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/rnaFoldClick.c src/hg/hgc/rnaFoldClick.c
index 6526ef5..e1539fa 100644
--- src/hg/hgc/rnaFoldClick.c
+++ src/hg/hgc/rnaFoldClick.c
@@ -54,39 +54,39 @@
     binArray[i] = assignBin(scores[i], minScore, maxScore, binCount);
 }
 
 void htmlColorPrintString(FILE *f, char *s, int *colorFormat, int *colors, int L)
 /* Prints s to f wrapping characters in html tags for coloring
  * according to colorFormat and colors. colorFormat must be of same
  * length as s. Each position of colorFormat defines which of the
  * colors to use. Use 0 for default color. If L is non-NULL it
  * defines a mximum length to print.*/
 {
 int i;
 
 if (!L || (L && strlen(s)<L) )
     L = strlen(s);
 
-fprintf(f, "<FONT COLOR=\"%06X\">", colors[0]); /* default color */
+fprintf(f, "<span style='color:#%06X;'>", colors[0]); /* default color */
 for (i = 0; i < L; i++)
     {
     if (colorFormat[i] == 0)
 	fprintf(f, "%c", s[i]);
     else
-	fprintf(f, "<FONT COLOR=\"%06X\">%c</FONT>", colors[ colorFormat[i] ], s[i]);
+	fprintf(f, "<span style='color:#%06X;'>%c</span>", colors[ colorFormat[i] ], s[i]);
     }
-fprintf(f, "</FONT>");
+fprintf(f, "</span>");
 }
 
 void mafAndFoldHeader(FILE *f)
 /* Print header for maf and fold the section*/
 {
 fprintf(f, "<center><h2> Multiple alignment and RNA secondary structure annotation </h2></center>");
 }
 
 void mkPosString(char *s, int size)
 /* Make a string-ruler with a decimal every tenth position */
 {
 int i, d;
 for (i = 0, d = 0; i < size; i++)
     if (i%10 == 0) 
 	{
@@ -252,38 +252,38 @@
     freeMem(scoreColorFormat);
     }
 for (i = 0; i < N; i++)
     freeMem(mafColorFormats[i]);
 freeMem(mafColorFormats);
 }
 
 void mafAndFoldLegend(FILE *f)
 /* Print legend for the maf and fold section */
 {
 char *s          = "0123456789";
 int colorFormat[] = {0,1,2,3,4,5,6,7,8,9};
 int colors[]      = {0x999999,0x888888,0x777777,0x666666,0x555555,0x444444,0x333333,0x222222,0x111111,0x000000};
 fprintf(f, "<h3> Color legend </h3>");
 fprintf(f, "<TABLE BORDER=0>");
-fprintf(f, "<TR> <TD> <FONT COLOR=\"%06X\">GRAY:       </TD> <TD> Not part of annotated pair, no substitution. <BR>             </TD> </TR>", LTGRAY);
-fprintf(f, "<TR> <TD> <FONT COLOR=\"%06X\">LT. PURPLE: </TD> <TD> Not part of annotated pair, substitution. <BR>                </TD> </TR>", LTPURPLE);
-fprintf(f, "<TR> <TD> <FONT COLOR=\"%06X\">BLACK:      </TD> <TD> Compatible with annotated pair, no substitutions.<BR>         </TD> </TR>", BLACK);
-fprintf(f, "<TR> <TD> <FONT COLOR=\"%06X\">BLUE:       </TD> <TD> Compatible with annotated pair, single substitution.<BR>      </TD> </TR>", BLUE);
-fprintf(f, "<TR> <TD> <FONT COLOR=\"%06X\">GREEN:      </TD> <TD> Compatible with annotated pair, double substitution.<BR>      </TD> </TR>", GREEN);
-fprintf(f, "<TR> <TD> <FONT COLOR=\"%06X\">RED:        </TD> <TD> Not compatible with annotated pair, single substitution. <BR> </TD> </TR>", RED);
-fprintf(f, "<TR> <TD> <FONT COLOR=\"%06X\">ORANGE:     </TD> <TD> Not compatible with annotated pair, double substitution. <BR> </TD> </TR>", ORANGE);
-fprintf(f, "<TR> <TD> <FONT COLOR=\"%06X\">MAGENTA:    </TD> <TD> Not compatible with annotated pair, involves gap. <BR>        </TD> </TR>", MAGENTA);
+fprintf(f, "<TR> <TD style='color:#%06X;'> GRAY:       </TD> <TD> Not part of annotated pair, no substitution. <BR>             </TD> </TR>", LTGRAY);
+fprintf(f, "<TR> <TD style='color:#%06X;'> LT. PURPLE: </TD> <TD> Not part of annotated pair, substitution. <BR>                </TD> </TR>", LTPURPLE);
+fprintf(f, "<TR> <TD style='color:#%06X;'> BLACK:      </TD> <TD> Compatible with annotated pair, no substitutions.<BR>         </TD> </TR>", BLACK);
+fprintf(f, "<TR> <TD style='color:#%06X;'> BLUE:       </TD> <TD> Compatible with annotated pair, single substitution.<BR>      </TD> </TR>", BLUE);
+fprintf(f, "<TR> <TD style='color:#%06X;'> GREEN:      </TD> <TD> Compatible with annotated pair, double substitution.<BR>      </TD> </TR>", GREEN);
+fprintf(f, "<TR> <TD style='color:#%06X;'> RED:        </TD> <TD> Not compatible with annotated pair, single substitution. <BR> </TD> </TR>", RED);
+fprintf(f, "<TR> <TD style='color:#%06X;'> ORANGE:     </TD> <TD> Not compatible with annotated pair, double substitution. <BR> </TD> </TR>", ORANGE);
+fprintf(f, "<TR> <TD style='color:#%06X;'> MAGENTA:    </TD> <TD> Not compatible with annotated pair, involves gap. <BR>        </TD> </TR>", MAGENTA);
 fprintf(f, "</TABLE>");
 /* Score legend */
 fprintf(f, "<BR>SCORE:   min ");
 htmlColorPrintString(f, s, colorFormat, colors, 0);
 fprintf(f, " max");
 }
 
 struct mafAli *mafFromRnaSecStrItem(char *mafTrack, struct rnaSecStr *item)
 {
 struct mafAli *maf;
 maf = hgMafFrag(database, mafTrack, item->chrom, item->chromStart, item->chromEnd, item->strand[0], NULL, NULL);
 return maf;
 }
 
 void mafSortBySpeciesOrder(struct mafAli *maf, char *speciesOrder)