src/hg/hgTables/custom.c 1.38
1.38 2009/03/17 17:24:51 kent
Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface.
Index: src/hg/hgTables/custom.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTables/custom.c,v
retrieving revision 1.37
retrieving revision 1.38
diff -b -B -U 1000000 -r1.37 -r1.38
--- src/hg/hgTables/custom.c 3 Sep 2008 19:18:58 -0000 1.37
+++ src/hg/hgTables/custom.c 17 Mar 2009 17:24:51 -0000 1.38
@@ -1,737 +1,723 @@
/* 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);
}
void flushCustomTracks()
/* Flush custom track list. */
{
theCtList = NULL;
}
struct customTrack *lookupCt(char *name)
/* Find named custom track. */
{
struct customTrack *ctList = getCustomTracks();
struct customTrack *ct;
for (ct=ctList; ct != NULL; ct=ct->next)
{
if (sameString(ct->tdb->tableName, name))
return ct;
}
return 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");
}
static void cgiToCharFilter(char *dd, char *pat, enum charFilterType *retCft,
char **retVals, boolean *retInv)
/* Given a "does/doesn't" and a (list of) literal chars from CGI, fill in
* retCft, retVals and retInv to make a filter. */
{
char *vals, *ptrs[32];
int numWords;
int i;
assert(retCft != NULL);
assert(retVals != NULL);
assert(retInv != NULL);
assert(sameString(dd, "does") || sameString(dd, "doesn't"));
/* catch null-constraint cases. ? will be treated as a literal match,
* which would make sense for bed strand and maybe other single-char things: */
if (pat == NULL)
pat = "";
pat = trimSpaces(pat);
if ((pat[0] == 0) || sameString(pat, "*"))
{
*retCft = cftIgnore;
return;
}
*retCft = cftMultiLiteral;
numWords = chopByWhite(pat, ptrs, ArraySize(ptrs));
vals = needMem((numWords+1) * sizeof(char));
for (i=0; i < numWords; i++)
vals[i] = ptrs[i][0];
vals[i] = 0;
*retVals = vals;
*retInv = sameString("doesn't", dd);
}
static void cgiToStringFilter(char *dd, char *pat, enum stringFilterType *retSft,
char ***retVals, boolean *retInv)
/* Given a "does/doesn't" and a (list of) regexps from CGI, fill in
* retCft, retVals and retInv to make a filter. */
{
char **vals, *ptrs[32];
int numWords;
int i;
assert(retSft != NULL);
assert(retVals != NULL);
assert(retInv != NULL);
assert(sameString(dd, "does") || sameString(dd, "doesn't"));
/* catch null-constraint cases: */
if (pat == NULL)
pat = "";
pat = trimSpaces(pat);
if ((pat[0] == 0) || sameString(pat, "*"))
{
*retSft = sftIgnore;
return;
}
*retSft = sftMultiRegexp;
numWords = chopByWhite(pat, ptrs, ArraySize(ptrs));
vals = needMem((numWords+1) * sizeof(char *));
for (i=0; i < numWords; i++)
vals[i] = cloneString(ptrs[i]);
vals[i] = NULL;
*retVals = vals;
*retInv = sameString("doesn't", dd);
}
static void cgiToIntFilter(char *cmp, char *pat, enum numericFilterType *retNft,
int **retVals)
/* Given a comparison operator and a (pair of) integers from CGI, fill in
* retNft and retVals to make a filter. */
{
char *ptrs[3];
int *vals;
int numWords;
assert(retNft != NULL);
assert(retVals != NULL);
/* catch null-constraint cases: */
if (pat == NULL)
pat = "";
pat = trimSpaces(pat);
if ((pat[0] == 0) || sameString(pat, "*") || sameString(cmp, "ignored"))
{
*retNft = nftIgnore;
return;
}
else if (sameString(cmp, "in range"))
{
*retNft = nftInRange;
numWords = chopString(pat, " \t,", ptrs, ArraySize(ptrs));
if (numWords != 2)
errAbort("For \"in range\" constraint, you must give two numbers separated by whitespace or comma.");
vals = needMem(2 * sizeof(int));
vals[0] = atoi(ptrs[0]);
vals[1] = atoi(ptrs[1]);
if (vals[0] > vals[1])
{
int tmp = vals[0];
vals[0] = vals[1];
vals[1] = tmp;
}
*retVals = vals;
}
else
{
if (sameString(cmp, "<"))
*retNft = nftLessThan;
else if (sameString(cmp, "<="))
*retNft = nftLTE;
else if (sameString(cmp, "="))
*retNft = nftEqual;
else if (sameString(cmp, "!="))
*retNft = nftNotEqual;
else if (sameString(cmp, ">="))
*retNft = nftGTE;
else if (sameString(cmp, ">"))
*retNft = nftGreaterThan;
else
errAbort("Unrecognized comparison operator %s", cmp);
vals = needMem(sizeof(int));
vals[0] = atoi(pat);
*retVals = vals;
}
}
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 = lookupCt(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 = lookupCt(track->tableName);
chosenFields = getBedFields(ct->fieldCount);
}
else
chosenFields = commaSepToSlNames(fields);
if (f == NULL)
- {
- hPrintf("#");
- for (field = chosenFields; field != NULL; field = field->next)
- {
- if (field != chosenFields)
- hPrintf("\t");
- hPrintf("%s", field->name);
- }
- hPrintf("\n");
- }
-else
- {
- fprintf(f, "#");
- for (field = chosenFields; field != NULL; field = field->next)
+ 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");
- }
+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)
{
- if (f == NULL)
- tabBedRow(bed, chosenFields);
- else
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);
}