111cb8c8dd6e03b2bee2628f5d8ff158710e61c9
tdreszer
  Wed Jul 11 10:58:51 2012 -0700
Format changes as dictated by Jim.  Formatting lines to 100 chars.  Only touching lines git blames on 'tdreszer'.  Because most of file has formatting differences from kent style, changes here conform to the local style.  These changes should affect executable in any way.
diff --git src/hg/hgc/lowelab.c src/hg/hgc/lowelab.c
index d6fc9ce..91911bd 100644
--- src/hg/hgc/lowelab.c
+++ src/hg/hgc/lowelab.c
@@ -299,33 +299,35 @@
     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%%; background-color:#%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; background-color:#%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"))
@@ -2099,31 +2101,32 @@
                "<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; background-color:#%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);
@@ -2191,31 +2194,32 @@
                "<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; background-color:#%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);
@@ -2441,31 +2445,32 @@
     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; background-color:#%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");
@@ -2846,31 +2851,32 @@
     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; background-color:#%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");
@@ -3152,31 +3158,32 @@
             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; background-color:#%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)
     {
@@ -3716,31 +3723,32 @@
         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; background-color:#%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");