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 8a15e5a..2a2ffd7 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 {
@@ -87,7 +88,6 @@ final class ControlPanel extends JPanel implements ActionListener {
     private JCheckBox            _show_node_names;
     private JCheckBox            _show_taxo_code;
     private JCheckBox            _write_confidence;
-    private JCheckBox            _write_confidence_sd;
     private JCheckBox            _show_events;
     private JCheckBox            _color_acc_species;
     private JCheckBox            _color_branches_cb;
@@ -125,6 +125,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     private int                  _subtree_cb_item;
     private int                  _color_subtree_cb_item;
     private int                  _open_seq_web_item;
+    private int                  _sort_descendents_item;
     private int                  _open_tax_web_item;
     private int                  _cut_subtree_item;
     private int                  _copy_subtree_item;
@@ -438,11 +439,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                 addJCheckBox( getWriteConfidenceCb(), ch_panel );
                 add( ch_panel );
                 break;
-            case Configuration.write_confidence_values_sd:
-                _write_confidence_sd = new JCheckBox( title );
-                addJCheckBox( getWriteConfidenceSDCb(), ch_panel );
-                add( ch_panel );
-                break;
             case Configuration.write_events:
                 _show_events = new JCheckBox( title );
                 addJCheckBox( getShowEventsCb(), ch_panel );
@@ -762,10 +758,6 @@ final class ControlPanel extends JPanel implements ActionListener {
         return _write_confidence;
     }
 
-    public JCheckBox getWriteConfidenceSDCb() {
-        return _write_confidence_sd;
-    }
-
     private void init() {
         _draw_phylogram = new ArrayList<Boolean>();
         setSpeciesColors( new HashMap<String, Color>() );
@@ -824,10 +816,6 @@ final class ControlPanel extends JPanel implements ActionListener {
         return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
     }
 
-    boolean isShowConfidenceSDValues() {
-        return ( ( getWriteConfidenceSDCb() != null ) && getWriteConfidenceSDCb().isSelected() );
-    }
-
     boolean isShowDomainArchitectures() {
         return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
     }
@@ -1054,11 +1042,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                     getWriteConfidenceCb().setSelected( state );
                 }
                 break;
-            case Configuration.write_confidence_values_sd:
-                if ( getWriteConfidenceSDCb() != null ) {
-                    getWriteConfidenceSDCb().setSelected( state );
-                }
-                break;
             case Configuration.write_events:
                 if ( getShowEventsCb() != null ) {
                     getShowEventsCb().setSelected( state );
@@ -1159,6 +1142,9 @@ final class ControlPanel extends JPanel implements ActionListener {
         else if ( action == _open_seq_web_item ) {
             setActionWhenNodeClicked( NodeClickAction.OPEN_SEQ_WEB );
         }
+        else if ( action == _sort_descendents_item ) {
+            setActionWhenNodeClicked( NodeClickAction.SORT_DESCENDENTS );
+        }
         else if ( action == _blast_item ) {
             if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
                 setActionWhenNodeClicked( NodeClickAction.BLAST );
@@ -1333,6 +1319,14 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             cb_index++;
         }
+        if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
+            _sort_descendents_item = cb_index;
+            addClickToOption( Configuration.sort_descendents, _configuration.getClickToTitle( Configuration.sort_descendents ) );
+            if ( default_option == Configuration.sort_descendents ) {
+                selected_index = cb_index;
+            }
+            cb_index++;
+        }
         if ( _configuration.doDisplayClickToOption( Configuration.color_subtree ) ) {
             _color_subtree_cb_item = cb_index;
             addClickToOption( Configuration.color_subtree, _configuration.getClickToTitle( Configuration.color_subtree ) );
@@ -1603,10 +1597,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                          _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
             setCheckbox( Configuration.write_confidence_values,
                          _configuration.doCheckOption( Configuration.write_confidence_values ) );
-            addCheckbox( Configuration.write_confidence_values_sd,
-                         _configuration.getDisplayTitle( Configuration.write_confidence_values_sd ) );
-            setCheckbox( Configuration.write_confidence_values_sd,
-                         _configuration.doCheckOption( Configuration.write_confidence_values_sd ) );
         }
         if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
             addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
@@ -1807,8 +1797,15 @@ 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();
         }
     }
@@ -1944,6 +1941,7 @@ final class ControlPanel extends JPanel implements ActionListener {
         PASTE_SUBTREE,
         ADD_NEW_NODE,
         EDIT_NODE_DATA,
+        SORT_DESCENDENTS,
         BLAST;
     }
 }