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/t2g.c src/hg/hgc/t2g.c
index 36c83c4..1bcb315 100644
--- src/hg/hgc/t2g.c
+++ src/hg/hgc/t2g.c
@@ -1,176 +1,176 @@
 /* t2g.c - display details of text2genome stuff */
 
 #include "common.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgc.h"
 #include "hgColors.h"
 #include "trackDb.h"
 #include "web.h"
 #include "hash.h"
 #include "obscure.h"
 
 #define PMCURL "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC"
 
 void printPubmedLink(char* pmid) 
 {
     printf("<B>PubMed:</B>&nbsp;<A HREF=\"http://www.ncbi.nlm.nih.gov/pubmed/%s\" TARGET=_blank>%s</A><BR>\n", pmid, pmid);
 }
 
 void printPmcLink(char* pmcId) 
 {
     printf("<B>PubMed&nbsp;Central:</B>&nbsp;<A HREF=\"%s%s\" TARGET=_blank>PMC%s</A><BR>\n", PMCURL, pmcId, pmcId);
 }
 
 void printT2gLink(char* pmcId) 
 {
     printf("<B>Text2Genome:</B>&nbsp;<A HREF=\"http://kumiho.smith.man.ac.uk/bergman/text2genome/inspector.cgi?pmcId=%s\" TARGET=_blank>%s</A><BR>\n", pmcId, pmcId);
 }
 
 void printLinks(char* pmid, char* pmcId) 
 {
     printPubmedLink(pmid);
     printPmcLink(pmcId);
     printT2gLink(pmcId);
     printf("<BR>\n");
 }
 
 char* printArticleInfo(struct sqlConnection *conn, struct trackDb* tdb, char* item) 
 /* Header with information about paper, return documentId */
 {
     char query[512];
     char* articleTable = hashMustFindVal(tdb->settingsHash, "articleTable");
 
     safef(query, sizeof(query), "SELECT pmid, pmcId, title,authors, abstract FROM %s WHERE displayId='%s'", articleTable, item);
     struct sqlResult *sr = sqlGetResult(conn, query);
     char **row;
     char *docId=0;
     if ((row = sqlNextRow(sr)) != NULL)
 	{
 	printLinks(row[0], row[1]);
 	printf("<A HREF=\"%s%s\"><b>%s</b></A>\n", PMCURL, row[1], row[2]);
 	printf("<p style=\"width:800px; font-size:96%%\">%s</p>\n", row[3]);
 	printf("<p style=\"width:800px; font-size:92%%\">%s</p>\n", row[4]);
         docId = row[1];
 	}
     sqlFreeResult(&sr);
     return docId;
 }
 
 void printSeqInfo(struct sqlConnection* conn, struct trackDb* tdb,
     char* docId, char* item, char* seqName, int start)
 {
     /* print table of sequences */
 
     /* get all sequences for paper identified by docId*/
     char query[512];
     char* sequenceTable = hashMustFindVal(tdb->settingsHash, "sequenceTable");
     safef(query, sizeof(query), "SELECT concat_ws('|',seqId, sequence) FROM %s WHERE pmcId='%s'", sequenceTable, docId);
     struct slName *seqList = sqlQuickList(conn, query);
 
     /* get sequence-Ids for feature that was clicked on (item&startPos are unique) and put into hash */
     // there must be an easier way to do this...
     // couldn't find a function that splits a string and converts it to a list
     safef(query, sizeof(query), "SELECT seqIds,'' FROM t2g WHERE name='%s' "
 	"and chrom='%s' and chromStart=%d", item, seqName, start);
     char* seqIdsString = sqlQuickString(conn, query);
     char* seqIds[1024];
     int partCount = chopString(seqIdsString, ",", seqIds, ArraySize(seqIds));
     int i;
     struct hash *seqIdHash = NULL;
     seqIdHash = newHash(0);
     for (i=0; i<partCount; i++) 
 	hashAdd(seqIdHash, seqIds[i], NULL);
     freeMem(seqIdsString);
 
     // output table
     webNewSection("Sequences in article");
     printf("<small>Sequences that map to the feature that was clicked "
 	"are highlighted in bold</small>");
     webPrintLinkTableStart();
 
     struct slName *listEl = seqList;
     while (listEl != NULL)
         {
         char* parts[2];
         chopString(listEl->name, "|", parts, 2);
         char* seqId    = parts[0];
         char* seq      = parts[1];
 
         if (hashLookup(seqIdHash, seqId)) 
             printf("<TD BGCOLOR=\"#%s\"><TT><B>%s</B></TT></TD>",
 		HG_COL_TABLE, seq);
         else
-            printf("<TD BGCOLOR=\"#%s\"><TT><FONT COLOR=\"#AAAAAA\">%s"
-		"</FONT></TT></TD>\n", HG_COL_TABLE, seq);
+            printf("<TD style='background-color:#%s; color:#AAAAAA;'><TT>%s"
+		"</TT></TD>\n", HG_COL_TABLE, seq);
         webPrintLinkTableNewRow();
         listEl=listEl->next;
         }
 	webPrintLinkTableEnd();
     printTrackHtml(tdb);
 
     slFreeList(seqList);
     freeHash(&seqIdHash);
 }
 
 void doT2gDetails(struct trackDb *tdb, char *item)
 /* text2genome.org custom display */
 {
 int start = cgiInt("o");
 int end = cgiInt("t");
 char versionString[256];
 char dateReference[256];
 char headerTitle[512];
 struct sqlConnection *conn = hAllocConn(database);
 
 /* see if hgFixed.trackVersion exists */
 boolean trackVersionExists = hTableExists("hgFixed", "trackVersion");
 
 if (trackVersionExists)
     {
     char query[256];
     safef(query, sizeof(query), "select version,dateReference from hgFixed.trackVersion where db = '%s' AND name = 't2g' order by updateTime DESC limit 1", database);
     struct sqlResult *sr = sqlGetResult(conn, query);
     char **row;
 
     /* in case of NULL result from the table */
     versionString[0] = 0;
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	safef(versionString, sizeof(versionString), "version %s",
 		row[0]);
 	safef(dateReference, sizeof(dateReference), "%s",
 		row[1]);
 	}
     sqlFreeResult(&sr);
     }
 else
     {
     versionString[0] = 0;
     dateReference[0] = 0;
     }
 
 if (versionString[0])
     safef(headerTitle, sizeof(headerTitle), "%s - %s", item, versionString);
 else
     safef(headerTitle, sizeof(headerTitle), "%s", item);
 
 genericHeader(tdb, headerTitle);
 
 printf("<B>Position:</B>&nbsp;"
            "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">",
                   hgTracksPathAndSettings(), database, seqName, start+1, end);
 char startBuf[64], endBuf[64];
 sprintLongWithCommas(startBuf, start + 1);
 sprintLongWithCommas(endBuf, end);
 printf("%s:%s-%s</A><BR>\n", seqName, startBuf, endBuf);
 long size = end - start;
 sprintLongWithCommas(startBuf, size);
 printf("<B>Genomic Size:</B>&nbsp;%s<BR>\n", startBuf);
 
 char* docId = printArticleInfo(conn, tdb, item);
 
 if (docId!=0) 
     printSeqInfo(conn, tdb, docId, item, seqName, start);
 hFreeConn(&conn);
 }