8c908f948b09826c6cb4452ee5b282aca41be85e galt Tue Dec 8 21:52:59 2015 -0800 Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it. diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c index 38d9b64..a1cf465 100644 --- src/hg/hgVai/hgVai.c +++ src/hg/hgVai/hgVai.c @@ -1,2366 +1,2370 @@ /* hgVai - Variant Annotation Integrator. */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "jksql.h" #include "htmshell.h" #include "web.h" #include "cheapcgi.h" #include "cart.h" #include "cartTrackDb.h" #include "hui.h" #include "grp.h" #include "hCommon.h" #include "hgFind.h" #include "hPrint.h" #include "jsHelper.h" #include "memalloc.h" #include "textOut.h" #include "trackHub.h" #include "hubConnect.h" #include "twoBit.h" #include "gpFx.h" #include "bigGenePred.h" #include "udc.h" #include "knetUdc.h" #include "md5.h" #include "regexHelper.h" #include "hAnno.h" #include "annoGratorQuery.h" #include "annoGratorGpVar.h" #include "annoFormatVep.h" #include "annoStreamBigBed.h" #include "libifyMe.h" /* Global Variables */ struct cart *cart; /* CGI and other variables */ struct hash *oldVars = NULL; /* The cart before new cgi stuff added. */ char *genome = NULL; /* Name of genome - mouse, human, etc. */ char *database = NULL; /* Current genome database - hg17, mm5, etc. */ char *regionType = NULL; /* genome, ENCODE pilot regions, or specific position range. */ struct grp *fullGroupList = NULL; /* List of all groups. */ struct trackDb *fullTrackList = NULL; /* List of all tracks in database. */ static struct pipeline *compressPipeline = (struct pipeline *)NULL; // Null terminated list of CGI Variables we don't want to save permanently: char *excludeVars[] = {"Submit", "submit", "hgva_startQuery", NULL,}; #define hgvaRange "position" #define hgvaRegionType "hgva_regionType" #define hgvaRegionTypeEncode "encode" #define hgvaRegionTypeGenome "genome" #define hgvaRegionTypeRange "range" #define hgvaPositionContainer "positionContainer" #define hgvaSampleVariants "hgva_internally_generated_sample_variants" #define hgvaSampleVariantsLabel "Artificial Example Variants" #define hgvaUseVariantIds "hgva_useVariantIds" #define hgvaVariantIdsLabel "Variant Identifiers" #define hgvaVariantIds "hgva_variantIds" #define hgvaVariantPasteContainer "variantPasteContainer" void addSomeCss() /*#*** This should go in a .css file of course. */ { printf("\n"); } INLINE void startCollapsibleSection(char *sectionSuffix, char *title, boolean onByDefault) // Wrap shared args to jsBeginCollapsibleSectionFontSize { jsBeginCollapsibleSectionFontSize(cart, "hgva", sectionSuffix, title, onByDefault, "1.1em"); } INLINE void startSmallCollapsibleSection(char *sectionSuffix, char *title, boolean onByDefault) // Wrap shared args to jsBeginCollapsibleSectionFontSize { jsBeginCollapsibleSectionFontSize(cart, "hgva", sectionSuffix, title, onByDefault, "0.9em"); } #define endCollapsibleSection jsEndCollapsibleSection static struct dyString *onChangeStart() /* Start up a javascript onChange command */ { struct dyString *dy = jsOnChangeStart(); jsTextCarryOver(dy, hgvaRegionType); jsTextCarryOver(dy, hgvaRange); return dy; } static char *onChangeClade() /* Return javascript executed when they change clade. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); dyStringAppend(dy, " document.hiddenForm.org.value=0;"); dyStringAppend(dy, " document.hiddenForm.db.value=0;"); dyStringAppend(dy, " document.hiddenForm." hgvaRange ".value='';"); return jsOnChangeEnd(&dy); } static char *onChangeOrg() /* Return javascript executed when they change organism. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "org"); dyStringAppend(dy, " document.hiddenForm.db.value=0;"); dyStringAppend(dy, " document.hiddenForm." hgvaRange ".value='';"); return jsOnChangeEnd(&dy); } static char *onChangeDb() /* Return javascript executed when they change database. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "db"); dyStringAppend(dy, " document.hiddenForm." hgvaRange ".value='';"); return jsOnChangeEnd(&dy); } INLINE void printOption(char *val, char *selectedVal, char *label) /* For rolling our own select without having to build conditional arrays/lists. */ { printf("