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/hgGeneRing/hgGeneRing.c src/hg/hgGeneRing/hgGeneRing.c
index 18a584b..f11d9e0 100644
--- src/hg/hgGeneRing/hgGeneRing.c
+++ src/hg/hgGeneRing/hgGeneRing.c
@@ -68,51 +68,49 @@
 char *position = cloneString(cartUsualString(cart, "position", defaultPosition));
 boolean gotClade = hGotClade();
 
 /* JavaScript to copy input data on the change genome button to a hidden form
 This was done in order to be able to flexibly arrange the UI HTML
 */
 char *onChangeDB = "onchange=\"document.orgForm.db.value = document.mainForm.db.options[document.mainForm.db.selectedIndex].value; document.orgForm.submit();\"";
 char *onChangeOrg = "onchange=\"document.orgForm.org.value = document.mainForm.org.options[document.mainForm.org.selectedIndex].value; document.orgForm.db.value = 0; document.orgForm.submit();\"";
 char *onChangeClade = "onchange=\"document.orgForm.clade.value = document.mainForm.clade.options[document.mainForm.clade.selectedIndex].value; document.orgForm.org.value = 0; document.orgForm.db.value = 0; document.orgForm.submit();\"";
 
 if (sameString(position, "genome") || sameString(position, "hgBatch"))
     position = defaultPosition;
 
 puts(
 "<FORM ACTION=\"/cgi-bin/hgTracks\" NAME=\"mainForm\" METHOD=\"GET\">\n"
-"<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='text-align:center; font-size:small;'>\n"
 "The UCSC Genome Browser was created by the \n"
 "<A HREF=\"/staff.html\">Genome Bioinformatics Group of UC Santa Cruz</A>.\n"
 "<BR>"
 "Software Copyright (c) The Regents of the University of California.\n"
 "All rights reserved.\n"
-"</CENTER>\n"
-"</FONT></TD></TR></TABLE></CENTER>\n"
+"</TD></TR></TABLE></span>\n"
 );
 
 puts(
 "<input TYPE=\"IMAGE\" BORDER=\"0\" NAME=\"hgt.dummyEnterButton\" src=\"/images/DOT.gif\" WIDTH=1 HEIGHT=1 ALT=dot>\n"
-"<center>\n"
-"<table bgcolor=\"cccc99\" border=\"0\" CELLPADDING=1 CELLSPACING=0>\n"
+"<span style='text-align:center;'>\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"
-"<table bgcolor=\"fffef3\" border=0>\n"
+"<table bgcolor='#FFFEF3' border=0>\n"
 "<tr>\n"
 "<td>\n"
 "<table><tr>");
 if (gotClade)
     puts("<td align=center valign=baseline>clade</td>");
 puts(
 "<td align=center valign=baseline>genome</td>\n"
 "<td align=center valign=baseline>assembly</td>\n"
 "<td align=center valign=baseline>position</td>\n"
 "<td align=center valign=baseline>image width</td>\n"
 "<td align=center valign=baseline> &nbsp; </td>\n"
 "</tr>\n<tr>"
 );
 
 if (gotClade)
@@ -158,42 +156,42 @@
     cartSetString(cart, "clade", clade);
 
 freez(&defaultPosition);
 position = NULL;
 
 puts("<td align=center>\n");
 cgiMakeIntVar("pix", cartUsualInt(cart, "pix", hgDefaultPixWidth), 4);
 cartSaveSession(cart);
 printf("</td>\n");
 printf("<td align=center>");
 cgiMakeButton("Submit", "Submit");
 printf("</td>\n");
 
 puts(
 "</tr></table>\n"
-"</td></tr><tr><td><center>\n"
+"</td></tr><tr><td><span style='text-align:center;'>\n"
 "<a HREF=\"../cgi-bin/cartReset\">Click here to reset</a> the browser user interface settings to their defaults.<BR>\n"
-"</center>\n"
-"</td></tr><tr><td><center>\n"
+"</span>\n"
+"</td></tr><tr><td><span style='text-align:center;'>\n"
 );
 cgiMakeButton("customTrackPage", "Add Your Own Custom Tracks");
-puts("</center>\n"
+puts("</span>\n"
 "</td></tr></table>\n"
 "</td></tr></table>\n"
 "</td></tr></table>\n"
 );
-puts("</center>");
+puts("</span>");
 
 hgPositionsHelpHtml(organism, db);
 
 puts("</FORM>\n"
 );
 
 puts("<FORM ACTION=\"/cgi-bin/hgGateway\" METHOD=\"GET\" NAME=\"orgForm\">");
 if (gotClade)
     printf("<input type=\"hidden\" name=\"clade\" value=\"%s\">\n", clade);
 printf("<input type=\"hidden\" name=\"org\" value=\"%s\">\n", organism);
 printf("<input type=\"hidden\" name=\"db\" value=\"%s\">\n", db);
 cartSaveSession(cart);
 puts("</FORM><BR>");
 }
 
@@ -369,64 +367,62 @@
 return result;
 }
 
 
 void getGeneList()
 /* hgGeneRing - Gene Network Browser. */
 {
 
 /* not much point in this, though called old it's the same as current
    at this point.  It is not the old value from before the last submit.
 char *oldGeneList = hashFindVal(oldVars, "ring_geneList");
 */
 
 if (!sameString(errMsg,""))
     {
-    printf("<CENTER>%s</CENTER>\n",errMsg);
+    printf("<span style='text-align:center;'>%s</span>\n",errMsg);
     }
 
 puts(
 "<FORM ACTION=\"/cgi-bin/hgGeneRing\" NAME=\"mainForm\" METHOD=\"GET\">\n"
-"<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='text-align:center; font-size:x-small;'>\n"
 "Enter gene list for gene network ring.\n"
-"</CENTER>\n"
-"</FONT></TD></TR></TABLE></CENTER>\n"
+"</TD></TR></TABLE></span>\n"
 );
 
 puts(
-"<center>"
-"<table bgcolor=\"cccc99\" border=\"0\" CELLPADDING=1 CELLSPACING=0>\n"
+"<span style='text-align:center;'>"
+"<table bgcolor='#CCCC99' border=0 CELLPADDING=1 CELLSPACING=0>\n"
 "<tr>\n"
 );
 
 puts("<td align=center>\n");
 cgiMakeTextArea("ring_geneList", geneList, 25, 30);
 printf("</td>\n");
 
 puts(
 "</tr><tr>\n"
 );
 
 printf("<td align=center>");
 cgiMakeButton("Submit", "Submit");
 printf("</td>\n");
 
 puts(
-"</tr></table></center>\n"
+"</tr></table></span>\n"
 );
 puts("</FORM>\n");
 
 cartSetString(cart, "ring_action", "saveGeneList");
 cartSetString(cart, "ring_errMsg", "");
 
 }
 
 
 int compareNodes(const void *va, const void *vb)
 {
 const struct nodelist *a = *((struct nodelist **)va);
 const struct nodelist *b = *((struct nodelist **)vb);
 if (a->node->ring && !b->node->ring) return -1;
 if (!a->node->ring && b->node->ring) return  1;
@@ -451,45 +447,45 @@
 */
 {
 struct interaction* intr;
 struct nodelist *nl;
 
 if (!getGenesAsList())
     {
     getGeneList();
     return FALSE;
     }
 
 
 if (showAll)
     {
     puts(
-    "<center>"
-    "<table bgcolor=\"cccc99\" border=\"0\" CELLPADDING=1 CELLSPACING=0>\n"
+    "<span style='text-align:center;'>"
+    "<table bgcolor='#CCCC99' border=0 CELLPADDING=1 CELLSPACING=0>\n"
     "<tr><td>\n"
     );
     printf("geneList: %s<br>\n", 
 	geneList
     );
     puts(
     "</td></tr><tr><td>"
     "<a href=\"/cgi-bin/hgGeneRing?ring_action=getGeneList\">gene-list</a>\n"
     "</td></tr><tr><td>"
     "<a href=\"/cgi-bin/hgGeneRing?ring_action=drawScreen\">screen</a>\n"
     );
     puts(
-    "</td></tr></table></center>\n"
+    "</td></tr></table></span>\n"
     );
 
     }
   
 
 interactions = getGenesFromTable("intrP2P");  /* adds geneList elements to hash */
 
 if (showAll)
     {
     uglyf("slCount = %d for result list for %s.<br><br>\n",slCount(interactions),geneList);
     }
 
 /* this might get moved later */
 /* add to hash the remaining interactions members */
 for(intr=interactions;intr;intr=intr->next)
@@ -764,43 +760,43 @@
 	    }
 	}
     }
     
     nl=nl->next;
     }
 
 
 printf("</MAP>\n");
 
 
 
 mgSaveGif(mg, filename.forCgi, FALSE);
  
 width=height=SCREEN_SIZE;
-printf("<CENTER><TABLE BORDER=0 CELLPADDING=0>");
+printf("<span style='text-align:center;'><TABLE BORDER=0 CELLPADDING=0>");
 printf("<TR><TD HEIGHT=5></TD></TR>");
 printf("<TR><TD><IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s >",
        filename.forHtml, width, height, mapName);
 printf("</TD></TR>");
 printf("<TR><TD HEIGHT=5></TD></TR>");
 printf(
     "<TR><TD>"
     "<a href = \"/cgi-bin/hgGeneRing?ring_action=saveGeneList\">back</a> "
     "<a href = \"/cgi-bin/hgGeneRing?ring_action=getGeneList\">gene-list</a> "
     "<a href = \"/cgi-bin/hgGeneRing?ring_action=drawScreen\">refresh</a> "
     "</TD></TR>");
-printf("<TR><TD HEIGHT=5></TD></TR></TABLE></CENTER>");
+printf("<TR><TD HEIGHT=5></TD></TR></TABLE></span>");
 			    
 }
 
 char *unAlias(char *gene)
 /* deal with alias mapping for gene names, return FBgn */
 {
 struct hashEl *hf=NULL;
 if (!startsWith("FBgn",gene))
     {
     if (hf=hashLookup(aliasHash,gene))
 	{
 	gene=(char *)hf->val;
 	}
     }
 return gene;