in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / ControlPanel.java

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 5509327..27930ec 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -64,6 +64,7 @@ import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.SequenceRelation;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
 
 final class ControlPanel extends JPanel implements ActionListener {
@@ -275,10 +276,10 @@ final class ControlPanel extends JPanel implements ActionListener {
             tp.requestFocus();
         }
         catch ( final Exception ex ) {
-            Util.unexpectedException( ex );
+            AptxUtil.unexpectedException( ex );
         }
         catch ( final Error err ) {
-            Util.unexpectedError( err );
+            AptxUtil.unexpectedError( err );
         }
     }
 
@@ -330,7 +331,7 @@ final class ControlPanel extends JPanel implements ActionListener {
         _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+Up]" );
         _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+Left]" );
         _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+Down]" );
-        if ( getConfiguration().isUseNativeUI() && Util.isMac() ) {
+        if ( getConfiguration().isUseNativeUI() && AptxUtil.isMac() ) {
             _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
             _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );
         }
@@ -810,7 +811,7 @@ final class ControlPanel extends JPanel implements ActionListener {
         return ( ( _show_binary_characters != null ) && _show_binary_characters.isSelected() );
     }
 
-    boolean isShowBootstrapValues() {
+    boolean isShowConfidenceValues() {
         return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
     }
 
@@ -1784,8 +1785,15 @@ final class ControlPanel extends JPanel implements ActionListener {
     void uncollapseAll( final TreePanel tp ) {
         final Phylogeny t = tp.getPhylogeny();
         if ( ( t != null ) && !t.isEmpty() ) {
-            t.setAllNodesToNotCollapse();
+            for( final PhylogenyNodeIterator iter = t.iteratorPreorder(); iter.hasNext(); ) {
+                final PhylogenyNode node = iter.next();
+                node.setCollapse( false );
+            }
+            tp.resetNodeIdToDistToLeafMap();
+            tp.updateSetOfCollapsedExternalNodes( t );
             t.recalculateNumberOfExternalDescendants( false );
+            tp.setNodeInPreorderToNull();
+            t.hashIDs();
             showWhole();
         }
     }