From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Mon, 25 Mar 2013 22:31:13 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2fe6ae39bef3f08ce521e2c16ff74bc651133bbd;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 533093c..92d1e75 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -2915,9 +2915,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
                         || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
                         || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
-                        .getNodeData().getTaxonomy().getIdentifier() != null )
-                        && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
-                        .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
+                        .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+                        .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
             return true;
         }
         else {
@@ -3294,6 +3293,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 e.printStackTrace();
             }
         }
+        else if ( ( tax.getIdentifier() != null )
+                && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+                && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
+                && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
+                        .equalsIgnoreCase( "uniprot" ) ) ) {
+            try {
+                uri_str = "http://www.uniprot.org/taxonomy/"
+                        + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
+            }
+            catch ( final UnsupportedEncodingException e ) {
+                AptxUtil.showErrorMessage( this, e.toString() );
+                e.printStackTrace();
+            }
+        }
         else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             try {
                 uri_str = "http://www.uniprot.org/taxonomy/?query="