src/hg/hgTables/seqOut.c 1.20

Index: src/hg/hgTables/seqOut.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTables/seqOut.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -b -B -U 1000000 -r1.19 -r1.20
--- src/hg/hgTables/seqOut.c	3 Sep 2008 19:18:59 -0000	1.19
+++ src/hg/hgTables/seqOut.c	17 Mar 2009 04:28:39 -0000	1.20
@@ -1,289 +1,289 @@
 /* seqOut - Output sequence. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "htmshell.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "web.h"
 #include "hui.h"
 #include "hdb.h"
 #include "trackDb.h"
 #include "customTrack.h"
 #include "hgSeq.h"
 #include "hgTables.h"
 
 static char const rcsid[] = "$Id$";
 
 static char *genePredMenu[] = 
     {
     "genomic",
     "protein",
     "mRNA",
     };
 
 static void genePredTypeButton(char *val, char *selVal)
 /* Make region radio button including a little Javascript
  * to save selection state. */
 {
 cgiMakeRadioButton(hgtaGeneSeqType, val, sameString(val, selVal));
 }
 
 static boolean isRefGeneTrack(char *table)
 /* Return TRUE if it's a refGene track. */
 {
 return sameString("refGene", table) || sameString("xenoRefGene", table);
 }
 
 static void genePredOptions(struct trackDb *track, char *type, 
 	struct sqlConnection *conn)
 /* Put up sequence type options for gene prediction tracks. */
 {
 char *predType = cartUsualString(cart, hgtaGeneSeqType, genePredMenu[0]);
 char *dupType = cloneString(type);
 char *typeWords[3];
 int typeWordCount, typeIx;
 
 /* Type field has 1-3 words which are in order:
  *     genePred pepTable mrnaTable */
 typeWordCount = chopLine(dupType, typeWords);
 /* TypeIx will be 0 (genomic) 1 (protein) 2(mrna). */
 typeIx = stringArrayIx(predType, genePredMenu, typeWordCount);
 if (typeIx < 0)
     predType = genePredMenu[0];
 htmlOpen("Select sequence type for %s", track->shortLabel);
 hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
 cartSaveSession(cart);
 
 if (isRefGeneTrack(track->tableName))
     {
     /* RefGene covers all 3 types, but in it's own way. */
     for (typeIx = 0; typeIx < 3; ++typeIx)
 	{
 	genePredTypeButton(genePredMenu[typeIx], predType);
 	hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
 	}
     }
 else
     {
     /* Otherwise we always have genomic, and we have
      * peptide/mrna only if there are corresponding table
      * in the type field. */
     for (typeIx = 0; typeIx < typeWordCount; ++typeIx)
 	{
 	if (typeIx == 0 || sqlTableExists(conn, typeWords[typeIx]))
 	    {
 	    genePredTypeButton(genePredMenu[typeIx], predType);
 	    hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
 	    }
 	}
     }
 cgiMakeButton(hgtaDoGenePredSequence, "submit");
 hPrintf(" ");
 cgiMakeButton(hgtaDoMainPage, "cancel");
 hPrintf("</FORM>\n");
 htmlClose();
 freez(&dupType);
 }
 
 
 void doRefGeneProteinSequence(struct sqlConnection *conn, struct bed *bedList)
 /* Fetch refGene proteins corresponding to names in bedList. */
 {
 struct hash *uniqHash = newHash(18);
 struct hash *protHash = newHash(18);
 struct sqlResult *sr;
 char **row;
 struct bed *bed;
 
 
 /* Get translation from mRNA to protein from refLink table. */
 sr = sqlGetResult(conn, "select mrnaAcc,protAcc from refLink");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *protAcc = row[1];
     if (protAcc != NULL && protAcc[0] != 0)
         hashAdd(protHash, row[0], lmCloneString(protHash->lm, protAcc));
     }
 sqlFreeResult(&sr);
 
 for (bed = bedList; bed != NULL; bed = bed->next)
     {
     char *protAcc = hashFindVal(protHash, bed->name);
     if (protAcc != NULL && !hashLookup(uniqHash, protAcc))
         {
 	char *fa = hGetSeqAndId(conn, protAcc, NULL);
 	hashAdd(uniqHash, protAcc, NULL);
 	if (fa != NULL)
 	    hPrintf("%s", fa);
 	freez(&fa);
 	}
     }
 hashFree(&protHash);
 hashFree(&uniqHash);
 }
 
 void doRefGeneMrnaSequence(struct sqlConnection *conn, struct bed *bedList)
 /* Fetch refGene mRNA sequence. */
 {
 struct hash *uniqHash = newHash(18);
 struct bed *bed;
 for (bed = bedList; bed != NULL; bed = bed->next)
     {
     if (!hashLookup(uniqHash, bed->name))
         {
 	char *fa = hGetSeqAndId(conn, bed->name, NULL);
 	hashAdd(uniqHash, bed->name, NULL);
 	if (fa != NULL)
 	    hPrintf("%s", fa);
 	freez(&fa);
 	}
     }
 hashFree(&uniqHash);
 }
 
 void doGenePredNongenomic(struct sqlConnection *conn, int typeIx)
 /* Get mrna or protein associated with selected genes. */
 {
 /* Note this does do the whole genome at once rather than one
  * chromosome at a time, but that's ok because the gene prediction
  * tracks this serves are on the small side. */
 char *typeWords[3];
 char *table;
 struct lm *lm = lmInit(64*1024);
 int fieldCount;
 struct bed *bed, *bedList = cookedBedsOnRegions(conn, curTable, getRegions(),
 	lm, &fieldCount);
 int typeWordCount;
 
 textOpen();
 
 /* Figure out which table to use. */
 if (isRefGeneTrack(curTable))
     {
     if (typeIx == 1) /* Protein */
         doRefGeneProteinSequence(conn, bedList);
     else
         doRefGeneMrnaSequence(conn, bedList);
     }
 else
     {
     char *dupType = cloneString(curTrack->type);
     typeWordCount = chopLine(dupType, typeWords);
     if (typeIx >= typeWordCount)
 	internalErr();
     table = typeWords[typeIx];
     if (sqlTableExists(conn, table))
 	{
 	struct sqlResult *sr;
 	char **row;
 	char query[256];
 	struct hash *hash = newHash(18);
 
 	/* Make hash of all id's passing filters. */
 	for (bed = bedList; bed != NULL; bed = bed->next)
 	    hashAdd(hash, bed->name, NULL);
 
 	/* Scan through table, outputting ones that match. */
 	safef(query, sizeof(query), "select name, seq from %s", table);
 	sr = sqlGetResult(conn, query);
 	while ((row = sqlNextRow(sr)) != NULL)
 	    {
 	    if (hashLookup(hash, row[0]))
 		{
 		hPrintf(">%s\n", row[0]);
 		writeSeqWithBreaks(stdout, row[1], strlen(row[1]), 60);
 		}
 	    }
 	sqlFreeResult(&sr);
 	hashFree(&hash);
 	}
     else
 	{
 	internalErr();
 	}
     freez(&dupType);
     }
 lmCleanup(&lm);
 }
 
 
 void genomicFormatPage(struct sqlConnection *conn)
 /* Put up page asking for what sort of genomic sequence. */
 {
-struct hTableInfo *hti = getHti(database, curTable);
+struct hTableInfo *hti = getHti(database, curTable, conn);
 htmlOpen("%s Genomic Sequence", curTableLabel());
 if (doGalaxy())
     startGalaxyForm();
 else
     hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
 cartSaveSession(cart);
 hgSeqOptionsHtiCart(hti, cart);
 hPrintf("<BR>\n");
 if (doGalaxy())
     {
     /* pass parameter to get sequence to Galaxy */
     cgiMakeHiddenVar(hgtaDoGenomicDna, "get sequence");
     printGalaxySubmitButtons();
     }
 else
     {
     cgiMakeButton(hgtaDoGenomicDna, "get sequence");
     hPrintf(" ");
     cgiMakeButton(hgtaDoMainPage, "cancel");
     hPrintf("</FORM>");
     }
 htmlClose();
 }
 
 void doGenomicDna(struct sqlConnection *conn)
 /* Get genomic sequence (UI has already told us how). */
 {
 struct region *region, *regionList = getRegions();
-struct hTableInfo *hti = getHti(database, curTable);
+struct hTableInfo *hti = getHti(database, curTable, conn);
 int fieldCount;
 textOpen();
 for (region = regionList; region != NULL; region = region->next)
     {
     struct lm *lm = lmInit(64*1024);
     struct bed *bedList = cookedBedList(conn, curTable, region, lm, &fieldCount);
     hgSeqBed(database, hti, bedList);
     lmCleanup(&lm);
     }
 }
 
 void doGenePredSequence(struct sqlConnection *conn)
 /* Output genePred sequence. */
 {
 char *type = cartString(cart, hgtaGeneSeqType);
 
 if (sameWord(type, "protein"))
     {
     if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
         sendParamsToGalaxy(hgtaDoGenePredSequence, "submit");
     else
         doGenePredNongenomic(conn, 1);
     }
 else if (sameWord(type, "mRNA"))
     {
     if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery))
         sendParamsToGalaxy(hgtaDoGenePredSequence, "submit");
     else
         doGenePredNongenomic(conn, 2);
     }
 else
     genomicFormatPage(conn);
 }
 
 void doOutSequence(struct sqlConnection *conn)
 /* Output sequence page. */
 {
 if (curTrack != NULL && sameString(curTrack->tableName, curTable) 
 	&& startsWith("genePred", curTrack->type))
     genePredOptions(curTrack, curTrack->type, conn);
 else
     genomicFormatPage(conn);
 }