From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 27 Sep 2014 00:19:27 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bde0d624895cd4624ff14c3af21835ef97914902;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
index fa70bf3..d6b2aa8 100644
--- a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
+++ b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
@@ -53,6 +53,8 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
     public final static Pattern  PDB_PATTERN       = Pattern.compile( "PDB;\\s+([0-9A-Z]{4});\\s+([^;]+)" );
     public final static Pattern  PharmGKB_PATTERN  = Pattern.compile( "PharmGKB;\\s+([0-9A-Z]+);" );
     public final static Pattern  Reactome_PATTERN  = Pattern.compile( "Reactome;\\s+([0-9A-Z]+);\\s+([^\\.]+)" );
+    public final static Pattern  HGNC_PATTERN      = Pattern.compile( "HGNC;\\s+HGNC:(\\d+);" );
+    
     private String               _ac;
     private SortedSet<Accession> _cross_references;
     private String               _gene_name;
@@ -282,6 +284,12 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
                         e.addCrossReference( new Accession( m.group( 1 ), "Reactome", m.group( 2 ) ) );
                     }
                 }
+                else if ( line.indexOf( "HGNC;" ) > 0 ) {
+                    final Matcher m = HGNC_PATTERN.matcher( line );
+                    if ( m.find() ) {
+                        e.addCrossReference( new Accession( m.group( 1 ), "HGNC" ) );
+                    }
+                }
             }
             else if ( line.startsWith( "OS" ) ) {
                 if ( line.indexOf( "(" ) > 0 ) {