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/hgText/hgText.c src/hg/hgText/hgText.c
index 660904f..68a0242 100644
--- src/hg/hgText/hgText.c
+++ src/hg/hgText/hgText.c
@@ -616,103 +616,101 @@
 return FALSE;
 }
 
 void doGateway()
 /* Table Browser gateway page: select organism, db */
 {
 webStart(cart, "Table Browser: Choose Organism and Assembly");
 
 if (! hDbIsActive(database))
     {
     database = hDefaultDb();
     organism = hGenome(database);
     }
 
 puts(
-"<CENTER>"
-"<TABLE BGCOLOR=\"FFFEF3\" BORDERCOLOR=\"cccc99\" BORDER=0 CELLPADDING=1>\n"
-"<TR><TD><FONT SIZE=\"2\">\n"
-"<CENTER>\n"
+"<span style='text-align:center;'>"
+"<TABLE BGCOLOR='#FFFEF3' BORDERCOLOR='#CCCC99' BORDER=0 CELLPADDING=1>\n"
+"<TR><TD style='font-size:small; text-align:center;'>\n"
 "The UCSC Table Browser was created by the \n"
 "<A HREF=\"/staff.html\">Genome Bioinformatics Group of UC Santa Cruz</A>. \n"
 "<BR>\n"
 "Software Copyright (c) The Regents of the University of California.\n"
 "All rights reserved.\n"
-"</CENTER>\n"
-"</FONT></TD></TR></TABLE></CENTER><P>\n"
+"</TD></TR></TABLE></span><P>\n"
 );
 
 puts("<P>This tool allows you to download portions of the Genome Browser \n"
      "database in several output formats. \n"
      "Choose a genome and assembly, \n"
      "then press the Submit button.\n");
 puts("See the <A HREF=\"/goldenPath/help/hgTextHelp.html\">Table Browser "
      "User Guide</A> for more information.<P>\n"
-     "<FONT COLOR=\"#FF0000\"><B>NOTE: This software has been replaced by a "
+     "<B style='color:#FF0000;'>NOTE: This software has been replaced by a "
      "<A HREF=\"hgTables\">newer version</A> of the Table Browser. "
      "This version of the tool is no longer "
      "maintained or updated by UCSC; therefore, we can make no guarantees "
      "about the completeness or correctness of the data returned. "
      "We are happy to assist you in the transition to the new Table "
      "Browser, which has many more features. Please "
      "email our public <A HREF=\"mailto:genome@soe.ucsc.edu\">mailing "
      "list</A> with questions or comments.</B> "
-     "</FONT><P> ");
+     "<P> ");
 
-puts("<center>");
+puts("<span style='text-align:center;'>");
 printf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=\"%s\">\n",
        hgTextName(), httpFormMethod);
 puts(
-"<table bgcolor=\"cccc99\" border=\"0\" CELLPADDING=1 CELLSPACING=0>\n"
+"<table bgcolor='#CCCC99' border=0 CELLPADDING=1 CELLSPACING=0>\n"
 "<tr><td>\n"
-"<table BGCOLOR=\"FEFDEF\" BORDERCOLOR=\"CCCC99\" BORDER=0 CELLPADDING=0 CELLSPACING=0>\n"  
+"<table BGCOLOR='#FEFDEF' BORDERCOLOR='#CCCC99' BORDER=0 CELLPADDING=0 CELLSPACING=0>\n"
 "<tr><td>\n"
 );
 
 puts(
-"<table bgcolor=\"FFFEF3\" border=0>\n"
+"<table bgcolor='#FFFEF3' border=0>\n"
 "<tr>\n"
 "<td>\n"
 );
 cartSaveSession(cart);
 puts(
 "<input TYPE=\"IMAGE\" BORDER=\"0\" NAME=\"tbDummyEnterButton\" src=\"/images/DOT.gif\">\n"
 "<table><tr>\n"
 "<td align=center valign=baseline>genome</td>\n"
 "<td align=center valign=baseline>assembly</td>\n"
 "</tr>"
 );
 
 puts("<tr><td align=center>\n");
 printGenomeListHtml(database, onChangeOrg);
 puts("</td>\n");
 
 puts("<td align=center>\n");
 printAssemblyListHtml(database, "");
 puts("</td><td>");
 cgiMakeButton("submit", "Submit");
 puts(
 "</td></tr></table>\n"
 "</td></tr>\n"
 "</table>\n"
 "</td></tr></table>\n"
 "</td></tr></table>\n"
 );
 cgiMakeHiddenVar("phase", chooseTablePhase);
 puts(
 "</FORM>"
-"</center>\n"
+"</span>\n"
 );
 
 printf("To reset <B>all</B> user cart settings (including custom tracks), \n"
        "<A HREF=\"/cgi-bin/cartReset?destination=%s\">click here</A>.\n",
        hgTextName());
 
 printf("<FORM ACTION=\"%s\" METHOD=\"%s\" NAME=\"orgForm\">\n", hgTextName(),
        httpFormMethod);
 cgiMakeHiddenVar("org", organism);
 cgiMakeHiddenVar("db", database);
 cartSetString(cart, "db",database);
 cartSetString(cart, "org", organism);
 cartSaveSession(cart);
 puts("</FORM>");
 
@@ -865,33 +863,33 @@
 cgiContinueHiddenVar("org");
 cgiContinueHiddenVar("db");
 cgiMakeHiddenVar("position", "genome");
 
 cgiMakeHiddenVar("table", getTableVar());
 cgiMakeHiddenVar("phase", chooseTablePhase);
 if (tableIsPositional)
     cgiMakeHiddenVar("tbPosOrKeys", "keys");
 cgiContinueHiddenVar("tbTrack");
 cgiContinueHiddenVar("tbCustomTrack");
 cgiContinueHiddenVar("table0");
 cgiContinueHiddenVar("table1");
 if (tableIsPositional)
     {
     puts("<TEXTAREA NAME=tbUserKeys ROWS=10 COLS=80></TEXTAREA><BR>\n");
-    puts("<CENTER>");
+    puts("<span style='text-align:center;'>");
     puts(" <INPUT TYPE=SUBMIT Name=tbShowPasteResults VALUE=\"Submit\"><P>\n");
-    puts("</CENTER>");
+    puts("</span>");
     }
 else
     {
     puts("<P><INPUT TYPE=SUBMIT Name=submit VALUE=\"Back\"><P>\n");
     }
 cartSaveSession(cart);
 printf("</FORM>\n");
 webEnd();
 }
 
 void uploadForm()
 /* Put up upload form. */
 {
 webStart(cart, "Table Browser: Upload File of Names/Accessions for Batch Query");
 puts("<A HREF=\"/goldenPath/help/hgTextHelp.html#UploadNames\">"
@@ -1101,40 +1099,40 @@
 struct hashEl *ctPosTableList = NULL;
 struct hashEl *posTableList;
 struct hashEl *nonposTableList;
 char *keyStr = getUserKeys();
 char *posOrKeys;
 
 webStart(cart, "Table Browser: %s %s: Choose a table",
 	 hOrganism(database), freezeName);
 
 printf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=\"%s\">\n\n",
        hgTextName(), httpFormMethod);
 cartSaveSession(cart);
 cgiMakeHiddenVar("db", database);
 cgiContinueHiddenVar("tbUserKeys");
 
-puts("<FONT COLOR=\"#FF0000\"><B>NOTE: This software has been replaced by a "
+puts("<B style='color:#FF0000;'>NOTE: This software has been replaced by a "
      "<A HREF=\"hgTables\">newer version</A> of the Table Browser. "
      "This version of the tool is no longer "
      "maintained or updated by UCSC; therefore, we can make no guarantees "
      "about the completeness or correctness of the data returned. "
      "We are happy to assist you in the transition to the new Table "
      "Browser, which has many more features. Please "
      "email our public <A HREF=\"mailto:genome@soe.ucsc.edu\">mailing "
      "list</A> with questions or comments.</B> "
-     "</FONT><P> ");
+     "<P> ");
 
 puts("<A HREF=\"/goldenPath/help/hgTextHelp.html#ChooseTable\">"
      "<B>Help</B></A>");
 
 ctPosTableList = getCustomTrackNames();
 categorizeTables(&posTableList, &nonposTableList);
 puts("<P> Choose a table: <BR>");
 printTrackDropList(database, onChangeTrack, "tbTrack");
 printf("<SELECT NAME=tbCustomTrack SIZE=1 %s>\n", onChangeCT);
 printf("<OPTION VALUE=\"Choose table\">Custom tracks</OPTION>\n");
 printSelectOptions(ctPosTableList, "tbCustomTrack");
 puts("</SELECT>");
 printf("<SELECT NAME=table0 SIZE=1 %s>\n", onChangePos);
 printf("<OPTION VALUE=\"Choose table\">Positional tables</OPTION>\n");
 printSelectOptions(posTableList, "table0");
@@ -3021,32 +3019,32 @@
  * offering histograms for the text/enum fields. */
 {
 char *db = getTableDb();
 struct sqlConnection *conn = hAllocOrConnect(db);
 struct sqlResult *sr;
 char **row;
 boolean tooBig = (sqlTableSize(conn, fullTableName) > TOO_BIG_FOR_HISTO);
 char button[64];
 char query[256];
 
 safef(query, sizeof(query), "desc %s", fullTableName);
 sr = sqlGetResult(conn, query);
 // For some reason BORDER=1 does not work in our web.c nested table scheme.
 // So use web.c's trick of using an enclosing table to provide a border.  
 puts("<!--outer table is for border purposes-->" "\n"
-     "<TABLE BGCOLOR=\"#"HG_COL_BORDER"\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>");
-puts("<TABLE BORDER=\"1\" BGCOLOR=\""HG_COL_INSIDE"\" CELLSPACING=\"0\">");
+     "<TABLE BGCOLOR='#" HG_COL_BORDER "' BORDER=0 CELLSPACING=0 CELLPADDING=1><TR><TD>");
+puts("<TABLE BGCOLOR='#" HG_COL_INSIDE "' BORDER=1 CELLSPACING=0>");
 printf("<TR> <TH>name</TH> <TH>SQL type</TH> ");
 histButtons = (histButtons && ! tooBig);
 if (histButtons)
     printf("<TH>text value histogram</TH> ");
 puts("</TR>");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     printf("<TR> <TD><TT>%s</TT></TD> <TD><TT>%s</TT></TD>", row[0], row[1]);
     if (histButtons)
 	{
 	printf(" <TD>");
 	if ((isSqlStringType(row[1]) || startsWith("enum", row[1])) &&
 	    ! sameString(row[1], "longblob"))
 	    {
 	    snprintf(button, sizeof(button), "%s for %s",histPhase,row[0]);
@@ -4628,32 +4626,32 @@
 if (typeWiggle)
     {
     wigDoStats(database, table, chromList, WIG_TABLE_1, constraints);
     wiggleDone = TRUE;
     }
 if (typeWiggle2)
     {
     wigDoStats(db2, table2, chromList, WIG_TABLE_2, constraints2);
     }
 
 if (! wiggleDone)
     {
     // For some reason BORDER=1 does not work in our web.c nested table scheme.
     // So use web.c's trick of using an enclosing table to provide a border.  
     puts("<!--outer table is for border purposes-->" "\n"
-	 "<TABLE BGCOLOR=\"#"HG_COL_BORDER"\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>");
-    puts("<TABLE BORDER=\"1\" BGCOLOR=\""HG_COL_INSIDE"\" CELLSPACING=\"0\">");
+	 "<TABLE BGCOLOR='#" HG_COL_BORDER "' BORDER=0 CELLSPACING=0 CELLPADDING=1><TR><TD>");
+    puts("<TABLE BGCOLOR='#" HG_COL_INSIDE "' BORDER=1 CELLSPACING=0>");
     /* Use fixed-font for decimal point/integer alignment. */
     /* All these non-blocking spaces are to widen the first column so that some 
      * row descriptions below do not get wrapped (which would mess up the <br> 
      * formatting of row contents). */
     puts("<TR><TH><TT>statistic&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TT></TH>");
     /* These non-blocking spaces are for decimal point/integer alignment: */
     puts("<TH ALIGN=\"RIGHT\"><TT>total&nbsp;&nbsp;&nbsp;</TT></TH>");
     if (numCols > 1)
 	for (chromPtr=chromList;  chromPtr != NULL;  chromPtr=chromPtr->next)
 	    printf("<TH><TT>%s</TT></TH>", breakChromRandomName(chromPtr->name));
     puts("</TR>");
     puts("<TR><TD><TT>items matching query</TT></TD>");
     for (i=0;  i < numCols;  i++)
 	printf("<TD ALIGN=\"RIGHT\"><TT>%d&nbsp;&nbsp;&nbsp;</TT></TD>",
 	       itemCounts[i]);