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/localization.c src/hg/hgGene/localization.c
index 0954126..01715ca 100644
--- src/hg/hgGene/localization.c
+++ src/hg/hgGene/localization.c
@@ -1,140 +1,143 @@
 /* localization - info/predictions from various sources about protein 
  * localization in cellular compartments */
 
+/* Copyright (C) 2013 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"
 
 
 
 static boolean localizationExists(struct section *section,
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if localization and existance tables exist and have something
  * on this one. */
 {
 char query[256];
 /* mitopred - prediction of nuclear-encoded mitochondrial proteins */
 if (swissProtAcc != NULL && sqlTableExists(conn, "mitopred"))
     {
     sqlSafef(query, sizeof(query),
 	  "select count(*) from mitopred where name = '%s' or name = '%s'",
 	  swissProtAcc, spAnyAccToId(spConn, swissProtAcc));
     if (sqlQuickNum(conn, query) > 0)
 	return TRUE;
     }
 /* SGD (Sacchromyces Genome Database) localization & abundance data */
 if (sqlTablesExist(conn, "sgdLocalization sgdAbundance"))
     {
     sqlSafef(query, sizeof(query),
 	  "select count(*) from sgdLocalization where name = '%s'", geneId);
     if (sqlQuickNum(conn, query) > 0)
 	return TRUE;
     sqlSafef(query, sizeof(query),
 	  "select count(*) from sgdAbundance where name = '%s'", geneId);
     if (sqlQuickNum(conn, query) > 0)
 	return TRUE;
     }
 return FALSE;
 }
 
 static void localizationPrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out localization and abundance links. */
 {
 char query[256], **row, *s = NULL;
 struct sqlResult *sr;
 boolean firstTime = TRUE;
 /* mitopred - prediction of nuclear-encoded mitochondrial proteins */
 if (swissProtAcc != NULL && sqlTableExists(conn, "mitopred"))
     {
     sqlSafef(query, sizeof(query), 
 	  "select confidence from mitopred where name = '%s' or name = '%s'",
 	  swissProtAcc, spAnyAccToId(spConn, swissProtAcc));
     sr = sqlGetResult(conn, query);
     firstTime = TRUE;
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	if (firstTime)
 	    {
 	    hPrintf("<B>Mitopred:</B> mitochondrion, confidence level: ");
 	    firstTime = FALSE;
 	    }
 	else
 	    {
 	    hPrintf(", ");
 	    }
 	hPrintf("%s", row[0]);
 	}
     sqlFreeResult(&sr);
     if (!firstTime)
 	{
 	hPrintf("<BR>");
 	hPrintf("Prediction of nuclear-encoded mitochondrial proteins from "
 	        "Guda et al., Bioinformatics. 2004 Jul 22;20(11):1785-94.<BR>"
 	        "For more information see "
 	        "<A HREF=\"http://mitopred.sdsc.edu/\" TARGET=_blank>"
 	        "http://mitopred.sdsc.edu/</A>.<P>");
 	}
     }
 /* SGD (Sacchromyces Genome Database) localization & abundance data */
 if (sqlTablesExist(conn, "sgdLocalization sgdAbundance"))
     {
     sqlSafef(query, sizeof(query), 
 	  "select value from sgdLocalization where name = '%s'", geneId);
     sr = sqlGetResult(conn, query);
     firstTime = TRUE;
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	if (firstTime)
 	    {
 	    hPrintf("<B>SGD Localization:</B> ");
 	    firstTime = FALSE;
 	    }
 	else
 	    {
 	    hPrintf(", ");
 	    }
 	hPrintf("%s", row[0]);
 	}
     sqlFreeResult(&sr);
     if (!firstTime)
 	{
 	hPrintf("<BR>");
 	}
 
     sqlSafef(query, sizeof(query), 
 	  "select abundance from sgdAbundance where name = '%s'", geneId);
     s = sqlQuickString(conn, query);
     if (s != NULL)
 	{
 	hPrintf("<B>SGD Abundance:</B> %s (range from 41 to 1590000)<BR>\n",
 		s);
 	freez(&s);
 	}
     hPrintf("Protein localization data from "
 	    "Huh et al. (2003), Nature 425:686-691<BR>"
 	    "Protein abundance data from "
 	    "Ghaemmaghami et al. (2003) Nature 425:737-741<BR>"
 	    "For more information see "
 	    "<A HREF=\"http://yeastgfp.yeastgenome.org\" TARGET=_blank>"
 	    "http://yeastgfp.yeastgenome.org</A>.");
     }
 }
 
 struct section *localizationSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create Localization section. */
 {
 struct section *section = sectionNew(sectionRa, "localization");
 if (section != NULL)
     {
     section->exists = localizationExists;
     section->print = localizationPrint;
     }
 return section;
 }