d3752edc12da1bf08427946150f564dbdd5d2254 angie Thu Oct 24 13:55:51 2019 -0700 bigDbSnp track handler code - initial commit. refs #23283 * dnautil: Added trimRefAltLeft to get left-justified trimming (a la VCF not HGVS). * bigBedClick: do hReplaceGbdb up front in parseDetailsTablUrls instead of waiting until endpoint. * trackDbCustom.c: consolidating type-handling for wig/bigWig vs. bigBed-based big*. diff --git src/hg/hgTrackUi/hgTrackUi.c src/hg/hgTrackUi/hgTrackUi.c index 95bc36a..3103fa2 100644 --- src/hg/hgTrackUi/hgTrackUi.c +++ src/hg/hgTrackUi/hgTrackUi.c @@ -934,46 +934,36 @@ void oregannoUi (struct trackDb *tdb) /* print the controls */ { int i = 0; /* variable to walk through array */ printf("<BR><B>Type of region to display: </B> "); printf(" (Click <A HREF=\"http://www.oreganno.org/oregano/help/records.html\" target=\"_blank\">here</A> for detailed information on these element types)<BR>"); for (i = 0; i < oregannoTypeSize; i++) { cartMakeCheckBox(cart, oregannoTypeString[i], TRUE); printf (" %s<BR>", oregannoTypeLabel[i]); } } -void labelMakeCheckBox(struct trackDb *tdb, char *sym, char *desc, boolean dflt) -/* add a checkbox use to choose labels to enable. */ -{ -char varName[64]; -safef(varName, sizeof(varName), "%s.label.%s", tdb->track, sym); -boolean option = cartUsualBoolean(cart, varName, dflt); -cgiMakeCheckBox(varName, option); -printf(" %s ", desc); -} - void gvIdControls (struct trackDb *tdb) /* print the controls for the label choice */ { printf("<B>Label:</B> "); -labelMakeCheckBox(tdb, "hgvs", "HGVS name", FALSE); -labelMakeCheckBox(tdb, "common", "Common name", FALSE); +labelMakeCheckBox(cart, tdb, "hgvs", "HGVS name", FALSE); +labelMakeCheckBox(cart, tdb, "common", "Common name", FALSE); printf("<BR>\n"); } void gvUi(struct trackDb *tdb) /* print UI for human mutation filters */ { int i = 0; /* variable to walk through arrays */ //char *def; gvIdControls(tdb); /* printf("<BR><B>Exclude data source</B><BR>"); for (i = 0; i < gvSrcSize; i++) { @@ -1652,100 +1642,100 @@ void hg17KgUI(struct trackDb *tdb) /* Put up refGene-specific controls */ { hg17KgIdConfig(tdb); baseColorDrawOptDropDown(cart, tdb); } void omimLocationConfig(struct trackDb *tdb) /* Put up OMIM Location track controls */ { char varName[64]; safef(varName, sizeof(varName), "%s.label", tdb->track); printf("<BR><B>Include Entries of:</B> "); printf("<UL>\n"); printf("<LI>"); -labelMakeCheckBox(tdb, "class1", "Phenotype map key 1: the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.", TRUE); +labelMakeCheckBox(cart, tdb, "class1", "Phenotype map key 1: the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.", TRUE); printf("<LI>"); -labelMakeCheckBox(tdb, "class2", "Phenotype map key 2: the disorder has been placed on the map by linkage; no mutation has been found.", TRUE); +labelMakeCheckBox(cart, tdb, "class2", "Phenotype map key 2: the disorder has been placed on the map by linkage; no mutation has been found.", TRUE); printf("<LI>"); -labelMakeCheckBox(tdb, "class3", "Phenotype map key 3: the molecular basis for the disorder is known; a mutation has been found in the gene.", TRUE); +labelMakeCheckBox(cart, tdb, "class3", "Phenotype map key 3: the molecular basis for the disorder is known; a mutation has been found in the gene.", TRUE); printf("<LI>"); -labelMakeCheckBox(tdb, "class4", "Phenotype map key 4: a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.", TRUE); +labelMakeCheckBox(cart, tdb, "class4", "Phenotype map key 4: a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.", TRUE); // removed the "others" option for the time being //printf("<LI>"); -//labelMakeCheckBox(tdb, "others", "Others: no associated OMIM phenotype map key info available.", TRUE); +//labelMakeCheckBox(cart, tdb, "others", "Others: no associated OMIM phenotype map key info available.", TRUE); printf("</UL>"); } void omimGene2Config(struct trackDb *tdb) /* Put up OMIM Genes track controls */ { char varName[64]; safef(varName, sizeof(varName), "%s.label", tdb->track); printf("<BR><B>Include Entries of:</B> "); printf("<UL>\n"); printf("<LI>"); -labelMakeCheckBox(tdb, "class1", "Phenotype map key 1: the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.", TRUE); +labelMakeCheckBox(cart, tdb, "class1", "Phenotype map key 1: the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.", TRUE); printf("<LI>"); -labelMakeCheckBox(tdb, "class2", "Phenotype map key 2: the disorder has been placed on the map by linkage; no mutation has been found.", TRUE); +labelMakeCheckBox(cart, tdb, "class2", "Phenotype map key 2: the disorder has been placed on the map by linkage; no mutation has been found.", TRUE); printf("<LI>"); -labelMakeCheckBox(tdb, "class3", "Phenotype map key 3: the molecular basis for the disorder is known; a mutation has been found in the gene.", TRUE); +labelMakeCheckBox(cart, tdb, "class3", "Phenotype map key 3: the molecular basis for the disorder is known; a mutation has been found in the gene.", TRUE); printf("<LI>"); -labelMakeCheckBox(tdb, "class4", "Phenotype map key 4: a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.", TRUE); +labelMakeCheckBox(cart, tdb, "class4", "Phenotype map key 4: a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.", TRUE); printf("<LI>"); -labelMakeCheckBox(tdb, "others", "Others: no associated OMIM phenotype map key info available.", TRUE); +labelMakeCheckBox(cart, tdb, "others", "Others: no associated OMIM phenotype map key info available.", TRUE); printf("</UL>"); } void omimGeneIdConfig(struct trackDb *tdb) /* Put up gene ID track controls */ { char varName[64]; char *geneLabel; safef(varName, sizeof(varName), "%s.label", tdb->track); geneLabel = cartUsualString(cart, varName, "OMIM ID"); printf("<BR><B>Label:</B> "); radioButton(varName, geneLabel, "OMIM ID"); radioButton(varName, geneLabel, "OMIM gene or syndrome"); radioButton(varName, geneLabel, "UCSC gene symbol"); } void knownGeneIdConfig(struct trackDb *tdb) /* Put up gene ID track controls */ { struct sqlConnection *conn = hAllocConn(database); char query[256]; char *omimAvail = NULL; sqlSafef(query, sizeof(query), "select kgXref.kgID from kgXref,%s r where kgXref.refseq = r.mrnaAcc and r.omimId != 0 limit 1", refLinkTable); omimAvail = sqlQuickString(conn, query); hFreeConn(&conn); boolean isGencode = trackDbSettingOn(tdb, "isGencode") || trackDbSettingOn(tdb, "isGencode2"); printf("<B>Label:</B> "); -labelMakeCheckBox(tdb, "gene", "gene symbol", FALSE); +labelMakeCheckBox(cart, tdb, "gene", "gene symbol", FALSE); if (isGencode) - labelMakeCheckBox(tdb, "gencodeId", "GENCODE Transcript ID", FALSE); -labelMakeCheckBox(tdb, "kgId", "UCSC Known Gene ID", FALSE); -labelMakeCheckBox(tdb, "prot", "UniProt Display ID", FALSE); + labelMakeCheckBox(cart, tdb, "gencodeId", "GENCODE Transcript ID", FALSE); +labelMakeCheckBox(cart, tdb, "kgId", "UCSC Known Gene ID", FALSE); +labelMakeCheckBox(cart, tdb, "prot", "UniProt Display ID", FALSE); if (omimAvail != NULL) { char sym[32]; safef(sym, sizeof(sym), "omim%s", cartString(cart, "db")); - labelMakeCheckBox(tdb, sym, "OMIM ID", FALSE); + labelMakeCheckBox(cart, tdb, sym, "OMIM ID", FALSE); } printf("<BR>\n"); } void knownGeneShowWhatUi(struct trackDb *tdb) /* Put up line of controls that describe what parts to show. */ { char varName[64]; printf("<B>Show:</B> "); safef(varName, sizeof(varName), "%s.show.noncoding", tdb->track); boolean option = cartUsualBoolean(cart, varName, TRUE); cgiMakeCheckBox(varName, option); printf(" %s ", "non-coding genes"); safef(varName, sizeof(varName), "%s.show.spliceVariants", tdb->track); option = cartUsualBoolean(cart, varName, TRUE); @@ -1779,32 +1769,32 @@ knownGeneShowWhatUi(tdb); baseColorDrawOptDropDown(cart, tdb); wigOption(cart, "knownGene", "UCSC Genes", tdb); } void omimLocationUI(struct trackDb *tdb) /* Put up omimLcation-specific controls */ { omimLocationConfig(tdb); } void omimGene2IdConfig(struct trackDb *tdb) /* Put up gene ID track controls */ { printf("<B>Label:</B> "); -labelMakeCheckBox(tdb, "omimId", "OMIM ID", FALSE); -labelMakeCheckBox(tdb, "gene", "gene symbol", FALSE); +labelMakeCheckBox(cart, tdb, "omimId", "OMIM ID", FALSE); +labelMakeCheckBox(cart, tdb, "gene", "gene symbol", FALSE); printf("<BR>\n"); } void omimGene2UI(struct trackDb *tdb) /* Put up omimGene2-specific controls */ { omimGene2IdConfig(tdb); omimGene2Config(tdb); } void omimGeneUI(struct trackDb *tdb) /* Put up omimGene-specific controls */ { omimGeneIdConfig(tdb); } @@ -1839,118 +1829,118 @@ static void hideNoncodingOpt(struct trackDb *tdb) /* Put up hide-noncoding options. */ { /* Put up option to hide non-coding elements. */ printf("<B>Hide non-coding genes:</B> "); char varName[64]; safef(varName, sizeof(varName), "%s.%s", tdb->track, HIDE_NONCODING_SUFFIX); cartMakeCheckBox(cart, varName, HIDE_NONCODING_DEFAULT); } void rgdGene2UI(struct trackDb *tdb) /* Put up rgdGene2 gene ID track controls, with checkboxes */ { /* Put up label line - boxes for gene and accession. */ printf("<B>Label:</B> "); -labelMakeCheckBox(tdb, "gene", "gene", FALSE); -labelMakeCheckBox(tdb, "acc", "accession", FALSE); +labelMakeCheckBox(cart, tdb, "gene", "gene", FALSE); +labelMakeCheckBox(cart, tdb, "acc", "accession", FALSE); printf("<BR>\n"); baseColorDrawOptDropDown(cart, tdb); } void refGeneUI(struct trackDb *tdb) /* Put up refGene or xenoRefGene gene ID track controls, with checkboxes */ { // Show label options only if top-level track; ncbiRefSeqUI (for refSeqComposite) shows // label options for all subtracks. if (tdb->parent == NULL) { /* Figure out if OMIM database is available. */ int omimAvail = 0; if (sameString(tdb->track, "refGene")) { struct sqlConnection *conn = hAllocConn(database); char query[128]; sqlSafef(query, sizeof(query), "select r.omimId from %s r, refGene where r.mrnaAcc = refGene.name and r.omimId != 0 limit 1", refLinkTable); omimAvail = sqlQuickNum(conn, query); hFreeConn(&conn); } /* Put up label line - boxes for gene, accession or maybe OMIM. */ printf("<BR><B>Label:</B> "); - labelMakeCheckBox(tdb, "gene", "gene", TRUE); - labelMakeCheckBox(tdb, "acc", "accession", FALSE); + labelMakeCheckBox(cart, tdb, "gene", "gene", TRUE); + labelMakeCheckBox(cart, tdb, "acc", "accession", FALSE); if (omimAvail != 0) { char sym[32]; safef(sym, sizeof(sym), "omim%s", cartString(cart, "db")); - labelMakeCheckBox(tdb, sym, "OMIM ID", FALSE); + labelMakeCheckBox(cart, tdb, sym, "OMIM ID", FALSE); } printf("<BR>\n"); } /* Put up noncoding option and codon coloring stuff. */ hideNoncodingOpt(tdb); baseColorDrawOptDropDown(cart, tdb); printf("<BR>\n"); // let the user choose to see the track in wiggle mode wigOption(cart, tdb->track, tdb->shortLabel, tdb); } void transMapUI(struct trackDb *tdb) /* Put up transMap-specific controls for table-based transMap */ { // FIXME: this can be deleted once table-based transMap is no longer supported. printf("<B>Label:</B> "); -labelMakeCheckBox(tdb, "orgCommon", "common name", FALSE); -labelMakeCheckBox(tdb, "orgAbbrv", "organism abbreviation", FALSE); -labelMakeCheckBox(tdb, "db", "assembly database", FALSE); -labelMakeCheckBox(tdb, "gene", "gene", FALSE); -labelMakeCheckBox(tdb, "acc", "accession", FALSE); +labelMakeCheckBox(cart, tdb, "orgCommon", "common name", FALSE); +labelMakeCheckBox(cart, tdb, "orgAbbrv", "organism abbreviation", FALSE); +labelMakeCheckBox(cart, tdb, "db", "assembly database", FALSE); +labelMakeCheckBox(cart, tdb, "gene", "gene", FALSE); +labelMakeCheckBox(cart, tdb, "acc", "accession", FALSE); baseColorDrawOptDropDown(cart, tdb); indelShowOptions(cart, tdb); } void retroGeneUI(struct trackDb *tdb) /* Put up retroGene-specific controls */ { printf("<B>Label:</B> "); -labelMakeCheckBox(tdb, "gene", "gene", FALSE); -labelMakeCheckBox(tdb, "acc", "accession", FALSE); +labelMakeCheckBox(cart, tdb, "gene", "gene", FALSE); +labelMakeCheckBox(cart, tdb, "acc", "accession", FALSE); baseColorDrawOptDropDown(cart, tdb); } void ncbiRefSeqUI(struct trackDb *tdb) /* Put up gene ID track controls */ { char varName[256]; safef(varName, sizeof(varName), "%s.label", tdb->track); printf("<br><b>Label:</b> "); -labelMakeCheckBox(tdb, "gene", "gene symbol", TRUE); -labelMakeCheckBox(tdb, "acc", "accession", FALSE); +labelMakeCheckBox(cart, tdb, "gene", "gene symbol", TRUE); +labelMakeCheckBox(cart, tdb, "acc", "accession", FALSE); struct sqlConnection *conn = hAllocConn(database); boolean omimAvail = sqlQuickNum(conn, NOSQLINJ"select 1 from ncbiRefSeqLink where omimId != 0 limit 1"); if (omimAvail) { char sym[32]; safef(sym, sizeof(sym), "omim%s", cartString(cart, "db")); - labelMakeCheckBox(tdb, sym, "OMIM ID", FALSE); + labelMakeCheckBox(cart, tdb, sym, "OMIM ID", FALSE); } hFreeConn(&conn); } void ensGeneUI(struct trackDb *tdb) /* Put up Ensembl Gene track-specific controls */ { ensGeneIdConfig(tdb); printf("<BR>\n"); /* Put up codon coloring stuff. */ baseColorDrawOptDropDown(cart, tdb); } void vegaGeneUI(struct trackDb *tdb) @@ -3237,35 +3227,31 @@ break; } } grpFreeList(&grps); } } puts("<BR><BR>"); if (ct && sameString(tdb->type, "maf")) tdb->canPack = TRUE; else if (sameString(tdb->track, WIKI_TRACK_TABLE)) // special case wikiTrack (there's no trackDb entry); fixes redmine 2395 tdb->canPack = TRUE; else if (sameString(tdb->type, "halSnake")) tdb->canPack = TRUE; -else if (sameString(tdb->type, "bigPsl")) - tdb->canPack = TRUE; -else if (startsWith(tdb->type, "bigLolly")) - tdb->canPack = TRUE; -else if (sameString(tdb->type, "bigChain")) +else if (!startsWith("bigWig", tdb->type) && startsWith("big", tdb->type)) tdb->canPack = TRUE; else if (sameString(tdb->type, "bigNarrowPeak")) tdb->canPack = TRUE; // Don't bother with vis controls for downloadsOnly if (!tdbIsDownloadsOnly(tdb)) { /* Display visibility menu */ if (tdbIsComposite(tdb) && multViewCount(tdb) > 0) printf("<B>Maximum display mode: </B>"); else printf("<B>Display mode: </B>"); if (tdbIsSuper(tdb)) { superTrackDropDown(cart, tdb, 1);