From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 21 Aug 2014 19:34:38 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ab7f6b669b0e7e265ff84ff7539b83dab8a27f71;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 174ba35..d051dab 100644
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -2456,8 +2456,8 @@ final class ControlPanel extends JPanel implements ActionListener {
         COLOR_NODE_FONT;
     }
 
-    public boolean isShowSequences() {
+    public boolean isShowMolSequences() {
         // TODO Auto-generated method stub
-        return true;
+        return false;
     }
 }
diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 324153c..e8bbfea 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -656,6 +656,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     _longest_domain = d.getTotalLength();
                 }
             }
+            if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
+                    && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
+                    && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
+                // FIXME 
+                sum += 100;
+            }
             if ( sum >= max_length ) {
                 _longest_ext_node_info = max_length;
                 return;
@@ -4863,13 +4869,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 }
             }
         }
-        if ( getControlPanel().isShowSequences() && ( node.getNodeData().isHasSequence() )
+        if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
                 && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
                 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
             final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence()
                     .getMolecularSequence(), getConfiguration() );
             if ( rs != null ) {
-              
                 final int default_height = 7;
                 float y = getYdistance();
                 if ( getControlPanel().isDynamicallyHideData() ) {
@@ -4896,7 +4901,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                this,
                                to_pdf );
                 }
-               
             }
         }
     }