src/hg/hgTracks/transMapTracks.c 1.8

Index: src/hg/hgTracks/transMapTracks.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/transMapTracks.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 1000000 -r1.7 -r1.8
--- src/hg/hgTracks/transMapTracks.c	6 Nov 2008 06:46:36 -0000	1.7
+++ src/hg/hgTracks/transMapTracks.c	10 Jul 2009 04:51:06 -0000	1.8
@@ -1,165 +1,166 @@
 /* transMapTracks - transMap track methods */
 #include "common.h"
 #include "transMapTracks.h"
 #include "hgTracks.h"
 #include "hdb.h"
 #include "transMapStuff.h"
 #include "transMapInfo.h"
 #include "transMapSrc.h"
 #include "transMapGene.h"
 
 static void addToLabel(struct dyString *label, char *val)
 /* append a label to the label, separating with a space, do nothing if val is
  * NULL.*/
 {
 if (val != NULL)
     {
     if (label->stringSize > 0)
         dyStringAppendC(label, ' ');
     dyStringAppend(label, val);
     }
 }
 
 /* bit set of labels to use */
 enum {useOrgCommon = 0x01,
       useOrgAbbrv  = 0x02,
       useOrgDb     = 0x04,
       useGene      = 0x08,
       useAcc       = 0x10};
 
 static unsigned getLabelTypes(struct track *tg)
 /* get set of labels to use */
 {
 unsigned labelSet = 0;
 
 // label setting are on parent track
 char prefix[128];
 safef(prefix, sizeof(prefix), "%s.label", tg->tdb->tableName);
 struct hashEl *labels = cartFindPrefix(cart, prefix);
 
 if (labels == NULL)
     {
     // default to common name+accession and save this in cart so it makes sense in trackUi
     labelSet = useOrgCommon|useAcc;
     char setting[64];
     safef(setting, sizeof(setting), "%s.label.acc", tg->tdb->tableName);
     cartSetBoolean(cart, setting, TRUE);
     safef(setting, sizeof(setting), "%s.label.orgCommon", tg->tdb->tableName);
     cartSetBoolean(cart, setting, TRUE);
     }
 struct hashEl *label;
 for (label = labels; label != NULL; label = label->next)
     {
     if (endsWith(label->name, ".orgCommon") && differentString(label->val, "0"))
         labelSet |= useOrgCommon;
     else if (endsWith(label->name, ".orgAbbrv") && differentString(label->val, "0"))
         labelSet |= useOrgAbbrv;
     else if (endsWith(label->name, ".db") && differentString(label->val, "0"))
         labelSet |= useOrgDb;
     else if (endsWith(label->name, ".gene") && differentString(label->val, "0"))
         labelSet |= useGene;
     else if (endsWith(label->name, ".acc") && differentString(label->val, "0"))
         labelSet |= useAcc;
     }
 return labelSet;
 }
 
 static void getItemLabel(struct sqlConnection *conn, char *transMapInfoTbl, 
                          struct sqlConnection *geneConn, char *transMapGeneTbl,
                          unsigned labelSet,
                          struct linkedFeatures *lf)
 /* get label for a transMap item */
 {
 struct transMapInfo *info = NULL;
 struct transMapGene *gene = NULL;
 boolean srcDbExists = FALSE;
 if (labelSet & (useOrgCommon|useOrgAbbrv|useOrgDb|useGene))
     {
     info = transMapInfoQuery(conn, transMapInfoTbl, lf->name);
     srcDbExists = sqlDatabaseExists(info->srcDb);
     }
 if ((labelSet & useGene) && (geneConn != NULL))
     {
     gene = transMapGeneQuery(geneConn, transMapGeneTbl,
                              info->srcDb, transMapIdToAcc(info->srcId));
     }
 
 struct dyString *label = dyStringNew(64);
 if (labelSet & useOrgAbbrv && srcDbExists)
     addToLabel(label, orgShortForDb(info->srcDb));
 if (labelSet & useOrgCommon && srcDbExists)
     addToLabel(label, hOrganism(info->srcDb));
 if (labelSet & useOrgDb)
     addToLabel(label, info->srcDb);
 if (labelSet & useGene) 
     {
     if ((gene != NULL) && (strlen(gene->geneName) > 0))
         addToLabel(label, gene->geneName);
     else
         labelSet |= useAcc;  // no gene, so force acc
     }
 if (labelSet & useAcc)
     addToLabel(label, transMapIdToAcc(lf->name));
 
 transMapInfoFree(&info);
 transMapGeneFree(&gene);
 lf->extra = dyStringCannibalize(&label);
 }
 
 static void lookupTransMapLabels(struct track *tg)
 /* This converts the transMap ids to labels. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 char *transMapInfoTbl = trackDbRequiredSetting(tg->tdb, transMapInfoTblSetting);
 char *transMapGeneTbl = trackDbSetting(tg->tdb, transMapGeneTblSetting);
 struct sqlConnection *geneConn = NULL;
 if (transMapGeneTbl != NULL)
     geneConn = hAllocConnDbTbl(transMapGeneTbl, &transMapGeneTbl, database);
     
 
 struct linkedFeatures *lf;
 unsigned labelSet = getLabelTypes(tg);
 
 for (lf = tg->items; lf != NULL; lf = lf->next)
     getItemLabel(conn, transMapInfoTbl, geneConn, transMapGeneTbl, labelSet, lf);
 hFreeConn(&geneConn);
 hFreeConn(&conn);
 }
 
 static void loadTransMap(struct track *tg)
 /* Load up transMap alignments. */
 {
 loadXenoPsl(tg);
 enum trackVisibility vis = limitVisibility(tg);
 if (!((vis == tvDense) || (vis == tvSquish)))
     lookupTransMapLabels(tg);
 if (vis != tvDense)
     slSort(&tg->items, linkedFeaturesCmpStart);
 }
 
 static char *transMapGetItemDataName(struct track *tg, char *itemName)
 /* translate itemName to data name (source accession).
  * WARNING: static return */
 {
 return transMapIdToAcc(itemName);
 }
 
 static void transMapMethods(struct track *tg)
 /* Make track for transMap alignments. */
 {
 tg->loadItems = loadTransMap;
 tg->itemName = refGeneName;
 tg->mapItemName = refGeneMapName;
 tg->itemDataName = transMapGetItemDataName;
 }
 
 void transMapRegisterTrackHandlers()
 /* register track handlers for transMap tracks */
 {
+registerTrackHandler("transMap", transMapMethods);
 registerTrackHandler("transMapAlnRefSeq", transMapMethods);
 registerTrackHandler("transMapAlnMRna", transMapMethods);
 registerTrackHandler("transMapAlnSplicedEst", transMapMethods);
 registerTrackHandler("transMapAlnUcscGenes", transMapMethods);
 // reconstruction
 registerTrackHandler("reconTransMapAlnRefSeq", transMapMethods);
 }