src/hg/hgGenome/custom.c 1.5

Index: src/hg/hgGenome/custom.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgGenome/custom.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/hgGenome/custom.c	10 Apr 2009 20:02:13 -0000	1.4
+++ src/hg/hgGenome/custom.c	11 May 2010 01:43:24 -0000	1.5
@@ -1,269 +1,270 @@
 /* custom - stuff related to custom tracks. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "obscure.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "trackDb.h"
 #include "grp.h"
 #include "customTrack.h"
 
 #include "hgGenome.h"
 
 static char const rcsid[] = "$Id$";
 
 struct customTrack *theCtList = NULL;	/* List of custom tracks. */
 struct slName *browserLines = NULL;	/* Browser lines in custom tracks. */
 
 struct customTrack *getCustomTracks()
 /* Get custom track list. */
 {
 //fprintf(stdout,"database %s in cart %s", database, cartString(cart, "db"));
 cartSetString(cart, "db", database);
 if (theCtList == NULL)
     theCtList = customTracksParseCart(database, cart, &browserLines, NULL);
 return(theCtList);
 }
 
 void flushCustomTracks()
 /* Flush custom track list. */
 {
 theCtList = NULL;
 }
 
 struct customTrack *newCt(char *ctName, char *ctDesc, int visNum, char *ctUrl,
 			  int fields)
 /* Make a new custom track record for the query results. */
 {
 struct customTrack *ct;
 struct trackDb *tdb;
 char buf[256];
 
 AllocVar(ct);
 AllocVar(tdb);
-tdb->tableName = customTrackTableFromLabel(ctName);
+tdb->table = customTrackTableFromLabel(ctName);
+tdb->track = cloneString(tdb->table);
 tdb->shortLabel = ctName;
 tdb->longLabel = ctDesc;
 safef(buf, sizeof(buf), "bed %d .", fields);
 tdb->type = cloneString(buf);
 tdb->visibility = visNum;
 tdb->url = ctUrl;
 ct->tdb = tdb;
 ct->fieldCount = fields;
 ct->needsLift = FALSE;
 ct->fromPsl = FALSE;
 ct->wiggle = FALSE;
 ct->wigAscii = (char *)NULL;
 ct->wigFile = (char *)NULL;
 ct->wibFile = (char *)NULL;
 ctAddToSettings(ct, CT_UNPARSED, "true");
 return ct;
 }
 
 
 struct hTableInfo *ctToHti(struct customTrack *ct)
 /* Create an hTableInfo from a customTrack. */
 {
 struct hTableInfo *hti;
 
 if (ct == NULL)
     return(NULL);
 
 AllocVar(hti);
-hti->rootName = cloneString(ct->tdb->tableName);
+hti->rootName = cloneString(ct->tdb->table);
 hti->isPos = TRUE;
 hti->isSplit = FALSE;
 hti->hasBin = FALSE;
 hti->type = cloneString(ct->tdb->type);
 if (ct->fieldCount >= 3)
     {
     strncpy(hti->chromField, "chrom", 32);
     strncpy(hti->startField, "chromStart", 32);
     strncpy(hti->endField, "chromEnd", 32);
     }
 if (ct->fieldCount >= 4)
     {
     strncpy(hti->nameField, "name", 32);
     }
 if (ct->fieldCount >= 5)
     {
     strncpy(hti->scoreField, "score", 32);
     }
 if (ct->fieldCount >= 6)
     {
     strncpy(hti->strandField, "strand", 32);
     }
 if (ct->fieldCount >= 8)
     {
     strncpy(hti->cdsStartField, "thickStart", 32);
     strncpy(hti->cdsEndField, "thickEnd", 32);
     hti->hasCDS = TRUE;
     }
 if (ct->fieldCount >= 12)
     {
     strncpy(hti->countField, "blockCount", 32);
     strncpy(hti->startsField, "chromStarts", 32);
     strncpy(hti->endsSizesField, "blockSizes", 32);
     hti->hasBlocks = TRUE;
     }
 
 return(hti);
 }
 
 struct slName *getBedFields(int fieldCount)
 /* Get list of fields for bed of given size. */
 {
 struct slName *fieldList = NULL, *field;
 if (fieldCount >= 3)
     {
     field = newSlName("chrom");
     slAddHead(&fieldList, field);
     field = newSlName("chromStart");
     slAddHead(&fieldList, field);
     field = newSlName("chromEnd");
     slAddHead(&fieldList, field);
     }
 if (fieldCount >= 4)
     {
     field = newSlName("name");
     slAddHead(&fieldList, field);
     }
 if (fieldCount >= 5)
     {
     field = newSlName("score");
     slAddHead(&fieldList, field);
     }
 if (fieldCount >= 6)
     {
     field = newSlName("strand");
     slAddHead(&fieldList, field);
     }
 if (fieldCount >= 8)
     {
     field = newSlName("thickStart");
     slAddHead(&fieldList, field);
     field = newSlName("thickEnd");
     slAddHead(&fieldList, field);
     }
 if (fieldCount >= 9)
     {
     field = newSlName("itemRgb");
     slAddHead(&fieldList, field);
     }
 if (fieldCount >= 12)
     {
     field = newSlName("blockCount");
     slAddHead(&fieldList, field);
     field = newSlName("blockSizes");
     slAddHead(&fieldList, field);
     field = newSlName("chromStarts");
     slAddHead(&fieldList, field);
     }
 if (fieldCount >= 15)
     {
     field = newSlName("expCount");
     slAddHead(&fieldList, field);
     field = newSlName("expIds");
     slAddHead(&fieldList, field);
     field = newSlName("expScores");
     slAddHead(&fieldList, field);
     }
 slReverse(&fieldList);
 return fieldList;
 }
 
 
 
 void removeNamedCustom(struct customTrack **pList, char *name)
 /* Remove named custom track from list if it's on there. */
 {
 struct customTrack *newList = NULL, *ct, *next;
 for (ct = *pList; ct != NULL; ct = next)
     {
     next = ct->next;
-    if (!sameString(ct->tdb->tableName, name))
+    if (!sameString(ct->tdb->table, name))
         {
 	slAddHead(&newList, ct);
 	}
     }
 slReverse(&newList);
 *pList = newList;
 }
 
 static void customTrackBedOnChrom(
 	char *chrom,	        /* chrom to get data from. */
 	struct customTrack *ct, /* Custom track. */
 	struct lm *lm,		/* Local memory pool. */
 	struct bed **pBedList   /* Output get's appended to this list */
 	)
 /* Get the custom tracks passing filter on a single chrom. */
 {
 struct bed *bed;
 
 if (ct->dbTrack)
     {
     int fieldCount = ct->fieldCount;
     char query[512];
     int rowOffset = 0;
     char **row;
     struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
     struct sqlResult *sr = NULL;
 
     safef(query, sizeof(query), "select * from %s where chrom='%s'", ct->dbTableName, chrom);
     sr = sqlGetResult(conn, query);
     if (sameString("bin",sqlFieldName(sr)))
 	++rowOffset;
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	bed = bedLoadN(row+rowOffset, fieldCount);
 	struct bed *copy = lmCloneBed(bed, lm);
 	slAddHead(pBedList, copy);
 	}
     sqlFreeResult(&sr);
     hFreeConn(&conn);
     }
 else
     {
     for (bed = ct->bedList; bed != NULL; bed = bed->next)
 	{
 	if (sameString(bed->chrom, chrom))
 	    {
 	    struct bed *copy = lmCloneBed(bed, lm);
 	    slAddHead(pBedList, copy);
 	    }
 	}
     }
 }
 
 
 
 struct bed *customTrackGetBedsForChrom(char *name, char *chrom,
 	struct lm *lm,	int *retFieldCount)
 /* Get list of beds from custom track of given name that are
  * in given chrom. You can bedFree this when done. */
 {
 struct customTrack *ct = lookupCt(name);
 struct bed *bedList = NULL;
 int fieldCount;
 
 if (ct == NULL)
     errAbort("Can't find custom track %s", name);
 
 /* Figure out how to filter things. */
 fieldCount = ct->fieldCount;
 
 /* Grab beds for a chrom. */
 customTrackBedOnChrom(chrom, ct, lm, &bedList);
 
 /* Set return variables and clean up. */
 slReverse(&bedList);
 
 if (retFieldCount != NULL)
     *retFieldCount = fieldCount;
 return bedList;
 }