src/hg/hgTables/custom.c 1.42

Index: src/hg/hgTables/custom.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTables/custom.c,v
retrieving revision 1.41
retrieving revision 1.42
diff -b -B -U 1000000 -r1.41 -r1.42
--- src/hg/hgTables/custom.c	20 May 2009 20:59:56 -0000	1.41
+++ src/hg/hgTables/custom.c	5 Jun 2009 21:59:00 -0000	1.42
@@ -1,586 +1,587 @@
 /* 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 "hgTables.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);
 }
 
 struct customTrack *ctLookupName(char *name)
 /* Lookup name in custom track list */
 {
 return ctFind(getCustomTracks(),name);
 }
 
 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];
 
 tdb = customTrackTdbDefault();
 tdb->tableName = customTrackTableFromLabel(ctName);
 tdb->shortLabel = ctName;
 tdb->longLabel = ctDesc;
 safef(buf, sizeof(buf), "bed %d .", fields);
 tdb->type = cloneString(buf);
 tdb->canPack = 0;
 tdb->visibility = visNum;
 tdb->url = ctUrl;
 
 AllocVar(ct);
 ct->tdb = tdb;
 ct->genomeDb = cloneString(database);
 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->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;
 }
 
 #ifdef UNUSED
 static void tabBedRow(struct bed *bed, struct slName *fieldList)
 /* Print out named fields from bed. */
 {
 struct slName *field;
 boolean needTab = FALSE;
 for (field = fieldList; field != NULL; field = field->next)
     {
     char *type = field->name;
     if (needTab)
         hPrintf("\t");
     else
         needTab = TRUE;
     if (sameString(type, "chrom"))
         hPrintf("%s", bed->chrom);
     else if (sameString(type, "chromStart"))
         hPrintf("%u", bed->chromStart);
     else if (sameString(type, "chromEnd"))
         hPrintf("%u", bed->chromEnd);
     else if (sameString(type, "name"))
         hPrintf("%s", bed->name);
     else if (sameString(type, "score"))
         hPrintf("%d", bed->score);
     else if (sameString(type, "strand"))
         hPrintf("%s", bed->strand);
     else if (sameString(type, "thickStart"))
         hPrintf("%u", bed->thickStart);
     else if (sameString(type, "thickEnd"))
         hPrintf("%u", bed->thickEnd);
     else if (sameString(type, "itemRgb"))
 	{
 	int rgb = bed->itemRgb;
 	hPrintf("%d,%d,%d", (rgb & 0xff0000) >> 16,
 		(rgb & 0xff00) >> 8, (rgb & 0xff));
 	}
     else if (sameString(type, "blockCount"))
         hPrintf("%u", bed->blockCount);
     else if (sameString(type, "blockSizes"))
 	{
 	unsigned i;
 	for (i=0; i<bed->blockCount; ++i)
 	    hPrintf("%u,", bed->blockSizes[i]);
 	}
     else if (sameString(type, "chromStarts"))
 	{
 	unsigned i;
 	for (i=0; i<bed->blockCount; ++i)
 	    hPrintf("%u,", bed->chromStarts[i]);
 	}
     else if (sameString(type, "expCount"))
         hPrintf("%u", bed->expCount);
     else if (sameString(type, "expIds"))
 	{
 	unsigned i;
 	for (i=0; i<bed->expCount; ++i)
 	    hPrintf("%u,", bed->expIds[i]);
 	}
     else if (sameString(type, "expScores"))
 	{
 	unsigned i;
 	for (i=0; i<bed->expCount; ++i)
 	    hPrintf("%f,", bed->expScores[i]);
 	}
     else
         errAbort("Unrecognized bed field %s", type);
     }
 hPrintf("\n");
 }
 #endif /* UNUSED */
 
 static void tabBedRowFile(struct bed *bed, struct slName *fieldList, FILE *f)
 /* Print out to a file named fields from bed. */
 {
 struct slName *field;
 boolean needTab = FALSE;
 for (field = fieldList; field != NULL; field = field->next)
     {
     char *type = field->name;
     if (needTab)
         fprintf(f, "\t");
     else
         needTab = TRUE;
     if (sameString(type, "chrom"))
         fprintf(f, "%s", bed->chrom);
     else if (sameString(type, "chromStart"))
         fprintf(f, "%u", bed->chromStart);
     else if (sameString(type, "chromEnd"))
         fprintf(f, "%u", bed->chromEnd);
     else if (sameString(type, "name"))
         fprintf(f, "%s", bed->name);
     else if (sameString(type, "score"))
         fprintf(f, "%d", bed->score);
     else if (sameString(type, "strand"))
         fprintf(f, "%s", bed->strand);
     else if (sameString(type, "thickStart"))
         fprintf(f, "%u", bed->thickStart);
     else if (sameString(type, "thickEnd"))
         fprintf(f, "%u", bed->thickEnd);
     else if (sameString(type, "itemRgb"))
 	{
 	int rgb = bed->itemRgb;
 	fprintf(f, "%d,%d,%d", (rgb & 0xff0000) >> 16,
 		(rgb & 0xff00) >> 8, (rgb & 0xff));
 	}
     else if (sameString(type, "blockCount"))
         fprintf(f, "%u", bed->blockCount);
     else if (sameString(type, "blockSizes"))
 	{
 	unsigned i;
 	for (i=0; i<bed->blockCount; ++i)
 	    fprintf(f, "%u,", bed->blockSizes[i]);
 	}
     else if (sameString(type, "chromStarts"))
 	{
 	unsigned i;
 	for (i=0; i<bed->blockCount; ++i)
 	    fprintf(f, "%u,", bed->chromStarts[i]);
 	}
     else if (sameString(type, "expCount"))
         fprintf(f, "%u", bed->expCount);
     else if (sameString(type, "expIds"))
 	{
 	unsigned i;
 	for (i=0; i<bed->expCount; ++i)
 	    fprintf(f, "%u,", bed->expIds[i]);
 	}
     else if (sameString(type, "expScores"))
 	{
 	unsigned i;
 	for (i=0; i<bed->expCount; ++i)
 	    fprintf(f, "%f,", bed->expScores[i]);
 	}
     else
         errAbort("Unrecognized bed field %s", type);
     }
 fprintf(f, "\n");
 }
 
 struct bedFilter *bedFilterForCustomTrack(char *ctName)
 /* If the user specified constraints, then translate them to a bedFilter. */
 {
 struct hashEl *var, *varList = cartFindPrefix(cart, hgtaFilterVarPrefix);
 int prefixSize = strlen(hgtaFilterVarPrefix);
 struct bedFilter *bf = NULL;
 int *trash;
 
 for (var = varList; var != NULL; var = var->next)
     {
     char *dbTrackFieldType = cloneString(var->name + prefixSize);
     char *parts[4];
     int partCount;
     partCount = chopByChar(dbTrackFieldType, '.', parts, ArraySize(parts));
     if (partCount == 4 && sameString(parts[1], ctName))
 	{
 	char *db = parts[0];
 	char *table = parts[1];
 	char *field = parts[2];
 	char *type = parts[3];
 	if (sameString(type, filterPatternVar))
 	    {
 	    char *pat = cloneString(var->val);
 	    char *varName, *dd, *cmp;
 	    if (bf == NULL)
 	        AllocVar(bf);
 	    varName = filterFieldVarName(db, table, field, filterDdVar);
 	    dd = cartOptionalString(cart, varName);
 	    varName = filterFieldVarName(db, table, field, filterCmpVar);
 	    cmp = cartOptionalString(cart, varName);
 	    if (sameString("chrom", field))
 		cgiToStringFilter(dd, pat, &(bf->chromFilter), &(bf->chromVals),
 				  &(bf->chromInvert));
 	    else if (sameString("chromStart", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->chromStartFilter), &(bf->chromStartVals));
 	    else if (sameString("chromEnd", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->chromEndFilter), &(bf->chromEndVals));
 	    else if (sameString("name", field))
 		cgiToStringFilter(dd, pat, &(bf->nameFilter), &(bf->nameVals),
 				  &(bf->nameInvert));
 	    else if (sameString("score", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->scoreFilter), &(bf->scoreVals));
 	    else if (sameString("strand", field))
 		cgiToCharFilter(dd, pat, &(bf->strandFilter), &(bf->strandVals),
 				&(bf->strandInvert));
 	    else if (sameString("thickStart", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->thickStartFilter), &(bf->thickStartVals));
 	    else if (sameString("thickEnd", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->thickEndFilter), &(bf->thickEndVals));
 	    else if (sameString("blockCount", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->blockCountFilter), &(bf->blockCountVals));
 	    else if (sameString("chromLength", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->chromLengthFilter), &(bf->chromLengthVals));
 	    else if (sameString("thickLength", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->thickLengthFilter), &(bf->thickLengthVals));
 	    else if (sameString("compareStarts", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->compareStartsFilter), &trash);
 	    else if (sameString("compareEnds", field))
 		cgiToIntFilter(cmp, pat,
 			       &(bf->compareEndsFilter), &trash);
 	    freez(&pat);
 	    }
 	}
     }
 
 hashElFreeList(&varList);
 return bf;
 }
 
 static void customTrackFilteredBedOnRegion(
 	struct region *region,	/* Region to get data from. */
 	struct customTrack *ct, /* Custom track. */
 	struct hash *idHash,	/* Hash of identifiers or NULL */
 	struct bedFilter *bf,	/* Filter or NULL */
 	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 region. */
 {
 struct bed *bed;
 
 if (ct->dbTrack)
     {
     int fieldCount = ct->fieldCount;
     char query[512];
     int rowOffset;
     char **row;
     struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
     struct sqlResult *sr = NULL;
 
     safef(query, sizeof(query), "select * from %s", ct->dbTableName);
     sr = hRangeQuery(conn, ct->dbTableName, region->chrom,
 	region->start, region->end, NULL, &rowOffset);
 
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	bed = bedLoadN(row+rowOffset, fieldCount);
 	if ((idHash == NULL || hashLookup(idHash, bed->name)) &&
 	    (bf == NULL || bedFilterOne(bf, bed)))
 	    {
 	    struct bed *copy = lmCloneBed(bed, lm);
 	    slAddHead(pBedList, copy);
 	    }
 	}
     sqlFreeResult(&sr);
     hFreeConn(&conn);
     }
 else
     {
     for (bed = ct->bedList; bed != NULL; bed = bed->next)
 	{
 	if (idHash == NULL || hashLookup(idHash, bed->name))
 	    {
 	    if (sameString(bed->chrom, region->chrom))
 		{
 		if (bed->chromStart < region->end && bed->chromEnd > region->start)
 		    {
 		    if (bf == NULL || bedFilterOne(bf, bed))
 			{
 			struct bed *copy = lmCloneBed(bed, lm);
 			slAddHead(pBedList, copy);
 			}
 		    }
 		}
 	    }
 	}
     }
 }
 
 struct bed *customTrackGetFilteredBeds(char *name, struct region *regionList,
 	struct lm *lm, int *retFieldCount)
 /* Get list of beds from custom track of given name that are
  * in current regions and that pass filters.  You can bedFree
  * this when done. */
 {
 struct customTrack *ct = ctLookupName(name);
 struct bedFilter *bf = NULL;
 struct bed *bedList = NULL;
 struct hash *idHash = NULL;
 struct region *region;
 int fieldCount;
 
 if (ct == NULL)
     errAbort("Can't find custom track %s", name);
 
 if (ct->wiggle)
     {
     struct bed *wigBedList = NULL, *bed;
 
     /* Grab filtered beds for each region. */
     for (region = regionList; region != NULL; region = region->next)
 	{
 	wigBedList = getWiggleAsBed(NULL, name, region, NULL, NULL, lm, NULL);
 	for (bed = wigBedList; bed != NULL; bed = bed->next)
 	    {
 	    struct bed *copy = lmCloneBed(bed, lm);
 	    slAddHead(&bedList, copy);
 	    }
 	/*bedFree(&wigBedList); do not free local memory*/
 	}
     fieldCount = 4;
     }
 else
     {
     /* Figure out how to filter things. */
     fieldCount = ct->fieldCount;
     bf = bedFilterForCustomTrack(name);
     if (ct->fieldCount > 3)
 	idHash = identifierHash(database, name);
 
     /* Grab filtered beds for each region. */
     for (region = regionList; region != NULL; region = region->next)
 	customTrackFilteredBedOnRegion(region, ct, idHash, bf, lm, &bedList);
 
     /* clean up. */
     hashFree(&idHash);
     slReverse(&bedList);
     }
 if (retFieldCount != NULL)
     *retFieldCount = fieldCount;
 return bedList;
 }
 
 void doTabOutCustomTracks(struct trackDb *track, struct sqlConnection *conn,
 	char *fields, FILE *f)
 /* Print out selected fields from custom track.  If fields
  * is NULL, then print out all fields. */
 {
 struct region *regionList = getRegions(), *region;
 struct slName *chosenFields, *field;
 int count = 0;
 if (fields == NULL)
     {
     struct customTrack *ct = ctLookupName(track->tableName);
     chosenFields = getBedFields(ct->fieldCount);
     }
 else
     chosenFields = commaSepToSlNames(fields);
 
 if (f == NULL)
     f = stdout;
 fprintf(f, "#");
 for (field = chosenFields; field != NULL; field = field->next)
     {
     if (field != chosenFields)
 	fprintf(f, "\t");
     fprintf(f, "%s", field->name);
     }
 fprintf(f, "\n");
 
 for (region = regionList; region != NULL; region = region->next)
     {
     struct lm *lm = lmInit(64*1024);
     struct bed *bed, *bedList = cookedBedList(conn, track->tableName,
     	region, lm, NULL);
     for (bed = bedList; bed != NULL; bed = bed->next)
 	{
 	tabBedRowFile(bed, chosenFields, f);
+	++count;
 	}
     lmCleanup(&lm);
     }
 if (count == 0)
     explainWhyNoResults(f);
 }
 
 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))
         {
 	slAddHead(&newList, ct);
 	}
     }
 slReverse(&newList);
 *pList = newList;
 }
 
 
 void doRemoveCustomTrack(struct sqlConnection *conn)
 /* Remove custom track file. */
 {
 getCustomTracks();
 if (theCtList)
     removeNamedCustom(&theCtList, curTable);
 customTracksSaveCart(database, cart, theCtList);
 initGroupsTracksTables(conn);
 doMainPage(conn);
 }