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("<br>\n"); printf("<b>Homologs within genome</b><BR>\n"); /* Print table */ - printf("<table style=\"width: 60%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); + printf("<table style='width:60%%; background-color:#%s;' border=0 cellpadding=1 cellspacing=0>", HG_COL_BORDER); printf("<tbody><tr><td>\n"); - printf("<table style=\"width: 100%%; text-align: left;\" bgcolor=\"%s\" border=\"1\" cellpadding=\"2\" cellspacing=\"2\">\n", HG_COL_INSIDE); + printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"20%%\"><b>Gene</b></td>\n"); printf("<td><b>Product</b></td>\n"); printf("<td width=\"30%%\"><b>BlastP E-value</b></td>\n"); printf("</tr>\n"); blastpHits = blastpHitsList; while (blastpHits != NULL) { parseDelimitedString(blastpHits->target, ':', blastpTarget, 2); if (hTableExists(blastpTarget[0], "lookup")) @@ -545,37 +545,37 @@ { printf("<B>UniProtKB:</B> "); printf("<A HREF="); printf(uniprotFormat, spAcc); if (spAcc == NULL) { printf(" TARGET=_blank>%s</A></B><BR>\n", item); } else { printf(" TARGET=_blank>%s</A></B><BR>\n", spAcc); } } /* print table of contents */ -printf("<br><hr style=\"width: 100%%; height: 2px;\"><font size=\"+1\">\n"); +printf("<br><hr style='width:100%%; height:2px;'><span style='font-size:larger;'>\n"); printf("<b>[<a href=\"#positions\">Positions and Sequence</a>] \n"); printf("[<a href=\"#COG\">COG</a>] \n"); printf("[<a href=\"#GO\">Gene Ontology</a>] \n"); printf("[<a href=\"#domain\">Protein Domain and Structure Infomation</a>] \n"); printf("[<a href=\"#homology\">Gene Homology</a>] \n"); -printf("[<a href=\"#pathway\">Pathway</a>]</b></font> <br>\n"); +printf("[<a href=\"#pathway\">Pathway</a>]</b></span> <br>\n"); printf("<hr style=\"width: 100%%; height: 2px;\"><br>\n"); /* Positions and sequence */ printf("<table style=\"text-align: left; width: 99%%;\" border=\"1\" cellpadding=\"5\" cellspacing=\"0\">\n"); printf("<tbody><tr><td style=\"background-color:#eee9e9;\">\n"); printf("<a name=\"positions\"></a><b>Positions and Sequence</b><br></td></tr>\n"); printf("<tr><td>\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("<FONT COLOR=\"#FF0000\">\n"); + printf("<span style='color:#FF0000;'>\n"); else - printf("<FONT COLOR=\"#000000\">\n"); + printf("<span style='color:#000000;'>\n"); printf("<B>Item:</B> %s<BR>\n",eg->name); printf("<B>Feature identifier:</B> %s<BR>\n",eg->feat); printf("<B>Start codon:</B> %s<BR>\n",eg->startCodon); printf("<B>EasyGene descriptor:</B> %s<BR>\n",eg->descriptor); if (eg->R >= 0.001) printf("<B>R value:</B> %.3f<BR>\n",eg->R); else printf("<B>R value:</B> %.2e<BR>\n",eg->R); printf("<B>Log-odds :</B> %.1f<BR>\n",eg->logOdds); printf("<B>Frame:</B> %d<BR>\n",eg->frame); printf("<B>Swiss-Prot match:</B> %s<BR>\n",eg->swissProt); printf("<B>ORF identifier:</B> %s<BR>\n",eg->orf); printPos(eg->chrom, eg->chromStart, eg->chromEnd, eg->strand, TRUE, eg->name); - printf("</FONT>\n"); + printf("</span>\n"); if (eg->next != NULL) printf("<hr>\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 @@ "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd); printf("%s:%d-%d</A><BR>\n", tigrOperon->chrom, tigrOperon->chromStart + 1, tigrOperon->chromEnd); printf("<B>Strand:</B> %s<BR>\n", tigrOperon->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (tigrOperon->chromEnd - tigrOperon->chromStart)); if (tigrOperon->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); printf("<br><B>OperonDB predicted gene pairs</B><br>\n"); /* Print table */ printf("<table style=\"width: 50%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); - printf("<table style=\"width: 100%%; text-align: left;\" bgcolor=\"%s\" border=\"1\" cellpadding=\"2\" cellspacing=\"2\">\n", HG_COL_INSIDE); + printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"25%%\"><b>Gene 1</b></td>\n"); printf("<td width=\"25%%\"><b>Gene 2</b></td>\n"); printf("<td width=\"25%%\"><b>Confidence</b></td>\n"); printf("<td width=\"25%%\"><b>Number of Conserved Genomes</b></td>\n"); printf("</tr>\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 @@ "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd); printf("%s:%d-%d</A><BR>\n", arkinOperon->chrom, arkinOperon->chromStart + 1, arkinOperon->chromEnd); printf("<B>Strand:</B> %s<BR>\n", arkinOperon->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (arkinOperon->chromEnd - arkinOperon->chromStart)); if (arkinOperon->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); printf("<br><B>Arkin operon predicted gene pairs</B><br>\n"); /* Print table */ printf("<table style=\"width: 50%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); - printf("<table style=\"width: 100%%; text-align: left;\" bgcolor=\"%s\" border=\"1\" cellpadding=\"2\" cellspacing=\"2\">\n", HG_COL_INSIDE); + printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"25%%\"><b>Gene 1</b></td>\n"); printf("<td width=\"25%%\"><b>Gene 2</b></td>\n"); printf("<td width=\"25%%\"><b>Probability of the Same Operon</b></td>\n"); printf("<td width=\"25%%\"><b>Gene neighbor score</b></td>\n"); printf("</tr>\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("<br>\n"); /* Print table */ printf("<table style=\"width: 100%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); - printf("<table style=\"width: 100%%; text-align: left;\" bgcolor=\"%s\" border=\"1\" cellpadding=\"2\" cellspacing=\"2\">\n", HG_COL_INSIDE); + printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"18%%\"><b>Organism</b></td>\n"); printf("<td width=\"7%%\"><b>Clade</b></td>\n"); printf("<td width=\"7%%\"><b>Gene</b></td>\n"); printf("<td><b>Product</b></td>\n"); printf("<td width=\"5%%\"><b>Percent Length of Full Protein</b></td>\n"); printf("<td width=\"8%%\"><b>Position in Source Protein</b></td>\n"); printf("<td width=\"5%%\"><b>Protein Identity (%%)</b></td>\n"); printf("<td width=\"5%%\"><b>E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Log of E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Bit Score</b></td>\n"); printf("<td width=\"6%%\"><b>Protein Alignment Length</b></td>\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("<br>\n"); /* Print table */ printf("<table style=\"width: 100%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); - printf("<table style=\"width: 100%%; text-align: left;\" bgcolor=\"%s\" border=\"1\" cellpadding=\"2\" cellspacing=\"2\">\n", HG_COL_INSIDE); + printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"10%%\"><b>Organism</b></td>\n"); printf("<td width=\"7%%\"><b>Clade</b></td>\n"); printf("<td width=\"7%%\"><b>Gene</b></td>\n"); printf("<td><b>Product</b></td>\n"); printf("<td width=\"7%%\"><b>Position in Query Genomic Sequence</b></td>\n"); printf("<td width=\"7%%\"><b>Position in Target Protein</b></td>\n"); printf("<td width=\"7%%\"><b>Percent Length of Target Protein</b></td>\n"); printf("<td width=\"5%%\"><b>Protein Identity (%%)</b></td>\n"); printf("<td width=\"5%%\"><b>E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Log of E-value</b></td>\n"); printf("<td width=\"5%%\"><b>Bit Score</b></td>\n"); @@ -3112,31 +3112,31 @@ printf("<B>nmole/OD<sub>260</sub>:</B> %0.3f <BR>\n", computeNMolePerOD(sequence->dna, sequence->size)); printf("<B>ug/OD<sub>260</sub>:</B> %0.3f <BR>\n", computeNMolePerOD(sequence->dna, sequence->size) * computeMolecularWeight(sequence->dna, sequence->size) * pow(10,-3)); } if (primer->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); printf("<br><B>Primer pairing</B><br>\n"); /* Print table */ printf("<table style=\"width: 90%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); - printf("<table style=\"width: 100%%; text-align: left;\" bgcolor=\"%s\" border=\"1\" cellpadding=\"2\" cellspacing=\"2\">\n", HG_COL_INSIDE); + printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"20%%\"><b>Primer Name</b></td>\n"); printf("<td width=\"10%%\"><b>Primer Type</b></td>\n"); printf("<td width=\"30%%\"><b>Primer Sequence</b></td>\n"); printf("<td width=\"10%%\"><b>PCR Region</b></td>\n"); printf("<td width=\"10%%\"><b>PCR Length (bp)</b></td>\n"); printf("<td width=\"10%%\"><b>PCR Region<BR>GC Content (%%)</b></td>\n"); printf("</tr>\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("<b>Hybridization Site:</b><br/><br/>"); /* print hybridization site */ - printf("<font face=\"Courier\">"); + printf("<span style='font-family:Courier;'>"); printf("Pattern 5%s3<br>", rnaHyb->patternSeq); printf("         "); for(i=0;i<rnaHyb->matchLength;i++) printf("|"); printf("<br/>"); printf("Target  3%s5", rnaHyb->targetSeq); - printf("</font><br/><br/>"); + printf("</span><br/><br/>"); printf("<BR><B>Genomic size: </B> %d nt<BR>\n",rnaHyb->matchLength); printf("<b>Percentage G-C base-pairs:</b> %d<br/>", (int)(rnaHyb->gcContent * 100)); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd); printf("%s:%d-%d</A><BR>\n", rnaHyb->chrom, rnaHyb->chromStart+1, rnaHyb->chromEnd); printf("<B>Strand:</B> %s<BR>\n", rnaHyb->strand); printf("<B>Target Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1); printf("%s:%d-%d</A><BR>\n", rnaHyb->chromTarget, rnaHyb->chromStartTarget+1, rnaHyb->chromEndTarget+1); @@ -3676,31 +3676,31 @@ printf("<B>Name: </B> %s<BR>\n", crisprName); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, crispr->chrom, crispr->chromStart + 1, crispr->chromEnd); printf("%s:%d-%d</A><BR>\n", crispr->chrom, crispr->chromStart + 1, crispr->chromEnd); printf("<B>Strand:</B> %s<BR>\n", crispr->strand); printf("<B>Genomic size:</B> %d nt<BR><BR>\n", (crispr->chromEnd - crispr->chromStart)); printf("<B>Number of spacers:</B> %u<BR><BR>\n", crispr->blockCount - 1); sequence = hDnaFromSeq(database, crispr->chrom, crispr->chromStart, crispr->chromEnd, dnaUpper); if (sequence != NULL) { /* Print table */ printf("<table style=\"width: 100%%;\" bgcolor=\"#%s\" border=\"0\" cellpadding=\"1\" cellspacing=\"0\">", HG_COL_BORDER); printf("<tbody><tr><td>\n"); - printf("<table style=\"width: 100%%; text-align: left;\" bgcolor=\"%s\" border=\"1\" cellpadding=\"2\" cellspacing=\"2\">\n", HG_COL_INSIDE); + printf("<table style='width:100%%; text-align:left; background-color:#%s;' border=1 cellpadding=2 cellspacing=2>\n", HG_COL_INSIDE); printf("<tbody>\n"); /* Print table column heading */ printf("<tr style=\"vertical-align: top;\">\n"); printf("<td colspan=\"3\"><b>Direct Repeat</b></td>\n"); printf("<td colspan=\"3\"><b>Spacer</b></td>\n"); printf("</tr>\n"); printf("<tr style=\"vertical-align: top;\">\n"); printf("<td width=\"8%%\"><b>Start Pos</b></td>\n"); printf("<td width=\"36%%\"><b>Sequence</b></td>\n"); printf("<td width=\"4%%\"><b>Length</b></td>\n"); printf("<td width=\"8%%\"><b>Start Pos</b></td>\n"); printf("<td><b>Sequence</b></td>\n"); printf("<td width=\"4%%\"><b>Length</b></td>\n"); printf("</tr>\n");