9b6958624673a00fdbe8447b7167e08301fd84bb
baertsch
  Fri May 20 13:31:58 2011 -0700
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
diff --git src/hg/hgTracks/retroGene.c src/hg/hgTracks/retroGene.c
index 5d40175..fd5324d 100644
--- src/hg/hgTracks/retroGene.c
+++ src/hg/hgTracks/retroGene.c
@@ -1,29 +1,41 @@
 
 #include "retroGene.h"
 #include "transMapStuff.h"
 
 static char const rcsid[] = "$Id: retroGene.c,v 1.19 2010/05/11 01:43:28 kent Exp $";
 
+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 retroMrnaInfo *pg)
+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;
 int blockCount = pg->blockCount, i;
 
 assert(starts != NULL && sizes != NULL && blockCount > 0);
 
 AllocVar(lf);
 lf->grayIx = grayIx;
 lf->name = cloneString(pg->name);
 lf->orientation = orientFromChar(pg->strand[0]);
@@ -37,45 +49,45 @@
     slAddHead(&sfList, sf);
     }
 slReverse(&sfList);
 lf->components = sfList;
 linkedFeaturesBoundsAndGrays(lf);
 lf->tallStart = pg->thickStart;
 lf->tallEnd = pg->thickEnd;
 lf->extra = pg;
 return lf;
 }
 void lfRetroGene(struct track *tg)
 /* Load the items in one custom track - just move beds in
  * window... */
 {
 struct linkedFeatures *lfList = NULL, *lf;
-struct retroMrnaInfo *pg = NULL, *list = NULL;
+struct ucscRetroInfo *pg = NULL, *list = NULL;
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 int rowOffset;
 int colCount ;
 
 sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
 colCount = sqlCountColumns(sr);
 while ((row = sqlNextRow(sr)) != NULL)
     {
-    if (colCount == 56)
-        pg = retroMrnaInfo56Load(row+rowOffset);
-    else
-        pg = retroMrnaInfoLoad(row+rowOffset);
+    //if (colCount == 56) 
+    //    pg = retroMrnaInfo56Load(row+rowOffset);
+    //else
+    pg = ucscRetroInfoLoad(row+rowOffset);
     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;
 }
 
@@ -85,60 +97,58 @@
 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 retroMrnaInfo *r, char *parentName)
+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];
-boolean isNative = sameString(tg->table, "pseudoGeneLink") ;
-boolean isRetroNative = startsWith( "ucscRetro", tg->table) || startsWith( "retroMrnaInfo", tg->table);
-safef(cartvar, sizeof(cartvar), "%s.label", (isNative ? "pseudoGeneLink.label" : (isRetroNative ? tg->track : "xenoRefGene.label")));
+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);
@@ -167,80 +177,73 @@
 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;
     char setting[64];
-    safef(setting, sizeof(setting), "%s.label.acc", tg->tdb->track);
-    cartSetBoolean(cart, setting, TRUE);
-    safef(setting, sizeof(setting), "%s.label.orgCommon", tg->tdb->track);
+    safef(setting, sizeof(setting), "%s.label.gene", tg->tdb->track);
     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 *retroMrnaInfoTbl , //char *transMapGeneTbl,
+                         char *retroInfoTbl , //char *transMapGeneTbl,
                          unsigned labelSet,
                          struct linkedFeatures *lf)
 /* get label for a retro item */
 {
-struct retroMrnaInfo *info = NULL;
-info = retroMrnaInfoQuery(conn, retroMrnaInfoTbl, lf->name);
+struct ucscRetroInfo *info = NULL;
+info = ucscRetroInfoQuery(conn, retroInfoTbl, lf->name);
 char *geneSymbol = getRetroParentSymbol(info, lf->name);
-lf->extra = geneSymbol;
-#ifdef junk
-if ((labelSet & useGene) && (transMapGeneTbl != NULL))
-    gene = transMapGeneQuery(conn, transMapGeneTbl,
-                             info->srcDb, transMapIdToAcc(info->srcId));
+//lf->extra = geneSymbol;
 
 struct dyString *label = dyStringNew(64);
-if (labelSet & useGene) 
+if ((labelSet & useGene) && (retroInfoTbl != NULL))
     {
-    if ((gene != NULL) && (strlen(gene->geneName) > 0))
-        addToLabel(label, gene->geneName);
+    if ((geneSymbol != NULL) && (strlen(geneSymbol) > 0))
+        addToLabel(label, geneSymbol);
     else
         labelSet |= useAcc;  // no gene, so force acc
     }
 if (labelSet & useAcc)
-    addToLabel(label, transMapIdToAcc(lf->name));
+    addToLabel(label, lf->name);
 
-retroMrnaInfoFree(&info);
+ucscRetroInfoFree(&info);
 lf->extra = dyStringCannibalize(&label);
-#endif
 }
 
 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);
 hFreeConn(&conn);
 }
@@ -274,26 +277,29 @@
 {
 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("pseudoGeneLink", retroGeneMethods);
+//registerTrackHandler("pseudoGeneLink2", retroGeneMethods);
+//registerTrackHandler("retroMrnaInfo", retroGeneMethods);
+//registerTrackHandler("retroMrnaInfo2", retroGeneMethods);
+//registerTrackHandler("retroMrnaInfo3", retroGeneMethods);
+registerTrackHandler("ucscRetroInfo", retroGeneMethods);
+registerTrackHandler("ucscRetroInfo2", retroGeneMethods);
 registerTrackHandler("ucscRetroInfo3", retroGeneMethods);
-registerTrackHandler("retroCdsAli", retroAliMethods);
-registerTrackHandler("retroCdsAli3", retroAliMethods);
+//registerTrackHandler("retroCdsAli", retroAliMethods);
+//registerTrackHandler("retroCdsAli3", retroAliMethods);
 registerTrackHandler("ucscRetroAli", retroAliMethods);
+registerTrackHandler("ucscRetroAli2", retroAliMethods);
 registerTrackHandler("ucscRetroAli3", retroAliMethods);
 }