256b87a01941403ecb6d5b6ce2ed34aa0fd77514
markd
  Fri Dec 19 21:50:42 2014 -0800
added support for transmap V3 which includes source databases in mapped alignment  idenitifier
diff --git src/hg/hgc/transMapClick.c src/hg/hgc/transMapClick.c
index b071b34..cd366e4 100644
--- src/hg/hgc/transMapClick.c
+++ src/hg/hgc/transMapClick.c
@@ -1,262 +1,262 @@
 /* transMapClick - transMap click handling */
 
 /* Copyright (C) 2010 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 /*
  * Per-genome tables associated with transMap:
  *   transMapAliXxx - mapped PSLs alignments
  *   transMapInfoXxx - information for mapped alignments
  * hgFixed tables associated with transMap:
  *   transMapSrcXxx - information about source alignments
  *   transMapGeneXxx - gene information
  *   transMapSeqXxx - seq table for accessing sequence
  *   transMapExtFileXxx - extFile table
  *
  * Xxx is:
  *    - UcscGene - UCSC genes
  *    - RefSeq - RefSeq mRNAs
  *    - MRna - GenBank mRNAs
  *    - SplicedEst - GenBank spliced ESTs
  */
 
 #include "common.h"
 #include "hgc.h"
 #include "hui.h"
 #include "hCommon.h"
 #include "transMapClick.h"
 #include "transMapStuff.h"
 #include "transMapInfo.h"
 #include "transMapSrc.h"
 #include "transMapGene.h"
 #include "genbank.h"
 
 
 struct transMapBag
 /* object contain collected information on a specific transMap mapping */
 {
     struct psl *psl;              // transMap alignment
     struct transMapInfo *info;    // addition information about mapping
     struct transMapSrc *src;      // source information
     struct transMapGene *gene;    // gene information
     boolean srcDbIsActive;        // source database is active
 };
 
 static struct transMapBag *transMapBagLoad(struct sqlConnection *conn,
                                            struct trackDb *tdb, char *mappedId,
                                            boolean getSrcRec)
 /* load information from various tables */
 {
 struct transMapBag *bag;
 AllocVar(bag);
 bag->psl = getAlignments(conn, tdb->table, mappedId);
 
 char *transMapInfoTbl = trackDbRequiredSetting(tdb, transMapInfoTblSetting);
 bag->info = transMapInfoQuery(conn, transMapInfoTbl, mappedId);
 
 if (getSrcRec)
     {
     char *transMapSrcTbl = trackDbRequiredSetting(tdb, transMapSrcTblSetting);
     bag->src = transMapSrcQuery(conn, transMapSrcTbl, bag->info->srcDb, bag->info->srcId);
     }
 
 char *transMapGeneTbl = trackDbSetting(tdb, transMapGeneTblSetting);
 if (transMapGeneTbl != NULL)
     bag->gene = transMapGeneQuery(conn, transMapGeneTbl,
-                                  bag->info->srcDb, transMapIdToAcc(bag->info->srcId));
+                                  bag->info->srcDb, transMapIdToSeqId(bag->info->srcId));
 bag->srcDbIsActive = hDbIsActive(bag->info->srcDb);
 return bag;
 }
 
 static void transMapBagFree(struct transMapBag **bagPtr)
 /* free the bag */
 {
 struct transMapBag *bag = *bagPtr;
 if (bag != NULL)
     {
     pslFree(&bag->psl);
     transMapInfoFree(&bag->info);
     transMapSrcFree(&bag->src);
     transMapGeneFree(&bag->gene);
     freez(bagPtr);
     }
 }
 
 static void prOrgScientific(char *db)
 /* print organism and scientific name for a database. */
 {
 char *org = hOrganism(db);
 char *sciName = hScientificName(db);
 if ((org != NULL) && (sciName != NULL))
     printf("%s (%s)", org, sciName);
 else
     printf("n/a");
 freeMem(org);
 freeMem(sciName);
 }
 
 static char *chainSubsetDesc(enum transMapInfoChainSubset cs)
 /* get description for chain subset */
 {
 switch (cs)
     {
     case transMapInfoUnknown:
         return "unknown";
     case transMapInfoAll:
         return "all";
     case transMapInfoSyn:
         return "syntenic";
     case transMapInfoRbest:
         return "reciprocal best";
     }
 return NULL;
 }
 
 static void displayMapped(struct transMapBag *bag)
 /* display information about the mapping alignment */
 {
 printf("<TABLE class=\"transMap\">\n");
 printf("<CAPTION>TransMap Alignment</CAPTION>\n");
 printf("<TBODY>\n");
 
 // organism/assembly
 printf("<TR CLASS=\"transMapLeft\"><TD>Organism<TD>");
 prOrgScientific(database);
 printf("</TR>\n");
 printf("<TR CLASS=\"transMapLeft\"><TD>Genome<TD>%s</TR>\n", database);
 
 // position
 printf("<TR CLASS=\"transMapLeft\">");
 printf("<TD>Position<TD CLASS=\"transMapNoWrap\">");
 printf("<A HREF=\"%s&position=%s:%d-%d\">",
       hgTracksPathAndSettings(),
       bag->psl->tName, bag->psl->tStart, bag->psl->tEnd);
 printf("%s:%d-%d</A>", bag->psl->tName, bag->psl->tStart, bag->psl->tEnd);
 printf("</TR>\n");
 
 // % identity and % aligned
 printf("<TR CLASS=\"transMapLeft\"><TD>Identity<TD>%0.1f%%</TR>\n",
        100.0*pslIdent(bag->psl));
 printf("<TR CLASS=\"transMapLeft\"><TD>Aligned<TD>%0.1f%%</TR>\n",
        100.0*pslQueryAligned(bag->psl));
 
 // chain used in mapping
 printf("<TR CLASS=\"transMapLeft\"><TD>Chain ID<TD>%s</TR>\n",
        bag->info->mappingId);
 printf("<TR CLASS=\"transMapLeft\"><TD>Chain subset<TD>%s</TR>\n",
        chainSubsetDesc(bag->info->chainSubset));
 printf("</TBODY></TABLE>\n");
 }
 
 static void displaySource(struct transMapBag *bag)
 /* display information about the source gene that was mapped */
 {
 printf("<TABLE class=\"transMap\">\n");
 printf("<CAPTION>Source Alignment</CAPTION>\n");
 printf("<TBODY>\n");
 // organism/assembly
 printf("<TR CLASS=\"transMapLeft\"><TD>Organism<TD>");
 prOrgScientific(bag->info->srcDb);
 printf("</TR>\n");
 printf("<TR CLASS=\"transMapLeft\"><TD>Genome<TD>%s</TR>\n", bag->info->srcDb);
 
 // position
 printf("<TR CLASS=\"transMapLeft\"><TD>Position\n");
 printf("<TD CLASS=\"transMapNoWrap\">");
 if (bag->srcDbIsActive)
     printf("<A HREF=\"%s?db=%s&position=%s:%d-%d\" target=_blank>"
            "%s:%d-%d</A>",
            hgTracksName(), bag->src->db,
            bag->src->chrom, bag->src->chromStart, bag->src->chromEnd,
            bag->src->chrom, bag->src->chromStart, bag->src->chromEnd);
 else
     printf("%s:%d-%d", bag->src->chrom, bag->src->chromStart, bag->src->chromEnd);
 printf("</TR>\n");
 
 // % identity and % aligned
 printf("<TR CLASS=\"transMapLeft\"><TD>Identity<TD>%0.1f%%</TR>\n",
        100.0*bag->src->ident);
 printf("<TR CLASS=\"transMapLeft\"><TD>Aligned<TD>%0.1f%%</TR>\n",
        100.0*bag->src->aligned);
 
 // gene and CDS
 printf("<TR CLASS=\"transMapLeft\"><TD>Gene<TD>%s</TR>\n",
        (((bag->gene != NULL) && (strlen(bag->gene->geneName) > 0))
         ? bag->gene->geneName : "&nbsp;"));
 printf("<TR CLASS=\"transMapLeft\"><TD>CDS<TD>%s</TR>\n",
        (((bag->gene != NULL) && (strlen(bag->gene->cds) > 0))
         ? bag->gene->cds : "&nbsp;"));
 printf("</TBODY></TABLE>\n");
 }
 
 static void displayAligns(struct trackDb *tdb, struct transMapBag *bag)
 /* display cDNA alignments */
 {
 int start = cartInt(cart, "o");
 printf("<H3>mRNA/Genomic Alignments</H3>");
 printAlignmentsSimple(bag->psl, start, "hgcTransMapCdnaAli", tdb->table, bag->info->mappedId);
 }
 
 void transMapClickHandler(struct trackDb *tdb, char *mappedId)
 /* Handle click on a transMap tracks */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct transMapBag *bag = transMapBagLoad(conn, tdb, mappedId, TRUE);
 
 genericHeader(tdb, mappedId);
 printf("<TABLE class=\"transMapLayout\">\n");
 
 printf("<TR><TD>\n");
 displayMapped(bag);
 printf("<TD>\n");
 displaySource(bag);
 printf("<TD>&nbsp;\n");
 printf("</TR>\n");
 printf("<TR><TD COLSPAN=3>\n");
 displayAligns(tdb, bag);
 printf("</TR>\n");
 printf("</TABLE>\n");
 
 printTrackHtml(tdb);
 transMapBagFree(&bag);
 hFreeConn(&conn);
 }
 
 static struct dnaSeq *getCdnaSeq(struct trackDb *tdb, char *name)
 /* look up sequence name in seq and extFile tables specified
  * for base coloring. */
 {
 /* FIXME: this is really a rip off of some of the code in
  * hgTracks/cds.c; really need to centralize it somewhere */
 char *spec = trackDbRequiredSetting(tdb, BASE_COLOR_USE_SEQUENCE);
 char *specCopy = cloneString(spec);
 
 // value is: extFile seqTbl extFileTbl
 char *words[3];
 int nwords = chopByWhite(specCopy, words, ArraySize(words));
 if ((nwords != ArraySize(words)) || !sameString(words[0], "extFile"))
     errAbort("invalid %s track setting: %s", BASE_COLOR_USE_SEQUENCE, spec);
-struct dnaSeq *seq = hDnaSeqGet(NULL, name, words[1], words[2]);
+struct dnaSeq *seq = hDnaSeqMustGet(NULL, name, words[1], words[2]);
 freeMem(specCopy);
 return seq;
 }
 
 void transMapShowCdnaAli(struct trackDb *tdb, char *mappedId)
 /* Show alignment for mappedId, mostly ripped off from htcCdnaAli */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct transMapBag *bag = transMapBagLoad(conn, tdb, mappedId, FALSE);
 struct genbankCds cds;
 if ((bag->gene == NULL) || (strlen(bag->gene->cds) == 0)
     || !genbankCdsParse(bag->gene->cds, &cds))
     ZeroVar(&cds);  /* can't get or parse cds */
-struct dnaSeq *seq = getCdnaSeq(tdb, transMapIdToAcc(mappedId));
+struct dnaSeq *seq = getCdnaSeq(tdb, transMapIdToSeqId(mappedId));
 
 writeFramesetType();
 puts("<HTML>");
 printf("<HEAD>\n<TITLE>%s vs Genomic</TITLE>\n</HEAD>\n\n", mappedId);
 showSomeAlignment(bag->psl, seq, gftDna, 0, seq->size, NULL, cds.start, cds.end);
 dnaSeqFree(&seq);
 transMapBagFree(&bag);
 hFreeConn(&conn);
 }