From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 25 Sep 2014 19:51:36 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3d2b4742a8c0f3c5e5abfc73139351b8aa6ec2dc;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 01adbb8..a885e3e 100644
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -251,6 +251,7 @@ final class ControlPanel extends JPanel implements ActionListener {
                     displayedPhylogenyMightHaveChanged( false );
                 }
                 else if ( e.getSource() == _show_whole ) {
+                    displayedPhylogenyMightHaveChanged( true );
                     showWhole();
                 }
                 else if ( e.getSource() == _return_to_super_tree ) {
@@ -275,7 +276,7 @@ final class ControlPanel extends JPanel implements ActionListener {
                     tp.getPhylogeny().recalculateNumberOfExternalDescendants( true );
                     tp.resetNodeIdToDistToLeafMap();
                     tp.setEdited( true );
-                    displayedPhylogenyMightHaveChanged( false );
+                    displayedPhylogenyMightHaveChanged( true );
                 }
                 else if ( e.getSource() == _uncollapse_all ) {
                     uncollapseAll( tp );
diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 611c354..387bba6 100644
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -480,7 +480,7 @@ final public class Options {
         _show_confidence_stddev = false;
         _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE;
         _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
-        _line_up_renderable_node_data = false;
+        _line_up_renderable_node_data = true;
         _right_align_domains = false;
     }