110f5e12a634db49ea9aa1ea23ff4965f1c2befe
galt
  Tue Aug 14 13:48:57 2018 -0700
changing cse to soe in domains, sometimes gi. ref #21876

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 84e8106..c9bcac3 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -1287,41 +1287,41 @@
     printf( "%4d %-10s %-5s %12d %12d %10d      %c      %-10s %-10s\n",
             ret.instance, ret.species,ret.chrom, ret.start + 1, ret.end,
             ret.end - ret.start + 1, ret.strand[0],ret.fivePrime,ret.threePrime);
     }
 printf("</A>");
 sqlFreeResult(&sr);
 
 if (!sameString("atom20080226d", table))
     return;
 
 printf("<TABLE>");
 printf("<THEAD>");
 printf("<TBODY>");
 printf("<TR><TH>");
 printf("Suh Trees<BR>\n");
-printf("<IMG src=http://hgwdev.cse.ucsc.edu/~braney/suhTrees/%s.tt.png><BR>",item);
-printf("<TD><IMG src=http://hgwdev.cse.ucsc.edu/~braney/suhTrees/%s.gt.png><BR>",item);
+printf("<IMG src=http://hgwdev.gi.ucsc.edu/~braney/suhTrees/%s.tt.png><BR>",item);
+printf("<TD><IMG src=http://hgwdev.gi.ucsc.edu/~braney/suhTrees/%s.gt.png><BR>",item);
 printf("<TR><TH>");
 printf("NJ Trees<BR>\n");
-printf("<IMG src=http://hgwdev.cse.ucsc.edu/~braney/njTrees/%s.tt.png><BR>",item);
-printf("<TD><IMG src=http://hgwdev.cse.ucsc.edu/~braney/njTrees/%s.gt.png><BR>",item);
+printf("<IMG src=http://hgwdev.gi.ucsc.edu/~braney/njTrees/%s.tt.png><BR>",item);
+printf("<TD><IMG src=http://hgwdev.gi.ucsc.edu/~braney/njTrees/%s.gt.png><BR>",item);
 printf("<TR><TH>");
 /*
 printf("Gap UPGMA Trees<BR>\n");
-printf("<IMG src=http://hgwdev.cse.ucsc.edu/~braney/gap992Trees/%s.tt.png><BR>",item);
-printf("<TD><IMG src=http://hgwdev.cse.ucsc.edu/~braney/gap992Trees/%s.gt.png><BR>",item);
+printf("<IMG src=http://hgwdev.gi.ucsc.edu/~braney/gap992Trees/%s.tt.png><BR>",item);
+printf("<TD><IMG src=http://hgwdev.gi.ucsc.edu/~braney/gap992Trees/%s.gt.png><BR>",item);
 printf("</TABLE>");
 
 */
 return;
 
 char buffer[4096];
 struct mafFile *mf;
 safef(buffer, sizeof buffer, "/gbdb/hgFixed/%s/%s.maf",table, item);
 mf = mafMayOpen(buffer);
 if (mf != NULL)
     {
     mafFileFree(&mf);
     mf = mafReadAll(buffer);
     struct mafAli *mafAli;
     int count = 1;
@@ -13932,31 +13932,31 @@
        psl->qName, psl->qStart+1, psl->qEnd);
 printf("<B>%s size:</B> %d<BR>\n", otherOrg, psl->qEnd - psl->qStart);
 printf("<B>%s position:</B> %s:%d-%d<BR>\n", thisOrg,
        psl->tName, psl->tStart+1, psl->tEnd);
 printf("<B>%s size:</B> %d<BR>\n", thisOrg,
        psl->tEnd - psl->tStart);
 printf("<B>Identical Bases:</B> %d<BR>\n", psl->match + psl->repMatch);
 printf("<B>Number of Gapless Aligning Blocks:</B> %d<BR>\n", psl->blockCount );
 printf("<B>Strand:</B> %s<BR>\n",psl->strand);
 printf("<B>Percent identity within gapless aligning blocks:</B> %3.1f%%<BR>\n", 0.1*(1000 - pslCalcMilliBad(psl, FALSE)));
 printf("<B>Browser window position:</B> %s:%d-%d<BR>\n", seqName, winStart, winEnd);
 printf("<B>Browser window size:</B> %d<BR>\n", winEnd - winStart);
 
 safef(anotherString, sizeof anotherString, "%s",otherOrg);
 toUpperN(anotherString,1);
-printf("Link to <a href=\"http://hgwdev-tcbruen.cse.ucsc.edu/cgi-bin/hgTracks?db=zoo%s1&position=chr1:%d-%d\">%s database</a><BR>\n",
+printf("Link to <a href=\"http://hgwdev-tcbruen.gi.ucsc.edu/cgi-bin/hgTracks?db=zoo%s1&position=chr1:%d-%d\">%s database</a><BR>\n",
        anotherString, psl->qStart, psl->qEnd, otherOrg);
 
 safef(otherString, sizeof otherString, "%d&pslTable=%s&otherOrg=%s&otherChromTable=%s", psl->tStart,
         tdb->table, otherOrg, otherChromTable);
 if (pslTrimToTargetRange(psl, winStart, winEnd) != NULL)
     {
     hgcAnchorSomewhere("htcLongXenoPsl2", item, otherString, psl->tName);
     printf("<BR>View details of parts of alignment within browser window</A>.<BR>\n");
     }
 printTrackHtml(tdb);
 }
 
 void doAlignmentOtherDb(struct trackDb *tdb, char *item)
 /* Put up cross-species alignment when the second species
  * is another db, indicated by the 3rd word of tdb->type. */
@@ -20309,31 +20309,31 @@
     }
 printTrackHtml(tdb);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 void chuckHtmlStart(char *title)
 /* Prints the header appropriate for the title
  * passed in. Links html to chucks stylesheet for
  * easier maintaince
  */
 {
 printf("<HTML>\n<HEAD>\n%s", getCspMetaHeader());
 // FIXME blueStyle should not be absolute to genome-test and should be called by:
 //       webIncludeResourceFile("blueStyle.css");
-printf("<LINK REL=STYLESHEET TYPE=\"text/css\" href=\"http://genome-test.cse.ucsc.edu/style/blueStyle.css\" title=\"Chuck Style\">\n");
+printf("<LINK REL=STYLESHEET TYPE=\"text/css\" href=\"http://genome-test.gi.ucsc.edu/style/blueStyle.css\" title=\"Chuck Style\">\n");
 printf("<title>%s</title>\n</head><body bgcolor=\"#f3f3ff\">",title);
 }
 
 void chuckHtmlContactInfo()
 /* Writes out Chuck's email so people bother Chuck instead of Jim */
 {
 puts("<br><br><span style='font-size:x-small;'><i>If you have comments and/or suggestions please email "
      "<a href=\"mailto:sugnet@cse.ucsc.edu\">sugnet@cse.ucsc.edu</a>.</span>\n");
 }
 
 
 void abbr(char *s, char *fluff)
 /* Cut out fluff from s. */
 {
 int len;