From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 19 Apr 2011 02:48:19 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4a4f1560c4784bfe8f84668997900dacb6cfa4c3;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index c01fb48..e1bcfb7 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -3344,6 +3344,17 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) {
                     x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " );
                 }
+                if ( getControlPanel().isShowGeneNames() ) {
+                    x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
+                }
+                if ( getControlPanel().isShowGeneSymbols() ) {
+                    x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
+                }
+                if ( getControlPanel().isShowSequenceAcc() ) {
+                    x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
+                            .toString()
+                            + " " );
+                }
                 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
                     x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
                 }
diff --git a/forester/java/src/org/forester/archaeopteryx/UniProtSequenceObtainer.java b/forester/java/src/org/forester/archaeopteryx/UniProtSequenceObtainer.java
index 4751335..fa5ae63 100644
--- a/forester/java/src/org/forester/archaeopteryx/UniProtSequenceObtainer.java
+++ b/forester/java/src/org/forester/archaeopteryx/UniProtSequenceObtainer.java
@@ -154,6 +154,12 @@ public class UniProtSequenceObtainer implements Runnable {
                 if ( query.indexOf( '/' ) > 0 ) {
                     query = query.substring( 0, query.indexOf( '/' ) );
                 }
+                if ( query.indexOf( '.' ) > 0 ) {
+                    query = query.substring( 0, query.indexOf( '.' ) );
+                }
+                if ( query.indexOf( '_' ) > 0 ) {
+                    query = query.substring( 0, query.indexOf( '_' ) );
+                }
                 final UniProtEntry upe = obtainUniProtEntry( query );
                 if ( upe != null ) {
                     final Sequence seq = new Sequence();