9723799cf6f1a8fb714ae1493b224b8e91aebf09
tdreszer
  Mon Jul 30 12:17:38 2012 -0700
Making final pass through tree of checkins as dictated by Jim. None of these changes should affect executables in any way. This pass is due to expanding fingerprint caused by kompare.
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 17581b4..9a27b7f 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -2643,32 +2643,31 @@
     char *autoTranslate = trackDbSetting(tdb, "autoTranslate");
     if (autoTranslate == NULL || differentString(autoTranslate, "0"))
         {
         puts("<LI>\n");
         /* put out correct message to describe translated mRNA */
         if ( sameString(geneTable, "ensGene")
         ||   sameString(geneTable, "vegaGene")
         ||   sameString(geneTable, "vegaPseudoGene")
         ||   genbankIsRefSeqNonCodingMRnaAcc(geneName)
         ||   sameString(geneTable, "lincRNAsTranscripts") )
             {
             printf("Non-protein coding gene or gene fragment, no protein prediction available.");
             }
         else
             {
-            hgcAnchorSomewhere("htcTranslatedPredMRna", geneName,
-                "translate", seqName);
+            hgcAnchorSomewhere("htcTranslatedPredMRna", geneName, "translate", seqName);
             printf("Translated Protein</A> from ");
             if (sameString(geneTable, "refGene") )
                 {
 		printf("genomic DNA\n");
                 }
 	    else
 		{
                 printf("predicted mRNA \n");
 		}
 	    foundPep = TRUE;
 	    }
 	puts("</LI>\n");
 	}
     }
 
@@ -8596,32 +8595,31 @@
     {
     warn("Organism %s not found!", organism); fflush(stdout);
     return;
     }
 
 /* print URL that links to Ensembl or Vega transcript details */
 if (isEnsembl)
     {
     if (archive != NULL)
        safef(dbUrl, sizeof(dbUrl), "http://%s.archive.ensembl.org/%s",
             archive, genomeStrEnsembl);
     else
         safef(dbUrl, sizeof(dbUrl), "http://www.ensembl.org/%s", genomeStrEnsembl);
     }
 else if (isVega)
-    safef(dbUrl, sizeof(dbUrl), "http://vega.sanger.ac.uk/%s",
-         genomeStrEnsembl);
+    safef(dbUrl, sizeof(dbUrl), "http://vega.sanger.ac.uk/%s", genomeStrEnsembl);
 
 boolean nonCoding = FALSE;
 char query[512];
 safef(query, sizeof(query), "name = \"%s\"", itemName);
 struct genePred *gpList = genePredReaderLoadQuery(conn, tdb->table, query);
 if (gpList && (gpList->cdsStart == gpList->cdsEnd))
     nonCoding = TRUE;
 genePredFreeList(&gpList);
 /* get gene and protein IDs */
 if ((isEnsembl && hasEnsGtp) || (isVega && hasVegaGtp))
     {
     /* shortItemName removes version number but sometimes the ensGtp */
     /* table has a transcript with version number so exact match not used */
     safef(cond_str, sizeof(cond_str), "transcript like '%s%%'", shortItemName);
     geneID=sqlGetField(database, gtpTable,"gene",cond_str);
@@ -11616,32 +11614,32 @@
         safef(chainTable_chrom,sizeof(chainTable_chrom), "%s_chainSelf",\
                 pg->chrom);
         if (hTableExists(database, chainTable_chrom) )
             {
                 /* lookup chain */
             dyStringPrintf(dy,
                            "select id, score, qStart, qEnd, qStrand, qSize from %s_%s where ",
                 pg->chrom, chainTable);
             hAddBinToQuery(pg->chromStart, pg->chromEnd, dy);
             if (sameString(pg->gStrand,pg->strand))
                 dyStringPrintf(dy,
                     "tEnd > %d and tStart < %d and qName = '%s' and qEnd > %d and qStart < %d and qStrand = '+' ",
                     pg->chromStart, pg->chromEnd, pg->gChrom, pg->gStart, pg->gEnd);
             else
                 {
-                dyStringPrintf(dy,
-                    "tEnd > %d and tStart < %d and qName = '%s' and qEnd > %d and qStart < %d and qStrand = '-'",
+                dyStringPrintf(dy,"tEnd > %d and tStart < %d and qName = '%s' and qEnd > %d "
+                                  "and qStart < %d and qStrand = '-'",
                     pg->chromStart, pg->chromEnd, pg->gChrom,
                     hChromSize(database, pg->gChrom)-(pg->gEnd),
                     hChromSize(database, pg->gChrom)-(pg->gStart));
                 }
             dyStringAppend(dy, " order by qStart");
             sr = sqlGetResult(conn, dy->string);
             while ((row = sqlNextRow(sr)) != NULL)
                 {
                 int chainId, score;
                 unsigned int qStart, qEnd, qSize;
                 char qStrand;
                 if (first == 0)
                     {
                     printf("<H4>Gene/PseudoGene Alignment (multiple records are a result of breaks in the human Self Chaining)</H4>\n");
                     printf("Shows removed introns, frameshifts and in frame stops.\n");
@@ -14081,31 +14079,32 @@
         if (strcmp(infoRow->rhName, ""))
             {
             printf("<TR><TH>&nbsp</TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH><TH ALIGN=left WIDTH=150>Score</TH?</TR>\n");
             printf("<TR><TH ALIGN=left>&nbsp</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD><TD WIDTH=150>%.2f</TD></TR>\n",
                    infoRow->rhName, infoRow->rhChr, infoRow->rhGeneticPos, infoRow->RHLOD);
             }
         printf("</TABLE><P>\n");
 
         /* Print out alignment information - full sequence */
         webNewSection("Genomic Alignments:");
         sprintf(stsid,"%d",infoRow->identNo);
 	sprintf(stsPrimer, "%d_%s", infoRow->identNo, infoRow->name);
         sprintf(stsClone, "%d_%s_clone", infoRow->identNo, infoRow->name);
 
         /* find sts in primer alignment info */
-        sprintf(query, "SELECT * FROM all_sts_primer WHERE  qName = '%s' AND  tStart = '%d' AND tEnd = '%d'",stsPrimer, start, end);
+        sprintf(query, "SELECT * FROM all_sts_primer WHERE  qName = '%s' AND  tStart = '%d' "
+                "AND tEnd = '%d'",stsPrimer, start, end);
         sr1 = sqlGetResult(conn1, query);
         i = 0;
         pslStart = 0;
         while ((row = sqlNextRow(sr1)) != NULL )
             {
             psl = pslLoad(row);
             fflush(stdout);
             if ((sameString(psl->tName, seqName)) && (abs(psl->tStart - start) < 1000))
 		pslStart = psl->tStart;
 	    slAddHead(&pslList, psl);
 	    i++;
 	  }
 	slReverse(&pslList);
         if (i > 0)
 	  {
@@ -14145,32 +14144,34 @@
 
 	if (stsRow.score == 1000)
 	    printf("<H3>This is the only location found for %s</H3>\n",marker);
         else
 	    {
             sqlFreeResult(&sr);
             printf("<H4>Other locations found for %s in the genome:</H4>\n", marker);
             printf("<TABLE>\n");
             sprintf(query, "SELECT * FROM %s WHERE name = '%s' "
                 "AND (chrom != '%s' OR chromStart != %d OR chromEnd != %d)",
                     table, marker, seqName, start, end);
             sr = sqlGetResult(conn,query);
             while ((row = sqlNextRow(sr)) != NULL)
             {
                 stsMapMouseNewStaticLoad(row, &stsRow);
-                printf("<TR><TD>%s:</TD><TD><A HREF = \"../cgi-bin/hgc?hgsid=%d&o=%u&t=%d&g=stsMapMouseNew&i=%s&c=%s\" target=_blank>%d</A></TD></TR>\n",
-                       stsRow.chrom, hgsid, stsRow.chromStart,stsRow.chromEnd, stsRow.name, stsRow.chrom,(stsRow.chromStart+stsRow.chromEnd)>>1);
+                printf("<TR><TD>%s:</TD><TD><A HREF = \"../cgi-bin/hgc?hgsid=%d&o=%u&t=%d&"
+                       "g=stsMapMouseNew&i=%s&c=%s\" target=_blank>%d</A></TD></TR>\n",
+                       stsRow.chrom, hgsid, stsRow.chromStart,stsRow.chromEnd, stsRow.name,
+                       stsRow.chrom,(stsRow.chromStart+stsRow.chromEnd)>>1);
 		}
 	    printf("</TABLE>\n");
 	    }
     }
 webNewSection("Notes:");
 printTrackHtml(tdb);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 hFreeConn(&conn1);
 }
 
 
 void doStsMapRat(struct trackDb *tdb, char *marker)
 /* Respond to click on an STS marker. */
 {
@@ -17624,32 +17625,32 @@
 struct sqlResult *sr;
 char **row;
 struct sqlConnection *conn = hAllocConn(database);
 int bedSize;
 
 genericHeader(tdb, item);
 bedSize = 8;
 hFindSplitTable(database, seqName, tdb->table, table, &hasBin);
 sprintf(query, "select * from %s where name = '%s'", table, item);
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     {
     ncRna = ncRnaLoad(row);
     printCustomUrl(tdb, item, TRUE);
     printf("<B>Type:</B> %s<BR>", ncRna->type);
-    if (ncRna->extGeneId != NULL)
-    if (!sameWord(ncRna->extGeneId, ""))
+    if (ncRna->extGeneId != NULL
+    &&  !sameWord(ncRna->extGeneId, ""))
         {
         printf("<B>External Gene ID:</B> %s<BR>", ncRna->extGeneId);
         }
     bed = bedLoadN(row+hasBin, bedSize);
     ncRnaPrintPos(bed, bedSize);
     }
 sqlFreeResult(&sr);
 printTrackHtml(tdb);
 }
 
 void doWgRna(struct trackDb *tdb, char *item)
 /* Handle click in wgRna track. */
 {
 struct wgRna *wgRna;
 char table[64];
@@ -21711,31 +21712,32 @@
     printf("</UL><B>Numbers of substitutions in rest of tree:</B>\n<UL>\n");
     printf("<LI>Null distribution: mean = %.2f, var = %.2f, 95%% c.i. = [%d, %d]\n",
            dless->priorMeanSup, dless->priorVarSup, dless->priorMinSup,
            dless->priorMaxSup);
     printf("<LI>Posterior distribution: mean = %.2f, var = %.2f\n</UL>\n",
            dless->postMeanSup, dless->postVarSup);
     if (approx)
         printf("* = Approximate p-value (usually conservative)<BR>\n");
     }
 
 printTrackHtml(tdb);
 hFreeConn(&conn);
 }
 
 void showSomeAlignment2(struct psl *psl, bioSeq *qSeq, enum gfType qType, int qStart,
-                        int qEnd, char *entryName, char *geneName, char *geneTable, int cdsS, int cdsE)
+                        int qEnd, char *entryName, char *geneName, char *geneTable, int cdsS,
+                        int cdsE)
 /* Display protein or DNA alignment in a frame. */
 {
 int blockCount = 0, i = 0, j= 0, *exnStarts = NULL, *exnEnds = NULL;
 struct tempName indexTn, bodyTn;
 FILE *index, *body;
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr = NULL;
 struct genePred *gene = NULL;
 char **row, query[256];
 int tStart = psl->tStart;
 int tEnd = psl->tEnd;
 char tName[256];
 struct dnaSeq *tSeq;
 char *tables[4] = {"luGene", "refGene", "mgcGenes", "luGene2"};
 
@@ -21795,32 +21797,31 @@
 
 freez(&tSeq->name);
 tSeq->name = cloneString(psl->tName);
 safef(tName, sizeof(tName), "%s.%s", organism, psl->tName);
 if (psl->qName == NULL)
     fprintf(body, "<H2>Alignment of %s and %s:%d-%d</H2>\n",
 	    entryName, psl->tName, psl->tStart+1, psl->tEnd);
 else
     fprintf(body, "<H2>Alignment of %s and %s:%d-%d</H2>\n",
 	    entryName, psl->tName, psl->tStart+1, psl->tEnd);
 
 fputs("Click on links in the frame to the left to navigate through "
       "the alignment.\n", body);
 
 safef(tName, sizeof(tName), "%s.%s", organism, psl->tName);
-blockCount = pslGenoShowAlignment(psl, qType == gftProt,
-        entryName, qSeq, qStart, qEnd,
+blockCount = pslGenoShowAlignment(psl, qType == gftProt, entryName, qSeq, qStart, qEnd,
         tName, tSeq, tStart, tEnd, exnStarts, exnEnds, j, body);
 freez(&exnStarts);
 freez(&exnEnds);
 freeDnaSeq(&tSeq);
 
 htmEnd(body);
 fclose(body);
 chmod(bodyTn.forCgi, 0666);
 
 /* Write index. */
 index = mustOpen(indexTn.forCgi, "w");
 if (entryName == NULL)
     entryName = psl->qName;
 htmStartDirDepth(index, entryName, 2);
 fprintf(index, "<H3>Alignment of %s</H3>", entryName);
@@ -24937,32 +24938,32 @@
     doTriangle(tdb, item, "dnaMotif");
     }
 else if (sameWord(table, "esRegGeneToMotif"))
     {
     doTriangle(tdb, item, "esRegMotif");
     }
 else if (sameWord(table, "transRegCode"))
     {
     doTransRegCode(tdb, item, "transRegCodeMotif");
     }
 else if (sameWord(table, "transRegCodeProbe"))
     {
     doTransRegCodeProbe(tdb, item, "transRegCode", "transRegCodeMotif",
         "transRegCodeCondition", "growthCondition");
     }
-else if (sameWord(table, "wgEncodeRegDnaseClustered") ||
-        sameWord(table, "wgEncodeRegDnaseClusteredOn7"))
+else if (sameWord(table, "wgEncodeRegDnaseClustered")
+     ||  sameWord(table, "wgEncodeRegDnaseClusteredOn7"))
     {
     doPeakClusters(tdb, item);
     }
 
 else if( sameWord( table, "humMusL" ) || sameWord( table, "regpotent" ))
     {
     humMusClickHandler( tdb, item, "Mouse", "mm2", "blastzBestMouse", 0);
     }
 else if( sameWord( table, "musHumL" ))
     {
     humMusClickHandler( tdb, item, "Human", "hg12", "blastzBestHuman_08_30" , 0);
     }
 else if( sameWord( table, "mm3Rn2L" ))
     {
     humMusClickHandler( tdb, item, "Rat", "rn2", "blastzBestRat", 0 );