");
printf(" ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN\n");
printf("---------------------------------------------------------------------------------------------------\n");
for (psl = pslList; psl != NULL; psl = psl->next)
{
+ if (customText)
+ printf("",
+ browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database,
+ customText, uiState, unhideTrack);
+ else
printf("",
browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database,
pslName, faName, uiState, unhideTrack);
printf("browser ");
printf("",
hgcUrl, psl->tStart, pslName, cgiEncode(faName), psl->qName, psl->tName,
psl->tStart, psl->tEnd, database, uiState);
printf("details ");
printf("%-14s %5d %5d %5d %5d %5.1f%% %4s %2s %9d %9d %6d\n",
psl->qName, pslScore(psl), psl->qStart+1, psl->qEnd, psl->qSize,
100.0 - pslCalcMilliBad(psl, TRUE) * 0.1,
skipChr(psl->tName), psl->strand, psl->tStart+1, psl->tEnd,
psl->tEnd - psl->tStart);
}
printf("\n");
@@ -479,33 +500,63 @@
int i, size = seq->size, count = 0;
char *s = seq->dna;
for (i=0; i
next)
subChar(seq->dna, 'u', 't');
}
-void blatSeq(char *userSeq, char *organism)
+static char *getUnusedName(char *database, struct cart *cart)
+// Find a track name that isn't currently a custom track.
+{
+struct slName *browserLines = NULL;
+struct customTrack *ctList = customTracksParseCart(database, cart, &browserLines, NULL);
+struct customTrack *ct;
+int count = 0;
+char buffer[4096];
+
+for(;;count++)
+ {
+ for (ct=ctList;
+ ct != NULL;
+ ct=ct->next)
+ {
+ safef(buffer, sizeof buffer, "ct_BlatResults%d", count);
+ if (startsWith(buffer, ct->tdb->track))
+ // Found a track with this name.
+ break;
+ }
+
+ if (ct == NULL)
+ break;
+ }
+safef(buffer, sizeof buffer, "Blat Results (%d)", count);
+
+return cloneString(buffer);
+}
+
+void blatSeq(char *userSeq, char *organism, char *database)
/* Blat sequence user pasted in. */
{
+boolean useBigPsl = cfgOptionBooleanDefault("useBlatBigPsl", FALSE);
FILE *f;
struct dnaSeq *seqList = NULL, *seq;
struct tempName pslTn, faTn;
int maxSingleSize, maxTotalSize, maxSeqCount;
int minSingleSize = minMatchShown;
char *genome, *db;
char *type = cgiString("type");
char *seqLetters = cloneString(userSeq);
struct serverTable *serve;
int conn;
int oneSize, totalSize = 0, seqCount = 0;
boolean isTx = FALSE;
boolean isTxTx = FALSE;
boolean txTxBoth = FALSE;
struct gfOutput *gvo;
@@ -680,32 +731,65 @@
else
{
gfAlignTrans(&conn, serve->nibDir, seq, 5, tFileCache, gvo);
}
}
else
{
gfAlignStrand(&conn, serve->nibDir, seq, FALSE, minMatchShown, tFileCache, gvo);
reverseComplement(seq->dna, seq->size);
conn = gfConnect(serve->host, serve->port);
gfAlignStrand(&conn, serve->nibDir, seq, TRUE, minMatchShown, tFileCache, gvo);
}
gfOutputQuery(gvo, f);
}
carefulClose(&f);
-showAliPlaces(pslTn.forCgi, faTn.forCgi, serve->db, qType, tType,
+
+if (useBigPsl)
+ {
+ // make bigPsl
+ struct tempName bigBedTn;
+ trashDirFile(&bigBedTn, "bigPsl", "bp", ".bb");
+ makeBigPsl(pslTn.forCgi, faTn.forCgi, serve->db, bigBedTn.forCgi);
+ struct tempName customTextTn;
+ trashDirFile(&customTextTn, "bigPsl", "ct", ".txt");
+ FILE *fp = fopen(customTextTn.forCgi, "w");
+ char* host = getenv("HTTP_HOST");
+ char* reqUrl = getenv("REQUEST_URI");
+ // remove everything after / in URL
+ char *e = strrchr(reqUrl, '/');
+ if (e) *e = 0;
+
+ char *trackName = getUnusedName(database, cart);
+ char *customTextTemplate = "track type=bigPsl visibility=pack showAll=on htmlUrl=http://%s/goldenPath/help/hgUserPsl.html %s bigDataUrl=http://%s/%s/%s name=\"%s\"\n";
+ char *extraForMismatch = "showDiffBasesAllScales=. baseColorUseSequence=lfExtra baseColorDefault=diffBases";
+
+ if (qIsProt)
+ extraForMismatch = "";
+ fprintf(fp, customTextTemplate, host, extraForMismatch, host, reqUrl, bigBedTn.forCgi, trackName);
+ fclose(fp);
+
+ char buffer[4096];
+ safef(buffer, sizeof buffer, "http://%s/%s/%s", host, reqUrl, customTextTn.forCgi);
+ showAliPlaces(pslTn.forCgi, faTn.forCgi, buffer, serve->db, qType, tType,
+ organism, feelingLucky);
+ }
+else
+ {
+ showAliPlaces(pslTn.forCgi, faTn.forCgi, NULL, serve->db, qType, tType,
organism, feelingLucky);
+ }
if(!feelingLucky)
cartWebEnd();
gfFileCacheFree(&tFileCache);
}
void askForSeq(char *organism, char *db)
/* Put up a little form that asks for sequence.
* Call self.... */
{
/* ignore struct serverTable* return, but can error out if not found */
findServer(db, FALSE);
/* JavaScript to update form when org changes */
char *onChangeText = "onchange=\""
"document.mainForm.changeInfo.value='orgChange';"
@@ -854,31 +938,31 @@
{
userSeq = cartOptionalString(cart, "seqFile");
}
if (isEmpty(userSeq) || orgChange)
{
cartWebStart(theCart, db, "%s BLAT Search", trackHubSkipHubName(organism));
if (differentString(oldDb, db))
printf("
Note: BLAT search is not available for %s %s; "
"defaulting to %s %s
\n",
hGenome(oldDb), hFreezeDate(oldDb), organism, hFreezeDate(db));
askForSeq(organism,db);
cartWebEnd();
}
else
{
- blatSeq(skipLeadingSpaces(userSeq), organism);
+ blatSeq(skipLeadingSpaces(userSeq), organism, db);
}
}
/* Null terminated list of CGI Variables we don't want to save
* permanently. */
char *excludeVars[] = {"Submit", "submit", "Clear", "Lucky", "type", "userSeq", "seqFile", "showPage", "changeInfo", NULL};
int main(int argc, char *argv[])
/* Process command line. */
{
long enteredMainTime = clock1000();
oldVars = hashNew(10);
cgiSpoof(&argc, argv);
setUdcCacheDir();