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/hgTracks/retroGene.c src/hg/hgTracks/retroGene.c
index 92bb334..65b29b3 100644
--- src/hg/hgTracks/retroGene.c
+++ src/hg/hgTracks/retroGene.c
@@ -1,21 +1,20 @@
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 
 #include "retroGene.h"
-#include "transMapStuff.h"
 
 /* bit set of labels to use */
 enum {useOrgCommon = 0x01,
       useOrgAbbrv  = 0x02,
       useOrgDb     = 0x04,
       useGene      = 0x08,
       useAcc       = 0x10};
 
 struct linkedFeatures *lfFromRetroGene(struct ucscRetroInfo *pg)
 /* Return a linked feature from a retroGene. */
 {
 struct linkedFeatures *lf;
 struct simpleFeature *sf, *sfList = NULL;
 int grayIx = grayInRange(pg->score, 0, 1000);
 int *starts = pg->chromStarts, start;
@@ -126,31 +125,31 @@
     {
     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 *retroInfoTbl , //char *transMapGeneTbl,
+                         char *retroInfoTbl,
                          unsigned labelSet,
                          struct linkedFeatures *lf)
 /* get label for a retro item */
 {
 struct ucscRetroInfo *info = NULL;
 info = ucscRetroInfoQuery(conn, retroInfoTbl, lf->name);
 char *geneSymbol = getRetroParentSymbol(info, lf->name);
 //lf->extra = geneSymbol;
 struct dyString *label = dyStringNew(64);
 dyStringAppend(label, "retro-");
 if ((labelSet & useGene) && (retroInfoTbl != NULL))
     {
     if ((geneSymbol != NULL) && (strlen(geneSymbol) > 0))
         dyStringAppend(label, geneSymbol);
     else
@@ -184,51 +183,51 @@
     getItemLabel(conn, retroInfoTbl, labelSet, lf);
 hFreeConn(&conn);
 }
 
 static void loadRetroAli(struct track *tg)
 /* Load up retro alignments. */
 {
 loadXenoPsl(tg);
 enum trackVisibility vis = limitVisibility(tg);
 if (!((vis == tvDense) || (vis == tvSquish)))
     lookupRetroAliLabels(tg);
 if (vis != tvDense)
     slSort(&tg->items, linkedFeaturesCmpStart);
 }
 
-char *transMapIdToAcc(char *id)
-/* remove all unique suffixes (starting with last `-') from any TransMap 
+char *retroGeneIdToAcc(char *id)
+/* remove all unique suffixes (starting with last `-') from any retrogene
  * id.  WARNING: static return */
 {
 static char acc[128];
 safecpy(acc, sizeof(acc), id);
 char *dash = strrchr(acc, '-');
 if (dash != NULL)
     *dash = '\0';
 return acc;
 }
 
-static char *transMapGetItemDataName(struct track *tg, char *itemName)
+static char *retroGeneGetItemDataName(struct track *tg, char *itemName)
 /* translate itemName to data name (source accession).
  * WARNING: static return */
 {
-return transMapIdToAcc(itemName);
+return retroGeneIdToAcc(itemName);
 }
 
 static void retroAliMethods(struct track *tg)
 /* Make track for retroGene psl alignments. */
 {
 tg->loadItems = loadRetroAli;
 tg->itemName = refGeneName;
 tg->mapItemName = linkedFeaturesName;
-tg->itemDataName = transMapGetItemDataName;
+tg->itemDataName = retroGeneGetItemDataName;
 }
 
 void retroRegisterTrackHandlers()
 {
 registerTrackHandler("ucscRetroAli1", retroAliMethods);
 registerTrackHandler("ucscRetroAli2", retroAliMethods);
 registerTrackHandler("ucscRetroAli3", retroAliMethods);
 registerTrackHandler("ucscRetroAli4", retroAliMethods);
 registerTrackHandler("ucscRetroAli5", retroAliMethods);
 }