Sorry, no matches found |
");
if (!sameString(output, "psl no header"))
pslxWriteHead(stdout, qType, tType);
for (psl = pslList; psl != NULL; psl = psl->next)
pslTabOut(psl, stdout);
printf("");
}
else
{
printf("Go back to %s on the Genome Browser.
\n", browserUrl, posStr); + if (useBigPsl) + { + char *trackName = NULL; + char *trackDescription = NULL; + getCustomName(database, cart, pslList, &trackName, &trackDescription); + psl = pslList; + printf("", + hgcUrl, psl->tStart, psl->tEnd,cgiEncode(trackName), cgiEncode(trackDescription), pslName, cgiEncode(faName), psl->qName, psl->tName, + psl->tStart, psl->tEnd, database, uiState); + + //printf( + //"", trackDescription); + //printf("Description: %s\n", trackDescription); + //printf("\n"); + //printf(""); + } + printf("");
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("",
@@ -605,68 +538,33 @@
else if (count == 2)
{
safef(shortName, sizeof shortName, "blat %s+%d", names->name, count - 1);
safef(description, sizeof description, "blat on %d queries (%s, %s)", count, names->name, names->next->name);
}
else
{
safef(shortName, sizeof shortName, "blat %s+%d", names->name, count - 1);
safef(description, sizeof description, "blat on %d queries (%s, %s, ...)", count, names->name, names->next->name);
}
*pName = makeNameUnique(shortName, database, cart);
*pDescription = cloneString(description);
}
-static char *outBigPsl(char *db, struct psl *pslList, char *pslFilename, char *faFilename, boolean isProt)
-// Make a bigPsl from a list of psls and return its name.
-{
-struct tempName bigBedTn;
-trashDirDateFile(&bigBedTn, "hgBlat", "bp", ".bb");
-char *bigBedFile = bigBedTn.forCgi;
-makeBigPsl(pslFilename, faFilename, db, bigBedFile);
-char *customTextFile = replaceSuffix(bigBedFile, "txt");
-FILE *fp = fopen(customTextFile, "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 = NULL;
-char *trackDescription = NULL;
-
-getCustomName(db, cart, pslList, &trackName, &trackDescription);
-char *customTextTemplate = "track type=bigPsl indelDoubleInsert=on indelQueryInsert=on pslFile=%s visibility=pack showAll=on htmlUrl=http://%s/goldenPath/help/hgUserPsl.html %s bigDataUrl=http://%s%s/%s name=\"%s\" description=\"%s\"\n";
-char *extraForMismatch = "showDiffBasesAllScales=. baseColorUseSequence=lfExtra baseColorDefault=diffBases";
-
-if (isProt)
- extraForMismatch = "";
-fprintf(fp, customTextTemplate, bigBedTn.forCgi, host, extraForMismatch, host, reqUrl, bigBedTn.forCgi, trackName, trackDescription);
-fclose(fp);
-
-char buffer[4096];
-safef(buffer, sizeof buffer, "http://%s%s/%s", host, reqUrl, customTextFile);
-
-return cloneString(buffer);
-}
-
void blatSeq(char *userSeq, char *organism, char *database)
/* Blat sequence user pasted in. */
{
-boolean doHyper = sameString(cartUsualString(cart, "output", outputList[0]), "hyperlink");;
-boolean useBigPsl = cfgOptionBooleanDefault("useBlatBigPsl", FALSE) && doHyper;
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;
@@ -842,48 +740,32 @@
{
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);
-if (useBigPsl)
- {
- struct psl *pslList = pslLoadAll(pslTn.forCgi);
-
- if (pslList != NULL)
- {
- char *customTrack = outBigPsl(database, pslList, pslTn.forCgi, faTn.forCgi, qIsProt);
- showAliPlaces(pslTn.forCgi, faTn.forCgi, customTrack, serve->db, qType, tType,
- organism, feelingLucky);
- }
- else
- puts("Sorry, no matches found |