClusterTreeAngle(cart, tdb, name, parentLevel); +vcfCfgHapClusterHeight(cart, tdb, vcff, name, parentLevel); puts("
"); } static void vcfCfgMinQual(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, - char *name, boolean compositeLevel) + char *name, boolean parentLevel) /* 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, +boolean applyFilter = cartUsualBooleanClosestToHome(cart, tdb, parentLevel, VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL); cgiMakeCheckBox(cartVar, applyFilter); printf("Exclude variants with Quality/confidence score (QUAL) score less than\n"); -double minQual = cartUsualDoubleClosestToHome(cart, tdb, compositeLevel, VCF_MIN_QUAL_VAR, +double minQual = cartUsualDoubleClosestToHome(cart, tdb, parentLevel, VCF_MIN_QUAL_VAR, VCF_DEFAULT_MIN_QUAL); safef(cartVar, sizeof(cartVar), "%s." VCF_MIN_QUAL_VAR, name); cgiMakeDoubleVar(cartVar, minQual, 10); printf("
\n"); } static void vcfCfgFilterColumn(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, - char *name, boolean compositeLevel) + char *name, boolean parentLevel) /* Show controls for filtering by value of VCF's FILTER column, which uses values defined * in the header. */ { int filterCount = slCount(vcff->filterDefs); if (filterCount < 1) return; printf("Exclude variants with these FILTER values:
\n"); char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s."VCF_EXCLUDE_FILTER_VAR, name); jsMakeCheckboxGroupSetClearButton(cartVar, TRUE); puts(" "); 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 (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) + char *name, boolean parentLevel) /* 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, +double cartMinFreq = cartUsualDoubleClosestToHome(cart, tdb, parentLevel, 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("
"); } 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) { - boolean compositeLevel = isNameAtCompositeLevel(tdb, name); + boolean parentLevel = isNameAtParentLevel(tdb, name); if (vcff->genotypeCount > 1) { puts("

Haplotype sorting display

"); puts("

When this display mode is enabled and genotypes are phased or homozygous, " "each genotype is split into two independent haplotypes. " "These local haplotypes are clustered by similarity around a central variant. " "Haplotypes are reordered for display using the clustering tree, which is " "drawn in the left label area. " "Local haplotype blocks can often be identified using this display.

"); - vcfCfgHapCluster(cart, tdb, vcff, name, compositeLevel); + vcfCfgHapCluster(cart, tdb, vcff, name, parentLevel); } puts("

Filters

"); - vcfCfgMinQual(cart, tdb, vcff, name, compositeLevel); - vcfCfgFilterColumn(cart, tdb, vcff, name, compositeLevel); - vcfCfgMinAlleleFreq(cart, tdb, vcff, name, compositeLevel); + vcfCfgMinQual(cart, tdb, vcff, name, parentLevel); + vcfCfgFilterColumn(cart, tdb, vcff, name, parentLevel); + vcfCfgMinAlleleFreq(cart, tdb, vcff, name, parentLevel); } else { printf("Sorry, couldn't access VCF file.
\n"); } puts(""); if (boxed && fileExists(hHelpFile("hgVcfTrackHelp"))) printf("VCF configuration help"); printf(""); if (!boxed && fileExists(hHelpFile("hgVcfTrackHelp"))) printf("

VCF " "configuration help

"); cfgEndBox(boxed); }