36650b61875fa047f2c9ebc3657d1a9d10ec77e6
braney
  Fri Nov 12 14:42:17 2021 -0800
Give developers a way to map sequence names to labels in maf display refs #28495

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index d108877..499b83e 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -1246,31 +1246,31 @@
     printf("<LI>");
     safef(extra,sizeof(extra),"%s=full",tdb->track);
     linkToOtherBrowserExtra(db, chrom, beg, end, extra);
     printf("%s</A></LI>\n",strSwapChar(title,'_',' '));
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 freeMem(setting);
 if (gotOne)
     printf("</UL>\n");
 else
     printf("<P>Currently the item \"%s\" has not been located in another genome.\n",name);
 }
 
 void mafPrettyOut(FILE *f, struct mafAli *maf, int lineSize,
-	boolean onlyDiff, int blockNo);
+	boolean onlyDiff, int blockNo, struct hash *hash);
 
 void doAtom( struct trackDb *tdb, char *item)
 {
 char table[HDB_MAX_TABLE_STRING];
 boolean hasBin;
 //struct bed *bed;
 char query[512];
 struct sqlResult *sr;
 char **row;
 //boolean firstTime = TRUE;
 int start = cartInt(cart, "o");
 //struct sqlConnection *conn = hAllocConn(database);
 char *user = cfgOption("db.user");
 char *password = cfgOption("db.password");
 struct sqlConnection *sc;
@@ -1367,31 +1367,31 @@
 if (mf != NULL)
     {
     mafFileFree(&mf);
     mf = mafReadAll(buffer);
     struct mafAli *mafAli;
     int count = 1;
     int numBlocks = 0;
 
     for (mafAli=mf->alignments; mafAli; mafAli = mafAli->next)
 	numBlocks++;
 
     for (mafAli=mf->alignments; mafAli; mafAli = mafAli->next)
 	{
 	printf("<BR><B>Multiple Alignment Block %d of %d</B><BR>",
 	    count, numBlocks);
-	mafPrettyOut(stdout, mafAli, 70, FALSE, count++);
+	mafPrettyOut(stdout, mafAli, 70, FALSE, count++, NULL);
 	if (mafAli->next != NULL)
 	    {
 	    struct mafAli *next = mafAli->next;
 	    struct mafComp *comp1 = mafAli->components;
 	    struct mafComp *comp2 = next->components;
 
 	    printf("<BR><B>Gaps:</B>\n");
 	    for(; comp1 ; comp1 = comp1->next, comp2 = comp2->next)
 		{
 		int diff;
 		char dbOnly[4096];
 
 		diff = comp2->start - (comp1->start + comp1->size);
 
 		safef(dbOnly, sizeof(dbOnly), "%s", comp1->src);