e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/hgGene/go.c src/hg/hgGene/go.c
index af2ffc2..8733071 100644
--- src/hg/hgGene/go.c
+++ src/hg/hgGene/go.c
@@ -1,108 +1,111 @@
 /* go - Gene Ontology annotations. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "spDb.h"
 #include "hgGene.h"
 #include "hdb.h"
 
 
 static boolean goExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if GO database exists and has something
  * on this one. */
 {
 char query[512];
 char *fbAcc = getFlyBaseId(conn, geneId);
 boolean useFbGo = (isFly() && fbAcc != NULL && sqlTableExists(conn, "fbGo"));
 if (!sqlDatabaseExists("go"))
     return(FALSE);
 if (useFbGo)
     {
     sqlSafef(query, sizeof(query),
 	  "select count(*) from fbGo where geneId = '%s'",
 	  fbAcc);
     return sqlQuickNum(conn, query) > 0;
     }
 else
     {
     if (swissProtAcc == NULL || !sqlTableExists(conn, "go.goaPart"))
 	return FALSE;
     sqlSafef(query, sizeof(query),
 	  "select count(*) from go.goaPart where dbObjectId = '%s'",
 	  swissProtAcc);
     return sqlQuickNum(conn, query) > 0;
     }
 }
 
 static void goPrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out GO annotations. */
 {
 struct sqlConnection *goConn = hAllocConn("go");
 char *fbAcc = getFlyBaseId(conn, geneId);
 boolean useFbGo = (isFly() && fbAcc != NULL && sqlTableExists(conn, "fbGo"));
 char *acc = useFbGo ? fbAcc : swissProtAcc;
 char query[512];
 struct sqlResult *sr;
 char **row;
 static char *aspects[3] = {"F", "P", "C"};
 static char *aspectNames[3] = {
     "Molecular Function",
     "Biological Process",
     "Cellular Component",
 };
 int aspectIx;
 
 for (aspectIx = 0; aspectIx < ArraySize(aspects); ++aspectIx)
     {
     boolean hasFirst = FALSE;
     if (useFbGo)
 	sqlSafef(query, sizeof(query),
 	      "select term.acc,term.name"
 	      " from %s.fbGo,term"
 	      " where %s.fbGo.geneId = '%s'"
 	      " and %s.fbGo.goId = term.acc"
 	      " and %s.fbGo.aspect = '%s'",
 	      database, database, acc, database, database, aspects[aspectIx]);
     else
 	sqlSafef(query, sizeof(query),
 	      "select term.acc,term.name"
 	      " from goaPart,term"
 	      " where goaPart.dbObjectId = '%s'"
 	      " and goaPart.goId = term.acc"
 	      " and goaPart.aspect = '%s'"
 	      , acc, aspects[aspectIx]);
     sr = sqlGetResult(goConn, query);
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	char *goID = row[0];
 	char *goTermName = row[1];
 	if (!hasFirst)
 	    {
 	    hPrintf("<B>%s:</B><BR>", aspectNames[aspectIx]);
 	    hasFirst = TRUE;
 	    }
         hPrintf("<A HREF = \"");
 	hPrintf("http://amigo1.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=%s", goID);
 	hPrintf("\" TARGET=_blank>%s</A> %s<BR>\n", goID, goTermName);
 	}
     if (hasFirst)
         hPrintf("<BR>");
     sqlFreeResult(&sr);
     }
 hFreeConn(&goConn);
 }
 
 struct section *goSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create GO annotations section. */
 {
 struct section *section = sectionNew(sectionRa, "go");
 section->exists = goExists;
 section->print = goPrint;
 return section;
 }