03d727b53edf7e9c1f5de4cd02c6664631cacef4
hartera
  Tue Apr 23 14:29:22 2013 -0700
Removed retroGeneMethods and its use and associated functions. This was used when a BED format track was loaded, now PSL is loaded and retroAliMethods are used. Added code to format the label for track items and to add the prefix, retro-.
diff --git src/hg/hgTracks/retroGene.c src/hg/hgTracks/retroGene.c
index d879fe9..cbf3aa6 100644
--- src/hg/hgTracks/retroGene.c
+++ src/hg/hgTracks/retroGene.c
@@ -1,32 +1,19 @@
 
 #include "retroGene.h"
 #include "transMapStuff.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};
 
 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;
 int *sizes = pg->blockSizes;
@@ -78,110 +65,52 @@
     slAddHead(&list, pg);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 
 for (pg = list; pg != NULL; pg = pg->next)
     {
     lf = lfFromRetroGene(pg);
     lf->grayIx = 9;
     slReverse(&lf->components);
     slAddHead(&lfList,lf);
     }
 tg->items = lfList;
 }
 
-void loadRetroGene(struct track *tg)
-/* Load up RetroGenes. */
-{
-enum trackVisibility vis = tg->visibility;
-lfRetroGene(tg);
-if (vis != tvDense)
-    {
-    slSort(&tg->items, linkedFeaturesCmpStart);
-    }
-vis = limitVisibility(tg);
-}
-
-Color retroGeneColor(struct track *tg, void *item, struct hvGfx *hvg)
-/* Return color to draw retroGene in. */
-{
-return hvGfxFindColorIx(hvg, CHROM_20_R, CHROM_20_G, CHROM_20_B);
-}
-
 char *getRetroParentSymbol(struct ucscRetroInfo *r, char *parentName)
 {
 struct sqlConnection *conn = hAllocConn(database);
 char cond_str[512];
 char *geneSymbol = NULL;
 if (r != NULL)
     {
     if (hTableExists(database, "kgXref") )
         {
         safef(cond_str, sizeof(cond_str), "kgID='%s'", parentName);
         geneSymbol = sqlGetField(database, "kgXref", "geneSymbol", cond_str);
         }
 
     if (hTableExists(database, "refLink") )
         {
         safef(cond_str, sizeof(cond_str), "mrnaAcc = '%s'", r->refSeq);
         geneSymbol = sqlGetField(database, "refLink", "name", cond_str);
         }
     }
 hFreeConn(&conn);
 return geneSymbol;
 }
-char *retroName(struct track *tg, void *item)
-/* Get name to use for retroGene item. */
-{
-struct linkedFeatures *lf = item;
-char cartvar[512];
-safef(cartvar, sizeof(cartvar), "%s.label", tg->table);
-char *refGeneLabel = cartUsualString(cart, cartvar, "gene") ;
-boolean useGeneName = sameString(refGeneLabel, "gene")
-    || sameString(refGeneLabel, "both");
-boolean useAcc = sameString(refGeneLabel, "accession")
-    || sameString(refGeneLabel, "both");
-struct dyString *name = dyStringNew(64);
-if  (useAcc || useGeneName)
-    dyStringAppend(name, "retro-");
-char *geneSymbol = NULL;
-if (lf->extra != NULL) 
-   {
-   geneSymbol = getRetroParentSymbol(lf->extra, lf->name);
-   if (geneSymbol != NULL)
-        {
-        dyStringAppend(name, geneSymbol);
-        if (useAcc)
-            dyStringAppendC(name, '/');
-        }
-   }
-if ((useGeneName) && sameString(name->string, "retro-"))
-    dyStringAppend(name, lf->name);
-if (useAcc)
-    dyStringAppend(name, lf->name);
-return dyStringCannibalize(&name);
-}
-
-void retroGeneMethods(struct track *tg)
-/* Make track of retroGenes from bed */
-{
-tg->loadItems = loadRetroGene;
-tg->itemName = retroName;
-tg->mapItemName = refGeneMapName;
-tg->itemColor = retroGeneColor;
-}
 
 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->track);
 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 = useAcc;
@@ -203,42 +132,50 @@
     else if (endsWith(label->name, ".acc") && differentString(label->val, "0"))
         labelSet |= useAcc;
     }
 return labelSet;
 }
 static void getItemLabel(struct sqlConnection *conn,
                          char *retroInfoTbl , //char *transMapGeneTbl,
                          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))
-        addToLabel(label, geneSymbol);
+        dyStringAppend(label, geneSymbol);
     else
         labelSet |= useAcc;  // no gene, so force acc
     }
+/* if both accession and gene are selected, add to item label */
 if (labelSet & useAcc)
-    addToLabel(label, lf->name);
-
+    {
+    if (labelSet & useGene)
+        {
+        dyStringAppend(label, "/");
+        dyStringAppend(label, lf->name);
+        }
+    else
+        dyStringAppend(label, lf->name);
+    }
 ucscRetroInfoFree(&info);
 lf->extra = dyStringCannibalize(&label);
 }
 
 static void lookupRetroAliLabels(struct track *tg)
 /* This converts the retro ids to labels. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 char *retroInfoTbl = trackDbRequiredSetting(tg->tdb, retroInfoTblSetting);
 
 struct linkedFeatures *lf;
 unsigned labelSet = getLabelTypes(tg);
 
 for (lf = tg->items; lf != NULL; lf = lf->next)
     getItemLabel(conn, retroInfoTbl, labelSet, lf);
@@ -274,35 +211,21 @@
 {
 return transMapIdToAcc(itemName);
 }
 
 static void retroAliMethods(struct track *tg)
 /* Make track for retroGene psl alignments. */
 {
 tg->loadItems = loadRetroAli;
 tg->itemName = refGeneName;
 tg->mapItemName = refGeneMapName;
 tg->itemDataName = transMapGetItemDataName;
 }
 
 void retroRegisterTrackHandlers()
 {
-//registerTrackHandler("pseudoGeneLink", retroGeneMethods);
-//registerTrackHandler("pseudoGeneLink2", retroGeneMethods);
-//registerTrackHandler("retroMrnaInfo", retroGeneMethods);
-//registerTrackHandler("retroMrnaInfo2", retroGeneMethods);
-//registerTrackHandler("retroMrnaInfo3", retroGeneMethods);
-registerTrackHandler("ucscRetroInfo", retroGeneMethods);
-registerTrackHandler("ucscRetroInfo1", retroGeneMethods);
-registerTrackHandler("ucscRetroInfo2", retroGeneMethods);
-registerTrackHandler("ucscRetroInfo3", retroGeneMethods);
-registerTrackHandler("ucscRetroInfo4", retroGeneMethods);
-registerTrackHandler("ucscRetroInfo5", retroGeneMethods);
-//registerTrackHandler("retroCdsAli", retroAliMethods);
-//registerTrackHandler("retroCdsAli3", retroAliMethods);
-registerTrackHandler("ucscRetroAli", retroAliMethods);
 registerTrackHandler("ucscRetroAli1", retroAliMethods);
 registerTrackHandler("ucscRetroAli2", retroAliMethods);
 registerTrackHandler("ucscRetroAli3", retroAliMethods);
 registerTrackHandler("ucscRetroAli4", retroAliMethods);
 registerTrackHandler("ucscRetroAli5", retroAliMethods);
 }