aab4f66a2aca5293f3536cc1d1438b17d2b09dfd tdreszer Thu May 5 16:14:15 2011 -0700 A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01. diff --git src/hg/hgc/lowelab.c src/hg/hgc/lowelab.c index 3756d67..7a822aa 100644 --- src/hg/hgc/lowelab.c +++ src/hg/hgc/lowelab.c @@ -300,33 +300,33 @@ char refSeq[50]; char xraTable[50]; char product[255]; struct blastTab *blastpHits; struct minGeneInfo *ginfo; char *blastpTarget[2]; char **buffer = NULL; boolean findTable = FALSE; unsigned int cdsStart = 0; unsigned int cdsEnd = 0; printf("
\n"); printf("Homologs within genome
\n"); /* Print table */ - printf("", HG_COL_BORDER); + printf("
", HG_COL_BORDER); printf("
\n"); - printf("\n", HG_COL_INSIDE); + printf("
\n", HG_COL_INSIDE); printf("\n"); /* Print table column heading */ printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); blastpHits = blastpHitsList; while (blastpHits != NULL) { parseDelimitedString(blastpHits->target, ':', blastpTarget, 2); if (hTableExists(blastpTarget[0], "lookup")) @@ -545,37 +545,37 @@ { printf("UniProtKB: "); printf("%s
\n", item); } else { printf(" TARGET=_blank>%s
\n", spAcc); } } /* print table of contents */ -printf("
\n"); +printf("
\n"); printf("[Positions and Sequence]   \n"); printf("[COG]   \n"); printf("[Gene Ontology]   \n"); printf("[Protein Domain and Structure Infomation]   \n"); printf("[Gene Homology]   \n"); -printf("[Pathway]
\n"); +printf("[Pathway]
\n"); printf("

\n"); /* Positions and sequence */ printf("
GeneProductBlastP E-value
\n"); printf("\n"); printf("
\n"); printf("Positions and Sequence
\n"); hFindSplitTable(database, seqName, table, tableName, &hasBin); safef(query, sizeof(query), "name = \"%s\"", item); gpList = genePredReaderLoadQuery(conn, tableName, query); for (gp = gpList; gp != NULL; gp = gp->next) { sequence = hDnaFromSeq(database, gp->chrom, gp->txStart, gp->txEnd, dnaUpper); if (sequence != NULL) @@ -1329,47 +1329,47 @@ char **row; int rowOffset; genericHeader(tdb,egName); rowOffset = hOffsetPastBin(database, seqName, tdb->table); sprintf(query, "select * from %s where name = '%s'", tdb->table, egName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) slAddTail(&egList,easyGeneLoad(row+rowOffset)); slReverse(&egList); sqlFreeResult(&sr); hFreeConn(&conn); for (eg = egList; eg != NULL; eg = eg->next) { if (eg->genbank[0] == 'Y') - printf("\n"); + printf("\n"); else - printf("\n"); + printf("\n"); printf("Item: %s
\n",eg->name); printf("Feature identifier: %s
\n",eg->feat); printf("Start codon: %s
\n",eg->startCodon); printf("EasyGene descriptor: %s
\n",eg->descriptor); if (eg->R >= 0.001) printf("R value: %.3f
\n",eg->R); else printf("R value: %.2e
\n",eg->R); printf("Log-odds : %.1f
\n",eg->logOdds); printf("Frame: %d
\n",eg->frame); printf("Swiss-Prot match: %s
\n",eg->swissProt); printf("ORF identifier: %s
\n",eg->orf); printPos(eg->chrom, eg->chromStart, eg->chromEnd, eg->strand, TRUE, eg->name); - printf("\n"); + printf("\n"); if (eg->next != NULL) printf("
\n"); } printTrackHtml(tdb); easyGeneFreeList(&egList); } void doCodeBlast(struct trackDb *tdb, char *trnaName) { struct pepPred *pp=NULL; struct codeBlast *cb=NULL; struct codeBlastScore *cbs=NULL, *cbs2, *list=NULL; struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[512]; @@ -2059,31 +2059,31 @@ "", hgTracksPathAndSettings(), database, tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd); printf("%s:%d-%d
\n", tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd); printf("Strand: %s
\n", tigrOperon->strand); printf("Genomic size: %d nt
\n", (tigrOperon->chromEnd - tigrOperon->chromStart)); if (tigrOperon->next != NULL) printf("
\n"); } sqlFreeResult(&sr); printf("
OperonDB predicted gene pairs
\n"); /* Print table */ printf("", HG_COL_BORDER); printf("
\n"); - printf("\n", HG_COL_INSIDE); + printf("
\n", HG_COL_INSIDE); printf("\n"); /* Print table column heading */ printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); sprintf(query, "select * from lowelabTIGROperonScore where name = '%s'", tigrOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { tigrOperonScore = lowelabTIGROperonScoreLoad(row); @@ -2151,31 +2151,31 @@ "", hgTracksPathAndSettings(), database, arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd); printf("%s:%d-%d
\n", arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd); printf("Strand: %s
\n", arkinOperon->strand); printf("Genomic size: %d nt
\n", (arkinOperon->chromEnd - arkinOperon->chromStart)); if (arkinOperon->next != NULL) printf("
\n"); } sqlFreeResult(&sr); printf("
Arkin operon predicted gene pairs
\n"); /* Print table */ printf("
Gene 1Gene 2ConfidenceNumber of Conserved Genomes
", HG_COL_BORDER); printf("
\n"); - printf("\n", HG_COL_INSIDE); + printf("
\n", HG_COL_INSIDE); printf("\n"); /* Print table column heading */ printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); sprintf(query, "select * from lowelabArkinOperonScore where name = '%s'", arkinOperonName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { arkinOperonScore = lowelabArkinOperonScoreLoad(row); @@ -2401,31 +2401,31 @@ char clade[50] = ""; unsigned int hitStart = 0; unsigned int hitEnd = 0; char **buffer = NULL; boolean findTable = FALSE; int tStart = cartInt(cart, "o"); int tEnd = cartInt(cart, "t"); char *tChrom = cartString(cart, "c"); printf("
\n"); /* Print table */ printf("
Gene 1Gene 2Probability of the Same OperonGene neighbor score
", HG_COL_BORDER); printf("
\n"); - printf("\n", HG_COL_INSIDE); + printf("
\n", HG_COL_INSIDE); printf("\n"); /* Print table column heading */ printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); @@ -2806,31 +2806,31 @@ unsigned int targetProteinStart = 0; unsigned int targetProteinEnd = 0; unsigned int hitStart = 0; unsigned int hitEnd = 0; char **buffer = NULL; int tStart = cartInt(cart, "o"); int tEnd = cartInt(cart, "t"); char *tChrom = cartString(cart, "c"); printf("
\n"); /* Print table */ printf("
OrganismCladeGeneProductPercent Length of Full ProteinPosition in Source ProteinProtein Identity (%%)E-valueLog of E-valueBit ScoreProtein Alignment Length
", HG_COL_BORDER); printf("
\n"); - printf("\n", HG_COL_INSIDE); + printf("
\n", HG_COL_INSIDE); printf("\n"); /* Print table column heading */ printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); @@ -3112,31 +3112,31 @@ printf("nmole/OD260: %0.3f
\n", computeNMolePerOD(sequence->dna, sequence->size)); printf("ug/OD260: %0.3f
\n", computeNMolePerOD(sequence->dna, sequence->size) * computeMolecularWeight(sequence->dna, sequence->size) * pow(10,-3)); } if (primer->next != NULL) printf("
\n"); } sqlFreeResult(&sr); printf("
Primer pairing
\n"); /* Print table */ printf("
OrganismCladeGeneProductPosition in Query Genomic SequencePosition in Target ProteinPercent Length of Target ProteinProtein Identity (%%)E-valueLog of E-valueBit Score
", HG_COL_BORDER); printf("
\n"); - printf("\n", HG_COL_INSIDE); + printf("
\n", HG_COL_INSIDE); printf("\n"); /* Print table column heading */ printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); memset(query, 0, 512); if (strcmp(primer->strand, "+") == 0) { @@ -3278,40 +3278,40 @@ cartWebStart(cart, database, "%s", "RNAHybridization Sites"); if (hTableExists(database, rnaHybridizationTable)) { /* Get query gene from refSeq */ sprintf(query, "select * from %s where name='%s'", rnaHybridizationTable, itemName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { rnaHyb = rnaHybridizationLoad(row); printf("Hybridization Site:

"); /* print hybridization site */ - printf(""); + printf(""); printf("Pattern 5%s3
", rnaHyb->patternSeq); printf("         "); for(i=0;imatchLength;i++) printf("|"); printf("
"); printf("Target  3%s5", rnaHyb->targetSeq); - printf("

"); + printf("

"); printf("
Genomic size: %d nt
\n",rnaHyb->matchLength); printf("Percentage G-C base-pairs: %d
", (int)(rnaHyb->gcContent * 100)); printf("Position: " "", hgTracksPathAndSettings(), database, rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd); printf("%s:%d-%d
\n", rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd); printf("Strand: %s
\n", rnaHyb->strand); printf("Target Position: " "", hgTracksPathAndSettings(), database, rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1); printf("%s:%d-%d
\n", rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1); @@ -3676,31 +3676,31 @@ printf("Name: %s
\n", crisprName); printf("Position: " "", hgTracksPathAndSettings(), database, crispr->chrom, crispr->chromStart + 1, crispr->chromEnd); printf("%s:%d-%d
\n", crispr->chrom, crispr->chromStart + 1, crispr->chromEnd); printf("Strand: %s
\n", crispr->strand); printf("Genomic size: %d nt

\n", (crispr->chromEnd - crispr->chromStart)); printf("Number of spacers: %u

\n", crispr->blockCount - 1); sequence = hDnaFromSeq(database, crispr->chrom, crispr->chromStart, crispr->chromEnd, dnaUpper); if (sequence != NULL) { /* Print table */ printf("
Primer NamePrimer TypePrimer SequencePCR RegionPCR Length (bp)PCR Region
GC Content (%%)
", HG_COL_BORDER); printf("
\n"); - printf("\n", HG_COL_INSIDE); + printf("
\n", HG_COL_INSIDE); printf("\n"); /* Print table column heading */ printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n"); printf("\n");
Direct RepeatSpacer
Start PosSequenceLengthStart PosSequenceLength