3c68ae03c7ec7a7e6b98c22e81f7a6489b50e515
braney
  Mon Feb 17 10:41:18 2020 -0800
delete long unused code for HIV, Cancer browser.   RIP Fan.

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 3e4c3c4..39ea344 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -4421,54 +4421,50 @@
 char *thisOrg = hOrganism(database);
 cartWebStart(cart, database, "Get DNA in Window (%s/%s)", database, thisOrg);
 printf("<H2>Get DNA for </H2>\n");
 printf("<FORM ACTION=\"%s\">\n\n", hgcName());
 cartSaveSession(cart);
 cgiMakeHiddenVar("g", "htcGetDna2");
 cgiMakeHiddenVar("table", tbl);
 cgiContinueHiddenVar("i");
 cgiContinueHiddenVar("o");
 cgiContinueHiddenVar("t");
 cgiContinueHiddenVar("l");
 cgiContinueHiddenVar("r");
 puts("Position ");
 savePosInTextBox(seqName, winStart+1, winEnd);
 
-/* bypass message about Table Browser for GSID server, since we haven't offered TB for GSID */
-if (!hIsGsidServer())
-    {
 if (tbl[0] == 0)
     {
     puts("<P>"
          "Note: This page retrieves genomic DNA for a single region. "
          "If you would prefer to get DNA for many items in a particular track, "
          "or get DNA with formatting options based on gene structure (introns, exons, UTRs, etc.), try using the ");
     printf("<A HREF=\"%s\" TARGET=_blank>", hgTablesUrl(TRUE, NULL));
     puts("Table Browser</A> with the \"sequence\" output format. You can also use the ");
     printf("<A HREF=\"../goldenPath/help/api.html\" TARGET=_blank>");
     puts("REST API</A> with the <b>/getData/sequence</b> endpoint function "
          "to extract sequence data with coordinates.");
     }
 else
     {
     puts("<P>"
          "Note: if you would prefer to get DNA for more than one feature of "
          "this track at a time, try the ");
     printf("<A HREF=\"%s\" TARGET=_blank>", hgTablesUrl(FALSE, tbl));
     puts("Table Browser</A> using the output format sequence.");
     }
-    }
 
 hgSeqOptionsHtiCart(hti,cart);
 puts("<P>");
 cgiMakeButton("submit", "get DNA");
 if (dbIsFound)
     cgiMakeButton("submit", EXTENDED_DNA_BUTTON);
 puts("</FORM><P>");
 if (dbIsFound)
     puts("Note: The \"Mask repeats\" option applies only to \"get DNA\", not to \"extended case/color options\". <P>");
 }
 
 boolean dnaIgnoreTrack(char *track)
 /* Return TRUE if this is one of the tracks too boring
  * to put DNA on. */
 {
@@ -4770,71 +4766,30 @@
 	    printf("</TD>");
 	    printf("<TD>");
 	    safef(buf, sizeof buf, "%s_green", tdb->track);
 	    cgiMakeIntVar(buf, cartUsualInt(cart, buf, 0), 3);
 	    printf("</TD>");
 	    printf("<TD>");
 	    safef(buf, sizeof buf, "%s_blue", tdb->track);
 	    cgiMakeIntVar(buf, cartUsualInt(cart, buf, 0), 3);
 	    printf("</TD>");
 	    printf("</TR>\n");
 	    }
 	}
     }
 printf("</TABLE>\n");
 printf("</FORM>\n");
-if (hIsGsidServer())
-    {
-    printf("<H3>Coloring Information and Examples</H3>\n");
-    puts("The color values range from 0 (darkest) to 255 (lightest) and are additive.\n");
-    puts("The examples below show a few ways to highlight individual tracks, "
-	 "and their interplay. It's good to keep it simple at first. It's easy "
-	 "to make pretty, but completely cryptic, displays with this feature.");
-    puts(
-	 "<UL>"
-	 "<LI>To put Genes in upper case red text, check the "
-	 "appropriate box in the Toggle Case column and set the color to pure "
-	 "red, RGB (255,0,0). Upon submitting, any Gene within the "
-	 "designated chromosomal interval will now appear in red capital letters.\n"
-	 "<LI>To see the overlap between Genes and InterPro Domains try "
-	 "setting the Genes/Regions to red (255,0,0) and InterPro to green (0,255,0). "
-	 "Places where the Genes and InterPro Domains overlap will be painted yellow "
-	 "(255,255,0).\n"
-	 "<LI>To get a level-of-coverage effect for tracks like Genes with "
-	 "multiple overlapping items, initially select a darker color such as deep "
-	 "green, RGB (0,64,0). Nucleotides covered by a single Gene will appear dark "
-	 "green, while regions covered with more Genes get progressively brighter &mdash; "
-	 "saturating at 4 Genes."
-	 "<LI>Another track can be used to mask unwanted features. Setting the "
-	 "InterPro track to RGB (255,255,255) will white-out Genes within InterPro "
-	 "domains. "
-	 "</UL>");
-    puts("<H3>Further Details and Ideas</H3>");
-    puts("<P>Copying and pasting the web page output to a text editor such as Word "
-	 "will retain upper case but lose colors and other formatting. That is still "
-	 "useful because other web tools such as "
-	 "<A HREF=\"https://www.ncbi.nlm.nih.gov/blast\" TARGET=_BLANK>NCBI Blast</A> "
-	 "can be set to ignore lower case.  To fully capture formatting such as color "
-	 "and underlining, view the output as \"source\" in your web browser, or download "
-	 "it, or copy the output page into an html editor.</P>");
-    puts("<P>The default line width of 60 characters is standard, but if you have "
-	 "a reasonable sized monitor it's useful to set this higher - to 125 characters "
-	 "or more.  You can see more DNA at once this way, and fewer line breaks help "
-	 "in finding DNA strings using the web browser search function.</P>");
-    }
-else
-    {
 printf("<H3>Coloring Information and Examples</H3>\n");
 puts("The color values range from 0 (darkest) to 255 (lightest) and are additive.\n");
 puts("The examples below show a few ways to highlight individual tracks, "
      "and their interplay. It's good to keep it simple at first.  It's easy "
      "to make pretty, but completely cryptic, displays with this feature.");
 puts(
      "<UL>"
      "<LI>To put exons from RefSeq Genes in upper case red text, check the "
      "appropriate box in the Toggle Case column and set the color to pure "
      "red, RGB (255,0,0). Upon submitting, any RefSeq Gene within the "
      "designated chromosomal interval will now appear in red capital letters.\n"
      "<LI>To see the overlap between RefSeq Genes and Genscan predictions try "
      "setting the RefSeq Genes to red (255,0,0) and Genscan to green (0,255,0). "
      "Places where the RefSeq Genes and Genscan overlap will be painted yellow "
      "(255,255,0).\n"
@@ -4852,31 +4807,30 @@
 puts("<P>Copying and pasting the web page output to a text editor such as Word "
      "will retain upper case but lose colors and other formatting. That is still "
      "useful because other web tools such as "
      "<A HREF=\"https://www.ncbi.nlm.nih.gov/blast\" TARGET=_BLANK>NCBI Blast</A> "
      "can be set to ignore lower case.  To fully capture formatting such as color "
      "and underlining, view the output as \"source\" in your web browser, or download "
      "it, or copy the output page into an html editor.</P>");
 puts("<P>The default line width of 60 characters is standard, but if you have "
      "a reasonable sized monitor it's useful to set this higher - to 125 characters "
      "or more.  You can see more DNA at once this way, and fewer line breaks help "
      "in finding DNA strings using the web browser search function.</P>");
 puts("<P>Be careful about requesting complex formatting for a very large "
      "chromosomal region.  After all the html tags are added to the output page, "
      "the file size may exceed size limits that your browser, clipboard, and "
      "other software can safely display.  The tool will format 10 Mb and more, however.</P>");
-    }
 trackDbFreeList(&tdbList);
 }
 
 void doGetBlastPep(char *readName, char *table)
 /* get predicted protein */
 {
 int qStart;
 struct psl *psl;
 int start, end;
 struct sqlResult *sr;
 struct sqlConnection *conn = hAllocConn(database);
 struct dnaSeq *tSeq;
 char query[256], **row;
 char fullTable[HDB_MAX_TABLE_STRING];
 boolean hasBin;
@@ -25443,35 +25397,30 @@
 
 cartSetString(cart, "i", "PrintAllSequences");
 hgCustom(newCts->tdb->track, NULL);
 }
 
 void doMiddle()
 /* Generate body of HTML. */
 {
 char *track = cartString(cart, "g");
 char *item = cloneString(cartOptionalString(cart, "i"));
 char *parentWigMaf = cartOptionalString(cart, "parentWigMaf");
 struct trackDb *tdb = NULL;
 
 hgBotDelayFrac(0.5);
 
-if (hIsGisaidServer())
-    {
-    validateGisaidUser(cart);
-    }
-
 /*	database and organism are global variables used in many places	*/
 getDbAndGenome(cart, &database, &genome, NULL);
 organism = hOrganism(database);
 scientificName = hScientificName(database);
 
 initGenbankTableNames(database);
 
 dbIsFound = trackHubDatabase(database) || sqlDatabaseExists(database);
 
 // Try to deal with virt chrom position used by hgTracks.
 // Hack the cart vars to set to a non virtual chrom mode position
 if (sameString("virt", cartString(cart, "c"))
  || sameString("getDna", cartUsualString(cart, "g", "")) )
     {
     char *nvPos = cartUsualString(cart, "nonVirtPosition", NULL);
@@ -26433,38 +26382,30 @@
     {
     doJaxAliasGenePred(tdb, item);
     }
 else if (sameWord(table, "wgRna"))
     {
     doWgRna(tdb, item);
     }
 else if (sameWord(table, "ncRna"))
     {
     doNcRna(tdb, item);
     }
 else if (sameWord(table, "gbProtAnn"))
     {
     doGbProtAnn(tdb, item);
     }
-else if (sameWord(table, "h1n1Gene"))
-    {
-    doH1n1Gene(tdb, item);
-    }
-else if (startsWith("h1n1_", table) || startsWith("h1n1b_", table))
-    {
-    doH1n1Seq(tdb, item);
-    }
 else if (sameWord(table, "bdgpGene") || sameWord(table, "bdgpNonCoding"))
     {
     doBDGPGene(tdb, item);
     }
 else if (sameWord(table, "flyBaseGene") || sameWord(table, "flyBaseNoncoding"))
     {
     doFlyBaseGene(tdb, item);
     }
 else if (sameWord(table, "bgiGene"))
     {
     doBGIGene(tdb, item);
     }
 else if (sameWord(table, "bgiSnp"))
     {
     doBGISnp(tdb, item);