Edited wiki page RIO through web user interface.

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

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 2f3df26..924eae9 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -89,21 +89,30 @@ import javax.swing.JTextArea;
 import javax.swing.Popup;
 import javax.swing.PopupFactory;
 
 import javax.swing.Popup;
 import javax.swing.PopupFactory;
 

+import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON;

 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;

+import org.forester.archaeopteryx.tools.Blast;
+import org.forester.archaeopteryx.tools.ImageLoader;

 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;

+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;

 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.BranchColor;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Event;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.BranchColor;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Event;

+import org.forester.phylogeny.data.NodeData.NODE_DATA;
+import org.forester.phylogeny.data.NodeVisualization;
+import org.forester.phylogeny.data.NodeVisualization.NodeFill;
+import org.forester.phylogeny.data.NodeVisualization.NodeShape;

 import org.forester.phylogeny.data.PhylogenyData;
 import org.forester.phylogeny.data.PhylogenyData;

+import org.forester.phylogeny.data.PhylogenyDataUtil;

 import org.forester.phylogeny.data.PropertiesMap;
 import org.forester.phylogeny.data.Property;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.PropertiesMap;
 import org.forester.phylogeny.data.Property;
 import org.forester.phylogeny.data.Sequence;

@@ -116,6 +125,7 @@ import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
 import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
 import org.forester.util.DescriptiveStatistics;
 import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;

+import org.forester.util.SequenceIdParser;

 
 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
 
 
 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
 

@@ -134,15 +144,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private final static int                EURO_D                            = 10;
     private final static String             NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
     private final static int                MIN_ROOT_LENGTH                   = 3;
     private final static int                EURO_D                            = 10;
     private final static String             NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
     private final static int                MIN_ROOT_LENGTH                   = 3;

-    private final static int                BOX_SIZE                          = 4;
-    private final static int                HALF_BOX_SIZE                     = TreePanel.BOX_SIZE / 2;

     private final static int                MAX_SUBTREES                      = 100;
     private final static int                MAX_NODE_FRAMES                   = 10;
     private final static int                MOVE                              = 20;
     private final static NumberFormat       FORMATTER_CONFIDENCE;
     private final static NumberFormat       FORMATTER_BRANCH_LENGTH;
     private final static int                WIGGLE                            = 2;
     private final static int                MAX_SUBTREES                      = 100;
     private final static int                MAX_NODE_FRAMES                   = 10;
     private final static int                MOVE                              = 20;
     private final static NumberFormat       FORMATTER_CONFIDENCE;
     private final static NumberFormat       FORMATTER_BRANCH_LENGTH;
     private final static int                WIGGLE                            = 2;

-    private final static int                HALF_BOX_SIZE_PLUS_WIGGLE         = HALF_BOX_SIZE + WIGGLE;

     private final static int                LIMIT_FOR_HQ_RENDERING            = 1000;
     private final static int                CONFIDENCE_LEFT_MARGIN            = 4;
     // TODO "rendering_hints" was static before. Need to make sure everything is OK with it not
     private final static int                LIMIT_FOR_HQ_RENDERING            = 1000;
     private final static int                CONFIDENCE_LEFT_MARGIN            = 4;
     // TODO "rendering_hints" was static before. Need to make sure everything is OK with it not

@@ -204,11 +211,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     final private static double             _180_OVER_PI                      = 180.0 / Math.PI;
     private static final float              ROUNDED_D                         = 8;
     private int                             _circ_max_depth;
     final private static double             _180_OVER_PI                      = 180.0 / Math.PI;
     private static final float              ROUNDED_D                         = 8;
     private int                             _circ_max_depth;

-    private int                             _circ_num_ext_nodes;

     private PhylogenyNode                   _root;
     final private Arc2D                     _arc                              = new Arc2D.Double();
     final private HashMap<Integer, Double>  _urt_nodeid_angle_map             = new HashMap<Integer, Double>();
     final private HashMap<Integer, Integer> _urt_nodeid_index_map             = new HashMap<Integer, Integer>();
     private PhylogenyNode                   _root;
     final private Arc2D                     _arc                              = new Arc2D.Double();
     final private HashMap<Integer, Double>  _urt_nodeid_angle_map             = new HashMap<Integer, Double>();
     final private HashMap<Integer, Integer> _urt_nodeid_index_map             = new HashMap<Integer, Integer>();

+    final private Set<Integer>              _collapsed_external_nodeid_set    = new HashSet<Integer>();

     HashMap<Integer, Short>                 _nodeid_dist_to_leaf              = new HashMap<Integer, Short>();
     private AffineTransform                 _at;
     private double                          _max_distance_to_root             = -1;
     HashMap<Integer, Short>                 _nodeid_dist_to_leaf              = new HashMap<Integer, Short>();
     private AffineTransform                 _at;
     private double                          _max_distance_to_root             = -1;

@@ -216,12 +223,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private boolean                         _edited                           = false;
     private Popup                           _node_desc_popup;
     private JTextArea                       _rollover_popup;
     private boolean                         _edited                           = false;
     private Popup                           _node_desc_popup;
     private JTextArea                       _rollover_popup;

+    // private final int                       _box_size;
+    // private final int                       _half_box_size;

     //private final short                     _skip_counter                     = 0;
     private final StringBuffer              _popup_buffer                     = new StringBuffer();
     final private static Font               POPUP_FONT                        = new Font( Configuration.getDefaultFontFamilyName(),
                                                                                           Font.PLAIN,
                                                                                           12 );
     //private final short                     _skip_counter                     = 0;
     private final StringBuffer              _popup_buffer                     = new StringBuffer();
     final private static Font               POPUP_FONT                        = new Font( Configuration.getDefaultFontFamilyName(),
                                                                                           Font.PLAIN,
                                                                                           12 );

-    private static final boolean            DRAW_MEAN_COUNTS                  = true;                                                     //TODO remove me later

     private Sequence                        _query_sequence                   = null;
     private final FontRenderContext         _frc                              = new FontRenderContext( null,
                                                                                                        false,
     private Sequence                        _query_sequence                   = null;
     private final FontRenderContext         _frc                              = new FontRenderContext( null,
                                                                                                        false,

@@ -263,7 +271,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         _main_panel = tjp;
         _configuration = configuration;
         _phylogeny = t;
         _main_panel = tjp;
         _configuration = configuration;
         _phylogeny = t;

-        _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
+        _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );

         init();
         // if ( !_phylogeny.isEmpty() ) {
         _phylogeny.recalculateNumberOfExternalDescendants( true );
         init();
         // if ( !_phylogeny.isEmpty() ) {
         _phylogeny.recalculateNumberOfExternalDescendants( true );

@@ -339,11 +347,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
         }
     }
 

+    @Override

     final public void actionPerformed( final ActionEvent e ) {
     final public void actionPerformed( final ActionEvent e ) {

-        int index;

         boolean done = false;
         final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
         boolean done = false;
         final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();

-        for( index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
+        for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {

             // NOTE: index corresponds to the indices of click-to options
             // in the control panel.
             if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
             // NOTE: index corresponds to the indices of click-to options
             // in the control panel.
             if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {

@@ -364,7 +372,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             errorMessageNoCutCopyPasteInUnrootedDisplay();
             return;
         }
             errorMessageNoCutCopyPasteInUnrootedDisplay();
             return;
         }

-        final String label = getASimpleTextRepresentationOfANode( node );
+        final String label = createASimpleTextRepresentationOfANode( node );

         String msg = "";
         if ( ForesterUtil.isEmpty( label ) ) {
             msg = "How to add the new, empty node?";
         String msg = "";
         if ( ForesterUtil.isEmpty( label ) ) {
             msg = "How to add the new, empty node?";

@@ -404,8 +412,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else {
             phy.addAsChild( node );
         }
         else {
             phy.addAsChild( node );
         }

+        setNodeInPreorderToNull();

         _phylogeny.externalNodesHaveChanged();
         _phylogeny.externalNodesHaveChanged();

-        _phylogeny.hashIDs();
+        _phylogeny.clearHashIdToNodeMap();

         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         setEdited( true );
         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         setEdited( true );

@@ -440,43 +449,75 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
         }
     }
 

-    final void assignGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node, final Graphics g ) {
+    final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {

         if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
         if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {

-            g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+            return ( PhylogenyMethods.getBranchColorValue( node ) );

         }
         else {
         }
         else {

-            g.setColor( getTreeColorSet().getBranchColor() );
+            return ( getTreeColorSet().getBranchColor() );

         }
     }
 
     final private void blast( final PhylogenyNode node ) {
         if ( !isCanBlast( node ) ) {
             JOptionPane.showMessageDialog( this,
         }
     }
 
     final private void blast( final PhylogenyNode node ) {
         if ( !isCanBlast( node ) ) {
             JOptionPane.showMessageDialog( this,

-                                           "No sequence information present",
+                                           "Insufficient information present",

                                            "Cannot Blast",
                                            "Cannot Blast",

-                                           JOptionPane.WARNING_MESSAGE );
+                                           JOptionPane.INFORMATION_MESSAGE );

             return;
         }
             return;
         }

-        if ( node.getNodeData().isHasSequence() ) {
-            String name = "";
-            if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
-                name = node.getNodeData().getSequence().getName();
-            }
-            else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
-                name = node.getNodeData().getSequence().getSymbol();
-            }
-            else if ( node.getNodeData().getSequence().getAccession() != null ) {
-                name = node.getNodeData().getSequence().getAccession().getValue();
-            }
-            if ( !ForesterUtil.isEmpty( name ) ) {
+        else {
+            final String query = Blast.obtainQueryForBlast( node );
+            System.out.println( "query for BLAST is: " + query );
+            char type = '?';
+            if ( !ForesterUtil.isEmpty( query ) ) {
+                if ( node.getNodeData().isHasSequence() ) {
+                    if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
+                        if ( node.getNodeData().getSequence().getType().toLowerCase()
+                                .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
+                            type = 'p';
+                        }
+                        else {
+                            type = 'n';
+                        }
+                    }
+                    else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+                        if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+                            type = 'p';
+                        }
+                        else {
+                            type = 'n';
+                        }
+                    }
+                }
+                if ( type == '?' ) {
+                    if ( SequenceIdParser.isProtein( query ) ) {
+                        type = 'p';
+                    }
+                    else {
+                        type = 'n';
+                    }
+                }
+                JApplet applet = null;
+                if ( isApplet() ) {
+                    applet = obtainApplet();
+                }

                 try {
                 try {

-                    System.out.println( "trying: " + name );
-                    final Blast s = new Blast();
-                    s.go( name );
+                    Blast.openNcbiBlastWeb( query, type == 'n', applet, this );

                 }
                 catch ( final Exception e ) {
                     e.printStackTrace();
                 }
                 }
                 catch ( final Exception e ) {
                     e.printStackTrace();
                 }

+                if ( Constants.ALLOW_DDBJ_BLAST ) {
+                    try {
+                        System.out.println( "trying: " + query );
+                        final Blast s = new Blast();
+                        s.ddbjBlast( query );
+                    }
+                    catch ( final Exception e ) {
+                        e.printStackTrace();
+                    }
+                }

             }
         }
     }
             }
         }
     }

@@ -526,7 +567,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
             return;
         }
         if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
             return;
         }

-        int longest = 20;
+        int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
+                * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
+        if ( max_length < 40 ) {
+            max_length = 40;
+        }
+        int longest = 30;

         for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
             int sum = 0;
             if ( node.isCollapse() ) {
         for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
             int sum = 0;
             if ( node.isCollapse() ) {

@@ -556,6 +602,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                             .asSimpleText()
                             + " " );
                 }
                             .asSimpleText()
                             + " " );
                 }

+                if ( getControlPanel().isShowDomainArchitectures()
+                        && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
+                    sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
+                            .getRenderingSize().getWidth();
+                }

             }
             if ( node.getNodeData().isHasTaxonomy() ) {
                 final Taxonomy tax = node.getNodeData().getTaxonomy();
             }
             if ( node.getNodeData().isHasTaxonomy() ) {
                 final Taxonomy tax = node.getNodeData().getTaxonomy();

@@ -570,25 +621,23 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
                 }
             }
                     sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
                 }
             }

+            if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+                sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
+            }

             if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
                 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
                         .getGainedCharactersAsStringBuffer().toString() );
             }
             if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
                 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
                         .getGainedCharactersAsStringBuffer().toString() );
             }

-            if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
-                    && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
-                sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
-                        .getRenderingSize().getWidth();
-            }
-            if ( sum >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
-                setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
+            if ( sum >= max_length ) {
+                setLongestExtNodeInfo( max_length );

                 return;
             }
             if ( sum > longest ) {
                 longest = sum;
             }
         }
                 return;
             }
             if ( sum > longest ) {
                 longest = sum;
             }
         }

-        if ( longest >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
-            setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
+        if ( longest >= max_length ) {
+            setLongestExtNodeInfo( max_length );

         }
         else {
             setLongestExtNodeInfo( longest );
         }
         else {
             setLongestExtNodeInfo( longest );

@@ -656,7 +705,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         // Look in species hash
         Color c = getControlPanel().getSpeciesColors().get( species );
         if ( c == null ) {
         // Look in species hash
         Color c = getControlPanel().getSpeciesColors().get( species );
         if ( c == null ) {

-            c = Util.calculateColorFromString( species );
+            c = AptxUtil.calculateColorFromString( species );

             getControlPanel().getSpeciesColors().put( species, c );
         }
         return c;
             getControlPanel().getSpeciesColors().put( species, c );
         }
         return c;

@@ -685,10 +734,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         if ( !node.isExternal() && !node.isRoot() ) {
             final boolean collapse = !node.isCollapse();
         }
         if ( !node.isExternal() && !node.isRoot() ) {
             final boolean collapse = !node.isCollapse();

-            Util.collapseSubtree( node, collapse );
+            AptxUtil.collapseSubtree( node, collapse );
+            updateSetOfCollapsedExternalNodes();

             _phylogeny.recalculateNumberOfExternalDescendants( true );
             resetNodeIdToDistToLeafMap();
             calculateLongestExtNodeInfo();
             _phylogeny.recalculateNumberOfExternalDescendants( true );
             resetNodeIdToDistToLeafMap();
             calculateLongestExtNodeInfo();

+            setNodeInPreorderToNull();
+            _control_panel.displayedPhylogenyMightHaveChanged( true );

             resetPreferredSize();
             updateOvSizes();
             _main_panel.adjustJScrollPane();
             resetPreferredSize();
             updateOvSizes();
             _main_panel.adjustJScrollPane();

@@ -701,10 +753,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return;
         }
         setWaitCursor();
             return;
         }
         setWaitCursor();

-        Util.collapseSpeciesSpecificSubtrees( _phylogeny );
+        AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
+        updateSetOfCollapsedExternalNodes();

         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         calculateLongestExtNodeInfo();
         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         calculateLongestExtNodeInfo();

+        setNodeInPreorderToNull();

         resetPreferredSize();
         _main_panel.adjustJScrollPane();
         setArrowCursor();
         resetPreferredSize();
         _main_panel.adjustJScrollPane();
         setArrowCursor();

@@ -755,7 +809,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return;
         }
         setWaitCursor();
             return;
         }
         setWaitCursor();

-        Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
+        AptxUtil.removeBranchColors( _phylogeny );
+        AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );

         _control_panel.setColorBranches( true );
         if ( _control_panel.getColorBranchesCb() != null ) {
             _control_panel.getColorBranchesCb().setSelected( true );
         _control_panel.setColorBranches( true );
         if ( _control_panel.getColorBranchesCb() != null ) {
             _control_panel.getColorBranchesCb().setSelected( true );

@@ -764,11 +819,57 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         repaint();
     }
 
         repaint();
     }
 

+    final void colorRank( final String rank ) {
+        if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+            return;
+        }
+        setWaitCursor();
+        AptxUtil.removeBranchColors( _phylogeny );
+        final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+        if ( colorizations > 0 ) {
+            _control_panel.setColorBranches( true );
+            if ( _control_panel.getColorBranchesCb() != null ) {
+                _control_panel.getColorBranchesCb().setSelected( true );
+            }
+            if ( _control_panel.getColorAccSpeciesCb() != null ) {
+                _control_panel.getColorAccSpeciesCb().setSelected( false );
+            }
+            _options.setColorLabelsSameAsParentBranch( true );
+            _control_panel.repaint();
+        }
+        setArrowCursor();
+        repaint();
+        if ( colorizations > 0 ) {
+            String msg = "Taxonomy colorization via " + rank + " completed:\n";
+            if ( colorizations > 1 ) {
+                msg += "colorized " + colorizations + " subtrees";
+            }
+            else {
+                msg += "colorized one subtree";
+            }
+            JOptionPane.showMessageDialog( this,
+                                           msg,
+                                           "Taxonomy Colorization Completed (" + rank + ")",
+                                           JOptionPane.INFORMATION_MESSAGE );
+        }
+        else {
+            String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
+            msg += "Possible solutions (given that suitable taxonomic information is present):\n";
+            msg += "select a different rank (e.g. phylum, genus, ...)\n";
+            msg += "  and/or\n";
+            msg += "execute:\n";
+            msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
+            msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
+            JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
+        }
+    }
+

     final private void copySubtree( final PhylogenyNode node ) {
         if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
             errorMessageNoCutCopyPasteInUnrootedDisplay();
             return;
         }
     final private void copySubtree( final PhylogenyNode node ) {
         if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
             errorMessageNoCutCopyPasteInUnrootedDisplay();
             return;
         }

+        setNodeInPreorderToNull();

         setCutOrCopiedTree( _phylogeny.copy( node ) );
         final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
         final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
         setCutOrCopiedTree( _phylogeny.copy( node ) );
         final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
         final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );

@@ -792,7 +893,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                            JOptionPane.ERROR_MESSAGE );
             return;
         }
                                            JOptionPane.ERROR_MESSAGE );
             return;
         }

-        final String label = getASimpleTextRepresentationOfANode( node );
+        final String label = createASimpleTextRepresentationOfANode( node );

         final int r = JOptionPane.showConfirmDialog( null,
                                                      "Cut subtree" + label + "?",
                                                      "Confirm Cutting of Subtree",
         final int r = JOptionPane.showConfirmDialog( null,
                                                      "Cut subtree" + label + "?",
                                                      "Confirm Cutting of Subtree",

@@ -800,10 +901,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( r != JOptionPane.OK_OPTION ) {
             return;
         }
         if ( r != JOptionPane.OK_OPTION ) {
             return;
         }

+        setNodeInPreorderToNull();

         setCopiedAndPastedNodes( null );
         setCutOrCopiedTree( _phylogeny.copy( node ) );
         _phylogeny.deleteSubtree( node, true );
         setCopiedAndPastedNodes( null );
         setCutOrCopiedTree( _phylogeny.copy( node ) );
         _phylogeny.deleteSubtree( node, true );

-        _phylogeny.hashIDs();
+        _phylogeny.clearHashIdToNodeMap();

         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         setEdited( true );
         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         setEdited( true );

@@ -844,7 +946,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                            JOptionPane.ERROR_MESSAGE );
             return;
         }
                                            JOptionPane.ERROR_MESSAGE );
             return;
         }

-        final String label = getASimpleTextRepresentationOfANode( node );
+        final String label = createASimpleTextRepresentationOfANode( node );

         final Object[] options = { "Node only", "Entire subtree", "Cancel" };
         final int r = JOptionPane.showOptionDialog( this,
                                                     "Delete" + label + "?",
         final Object[] options = { "Node only", "Entire subtree", "Cancel" };
         final int r = JOptionPane.showOptionDialog( this,
                                                     "Delete" + label + "?",

@@ -854,6 +956,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                                     null,
                                                     options,
                                                     options[ 2 ] );
                                                     null,
                                                     options,
                                                     options[ 2 ] );

+        setNodeInPreorderToNull();

         boolean node_only = true;
         if ( r == 1 ) {
             node_only = false;
         boolean node_only = true;
         if ( r == 1 ) {
             node_only = false;

@@ -868,7 +971,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             _phylogeny.deleteSubtree( node, true );
         }
         _phylogeny.externalNodesHaveChanged();
             _phylogeny.deleteSubtree( node, true );
         }
         _phylogeny.externalNodesHaveChanged();

-        _phylogeny.hashIDs();
+        _phylogeny.clearHashIdToNodeMap();

         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         setEdited( true );
         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         setEdited( true );

@@ -932,6 +1035,52 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         g.fill( _rectangle );
     }
 
         g.fill( _rectangle );
     }
 

+    final private void drawRectGradient( final double x,
+                                         final double y,
+                                         final double width,
+                                         final double heigth,
+                                         final Graphics2D g,
+                                         final Color color_1,
+                                         final Color color_2,
+                                         final Color color_border ) {
+        _rectangle.setFrame( x, y, width, heigth );
+        g.setPaint( new GradientPaint( ( float ) x,
+                                       ( float ) y,
+                                       color_1,
+                                       ( float ) ( x + width ),
+                                       ( float ) ( y + heigth ),
+                                       color_2,
+                                       false ) );
+        g.fill( _rectangle );
+        if ( color_border != null ) {
+            g.setPaint( color_border );
+            g.draw( _rectangle );
+        }
+    }
+
+    final private void drawOvalGradient( final double x,
+                                         final double y,
+                                         final double width,
+                                         final double heigth,
+                                         final Graphics2D g,
+                                         final Color color_1,
+                                         final Color color_2,
+                                         final Color color_border ) {
+        _ellipse.setFrame( x, y, width, heigth );
+        g.setPaint( new GradientPaint( ( float ) x,
+                                       ( float ) y,
+                                       color_1,
+                                       ( float ) ( x + width ),
+                                       ( float ) ( y + heigth ),
+                                       color_2,
+                                       false ) );
+        g.fill( _ellipse );
+        if ( color_border != null ) {
+            g.setPaint( color_border );
+            g.draw( _ellipse );
+        }
+    }
+

     final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
         JOptionPane.showMessageDialog( this,
                                        "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
     final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
         JOptionPane.showMessageDialog( this,
                                        "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",

@@ -950,20 +1099,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
             return null;
         }
         if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
             return null;
         }

+        final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;

         for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
         for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )

-                    && ( ( node.getXcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= x )
-                    && ( ( node.getXcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= x )
-                    && ( ( node.getYcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= y )
-                    && ( ( node.getYcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= y ) ) {
+                    && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
+                    && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
+                    && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
+                    && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {

                 return node;
             }
         }
         return null;
     }
 
                 return node;
             }
         }
         return null;
     }
 

-    final private String getASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
+    final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {

         final String tax = PhylogenyMethods.getSpecies( node );
         String label = node.getName();
         if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
         final String tax = PhylogenyMethods.getSpecies( node );
         String label = node.getName();
         if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {

@@ -1091,7 +1241,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
      * 
      * @return a pointer to the phylogeny
      */
      * 
      * @return a pointer to the phylogeny
      */

-    final Phylogeny getPhylogeny() {
+    public final Phylogeny getPhylogeny() {

         return _phylogeny;
     }
 
         return _phylogeny;
     }
 

@@ -1207,11 +1357,133 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             case EDIT_NODE_DATA:
                 showNodeEditFrame( node );
                 break;
             case EDIT_NODE_DATA:
                 showNodeEditFrame( node );
                 break;

+            case SORT_DESCENDENTS:
+                sortDescendants( node );
+                break;
+            case GET_EXT_DESC_DATA:
+                showExtDescNodeData( node );
+                break;

             default:
                 throw new IllegalArgumentException( "unknown action: " + action );
         }
     }
 
             default:
                 throw new IllegalArgumentException( "unknown action: " + action );
         }
     }
 

+    private void showExtDescNodeData( final PhylogenyNode node ) {
+        final List<String> data = new ArrayList<String>();
+        for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
+            switch ( getOptions().getExtDescNodeDataToReturn() ) {
+                case NODE_NAME:
+                    if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+                        data.add( n.getName() );
+                    }
+                    break;
+                case SEQUENCE_NAME:
+                    if ( n.getNodeData().isHasSequence()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
+                        data.add( n.getNodeData().getSequence().getName() );
+                    }
+                    break;
+                case SEQUENCE_SYMBOL:
+                    if ( n.getNodeData().isHasSequence()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+                        data.add( n.getNodeData().getSequence().getSymbol() );
+                    }
+                    break;
+                case SEQUENCE_MOL_SEQ:
+                    if ( n.getNodeData().isHasSequence()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+                        data.add( n.getNodeData().getSequence().getMolecularSequence() );
+                    }
+                    break;
+                case SEQUENCE_ACC:
+                    if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
+                            && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
+                        data.add( n.getNodeData().getSequence().getAccession().toString() );
+                    }
+                    break;
+                case TAXONOMY_SCIENTIFIC_NAME:
+                    if ( n.getNodeData().isHasTaxonomy()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                        data.add( n.getNodeData().getTaxonomy().getScientificName() );
+                    }
+                    break;
+                case TAXONOMY_CODE:
+                    if ( n.getNodeData().isHasTaxonomy()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+                        data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+                    }
+                    break;
+                case UNKNOWN:
+                    AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
+                    break;
+                default:
+                    throw new IllegalArgumentException( "unknown data element: "
+                            + getOptions().getExtDescNodeDataToReturn() );
+            }
+        } // for loop
+        if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
+            for( final String d : data ) {
+                if ( !ForesterUtil.isEmpty( d ) ) {
+                    System.out.println( d );
+                }
+            }
+        }
+        else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
+            final StringBuilder sb = new StringBuilder();
+            for( final String d : data ) {
+                if ( !ForesterUtil.isEmpty( d ) ) {
+                    sb.append( d );
+                    sb.append( "\n" );
+                }
+            }
+            if ( sb.length() < 1 ) {
+                AptxUtil.showInformationMessage( this,
+                                                 "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
+                                                 "Descendants of selected node do not contain selected data" );
+            }
+            else {
+                final String title = "External Descendants "
+                        + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
+                                : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
+                        + node.getNumberOfExternalNodes() + ") For Node " + node;
+                if ( getMainPanel().getMainFrame() == null ) {
+                    // Must be "E" applet version.
+                    final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
+                    final String s = sb.toString().trim();
+                    ae.showTextFrame( s, title );
+                    ae.setCurrentExternalNodesDataBuffer( s );
+                }
+                else {
+                    getMainPanel().getMainFrame().showTextFrame( sb.toString(), title );
+                }
+            }
+        }
+    }
+
+    private final String obtainTitleForExtDescNodeData() {
+        switch ( getOptions().getExtDescNodeDataToReturn() ) {
+            case NODE_NAME:
+                return "Node Names";
+            case SEQUENCE_NAME:
+                return "Sequence Names";
+            case SEQUENCE_SYMBOL:
+                return "Sequence Symbols";
+            case SEQUENCE_MOL_SEQ:
+                return "Molecular Sequences";
+            case SEQUENCE_ACC:
+                return "Sequence Accessors";
+            case TAXONOMY_SCIENTIFIC_NAME:
+                return "Scientific Names";
+            case TAXONOMY_CODE:
+                return "Taxonomy Codes";
+            case UNKNOWN:
+                return "User Selected Data";
+            default:
+                throw new IllegalArgumentException( "unknown data element: "
+                        + getOptions().getExtDescNodeDataToReturn() );
+        }
+    }
+

     final void increaseDomainStructureEvalueThreshold() {
         if ( _domain_structure_e_value_thr_exp < 3 ) {
             _domain_structure_e_value_thr_exp += 1;
     final void increaseDomainStructureEvalueThreshold() {
         if ( _domain_structure_e_value_thr_exp < 3 ) {
             _domain_structure_e_value_thr_exp += 1;

@@ -1219,9 +1491,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final private void increaseOvSize() {
     }
 
     final private void increaseOvSize() {

-        if ( ( getOvMaxWidth() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 )
-                && ( getOvMaxHeight() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
-                        .getHeight() / 2 ) ) {
+        if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) )
+                && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
+                        .getHeight() / 2 ) ) ) {

             setOvMaxWidth( getOvMaxWidth() + 5 );
             setOvMaxHeight( getOvMaxHeight() + 5 );
             updateOvSettings();
             setOvMaxWidth( getOvMaxWidth() + 5 );
             setOvMaxHeight( getOvMaxHeight() + 5 );
             updateOvSettings();

@@ -1234,7 +1506,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return;
         }
         setWaitCursor();
             return;
         }
         setWaitCursor();

-        Util.inferCommonPartOfScientificNames( _phylogeny );
+        AptxUtil.inferCommonPartOfScientificNames( _phylogeny );

         setArrowCursor();
         repaint();
     }
         setArrowCursor();
         repaint();
     }

@@ -1248,7 +1520,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         setTreeFile( null );
         setEdited( false );
         initializeOvSettings();
         setTreeFile( null );
         setEdited( false );
         initializeOvSettings();

-        setStartingAngle( TWO_PI * 3 / 4 );
+        setStartingAngle( ( TWO_PI * 3 ) / 4 );

         final ImageLoader il = new ImageLoader( this );
         new Thread( il ).start();
     }
         final ImageLoader il = new ImageLoader( this );
         new Thread( il ).start();
     }

@@ -1298,24 +1570,24 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final boolean inOv( final MouseEvent e ) {
     }
 
     final boolean inOv( final MouseEvent e ) {

-        return ( ( e.getX() > getVisibleRect().x + getOvXPosition() + 1 )
-                && ( e.getX() < getVisibleRect().x + getOvXPosition() + getOvMaxWidth() - 1 )
-                && ( e.getY() > getVisibleRect().y + getOvYPosition() + 1 ) && ( e.getY() < getVisibleRect().y
-                + getOvYPosition() + getOvMaxHeight() - 1 ) );
+        return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
+                && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
+                && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
+                + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );

     }
 
     final boolean inOvRectangle( final MouseEvent e ) {
     }
 
     final boolean inOvRectangle( final MouseEvent e ) {

-        return ( ( e.getX() >= getOvRectangle().getX() - 1 )
-                && ( e.getX() <= getOvRectangle().getX() + getOvRectangle().getWidth() + 1 )
-                && ( e.getY() >= getOvRectangle().getY() - 1 ) && ( e.getY() <= getOvRectangle().getY()
-                + getOvRectangle().getHeight() + 1 ) );
+        return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
+                && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
+                && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
+                + getOvRectangle().getHeight() + 1 ) ) );

     }
 
     final private boolean inOvVirtualRectangle( final int x, final int y ) {
     }
 
     final private boolean inOvVirtualRectangle( final int x, final int y ) {

-        return ( ( x >= getOvVirtualRectangle().x - 1 )
-                && ( x <= getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 )
-                && ( y >= getOvVirtualRectangle().y - 1 ) && ( y <= getOvVirtualRectangle().y
-                + getOvVirtualRectangle().height + 1 ) );
+        return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
+                && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
+                && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
+                + getOvVirtualRectangle().height + 1 ) ) );

     }
 
     final private boolean inOvVirtualRectangle( final MouseEvent e ) {
     }
 
     final private boolean inOvVirtualRectangle( final MouseEvent e ) {

@@ -1327,10 +1599,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final private boolean isCanBlast( final PhylogenyNode node ) {
     }
 
     final private boolean isCanBlast( final PhylogenyNode node ) {

-        return ( node.getNodeData().isHasSequence() && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil
-                .isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) )
-                || !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil.isEmpty( node
-                .getNodeData().getSequence().getSymbol() ) ) );
+        if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
+            return false;
+        }
+        return Blast.isContainsQueryForBlast( node );

     }
 
     final boolean isCanCollapse() {
     }
 
     final boolean isCanCollapse() {

@@ -1420,16 +1692,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( getControlPanel().isShowTaxonomyImages() ) {
             y_dist = 40 + ( int ) getYdistance();
         }
         if ( getControlPanel().isShowTaxonomyImages() ) {
             y_dist = 40 + ( int ) getYdistance();
         }

-        return ( ( node.getYcoord() < getVisibleRect().getMinY() - y_dist )
-                || ( node.getYcoord() > getVisibleRect().getMaxY() + y_dist ) || ( ( node.getParent() != null ) && ( node
+        return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
+                || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node

                 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
     }
 
     final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
                 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
     }
 
     final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {

-        return ( ( node.getYcoord() < getVisibleRect().getMinY() - 20 )
-                || ( node.getYcoord() > getVisibleRect().getMaxY() + 20 )
-                || ( node.getXcoord() < getVisibleRect().getMinX() - 20 ) || ( node.getXcoord() > getVisibleRect()
-                .getMaxX() + 20 ) );
+        return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
+                || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
+                || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
+                .getMaxX() + 20 ) ) );

     }
 
     final private boolean isNonLinedUpCladogram() {
     }
 
     final private boolean isNonLinedUpCladogram() {

@@ -1629,9 +1901,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
                 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {

-                if ( Constants.__RELEASE || Constants.__SNAPSHOT_RELEASE ) {
-                    continue;
-                }

                 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
                 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {

@@ -1672,7 +1941,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
                 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {

-                _node_popup_menu_items[ i ].setEnabled( isCanCollapse() );
+                _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );

             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
                 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
                 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );

@@ -1680,6 +1949,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
                 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
                 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
             }

+            else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
+                _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
+            }
+            else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
+                _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
+            }

             _node_popup_menu_items[ i ].addActionListener( this );
             _node_popup_menu.add( _node_popup_menu_items[ i ] );
         }
             _node_popup_menu_items[ i ].addActionListener( this );
             _node_popup_menu.add( _node_popup_menu_items[ i ] );
         }

@@ -1696,6 +1971,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                            JOptionPane.WARNING_MESSAGE );
             return;
         }
                                            JOptionPane.WARNING_MESSAGE );
             return;
         }

+        setNodeInPreorderToNull();

         setWaitCursor();
         PhylogenyMethods.midpointRoot( _phylogeny );
         resetNodeIdToDistToLeafMap();
         setWaitCursor();
         PhylogenyMethods.midpointRoot( _phylogeny );
         resetNodeIdToDistToLeafMap();

@@ -1707,9 +1983,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
             final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
             final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
         if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
             final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
             final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();

-            double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - getOvRectangle().getWidth() / 2.0 )
+            double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )

                     * w_ratio;
                     * w_ratio;

-            double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - getOvRectangle().getHeight() / 2.0 )
+            double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )

                     * h_ratio;
             if ( x < 0 ) {
                 x = 0;
                     * h_ratio;
             if ( x < 0 ) {
                 x = 0;

@@ -1806,8 +2082,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
         final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
         final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
         final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
         final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
         final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();

-        double dx = ( w_ratio * e.getX() - w_ratio * getLastDragPointX() );
-        double dy = ( h_ratio * e.getY() - h_ratio * getLastDragPointY() );
+        double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
+        double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );

         scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
         scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
         if ( scroll_position.x <= 0 ) {
         scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
         scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
         if ( scroll_position.x <= 0 ) {

@@ -1899,6 +2175,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         setCursor( ARROW_CURSOR );
     }
 
         setCursor( ARROW_CURSOR );
     }
 

+    @Override

     final public void mouseWheelMoved( final MouseWheelEvent e ) {
         final int notches = e.getWheelRotation();
         if ( inOvVirtualRectangle( e ) ) {
     final public void mouseWheelMoved( final MouseWheelEvent e ) {
         final int notches = e.getWheelRotation();
         if ( inOvVirtualRectangle( e ) ) {

@@ -2008,7 +2285,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
         }
         catch ( final UnsupportedEncodingException e ) {
             uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
         }
         catch ( final UnsupportedEncodingException e ) {

-            Util.showErrorMessage( this, e.toString() );
+            AptxUtil.showErrorMessage( this, e.toString() );

             e.printStackTrace();
         }
         if ( !ForesterUtil.isEmpty( uri_str ) ) {
             e.printStackTrace();
         }
         if ( !ForesterUtil.isEmpty( uri_str ) ) {

@@ -2017,14 +2294,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 if ( isApplet() ) {
                     applet = obtainApplet();
                 }
                 if ( isApplet() ) {
                     applet = obtainApplet();
                 }

-                Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
+                AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );

             }
             catch ( final IOException e ) {
             }
             catch ( final IOException e ) {

-                Util.showErrorMessage( this, e.toString() );
+                AptxUtil.showErrorMessage( this, e.toString() );

                 e.printStackTrace();
             }
             catch ( final URISyntaxException e ) {
                 e.printStackTrace();
             }
             catch ( final URISyntaxException e ) {

-                Util.showErrorMessage( this, e.toString() );
+                AptxUtil.showErrorMessage( this, e.toString() );

                 e.printStackTrace();
             }
         }
                 e.printStackTrace();
             }
         }

@@ -2048,7 +2325,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {
                 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {

-                Util.showErrorMessage( this, e.toString() );
+                AptxUtil.showErrorMessage( this, e.toString() );

                 e.printStackTrace();
             }
         }
                 e.printStackTrace();
             }
         }

@@ -2058,7 +2335,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
             }
             catch ( final URISyntaxException e ) {
                 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
             }
             catch ( final URISyntaxException e ) {

-                Util.showErrorMessage( this, e.toString() );
+                AptxUtil.showErrorMessage( this, e.toString() );

                 uri_str = null;
                 e.printStackTrace();
             }
                 uri_str = null;
                 e.printStackTrace();
             }

@@ -2069,7 +2346,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {
                         + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {

-                Util.showErrorMessage( this, e.toString() );
+                AptxUtil.showErrorMessage( this, e.toString() );

                 e.printStackTrace();
             }
         }
                 e.printStackTrace();
             }
         }

@@ -2079,7 +2356,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {
                         + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {

-                Util.showErrorMessage( this, e.toString() );
+                AptxUtil.showErrorMessage( this, e.toString() );

                 e.printStackTrace();
             }
         }
                 e.printStackTrace();
             }
         }

@@ -2089,7 +2366,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {
                         + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {

-                Util.showErrorMessage( this, e.toString() );
+                AptxUtil.showErrorMessage( this, e.toString() );

                 e.printStackTrace();
             }
         }
                 e.printStackTrace();
             }
         }

@@ -2099,14 +2376,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 if ( isApplet() ) {
                     applet = obtainApplet();
                 }
                 if ( isApplet() ) {
                     applet = obtainApplet();
                 }

-                Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
+                AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );

             }
             catch ( final IOException e ) {
             }
             catch ( final IOException e ) {

-                Util.showErrorMessage( this, e.toString() );
+                AptxUtil.showErrorMessage( this, e.toString() );

                 e.printStackTrace();
             }
             catch ( final URISyntaxException e ) {
                 e.printStackTrace();
             }
             catch ( final URISyntaxException e ) {

-                Util.showErrorMessage( this, e.toString() );
+                AptxUtil.showErrorMessage( this, e.toString() );

                 e.printStackTrace();
             }
         }
                 e.printStackTrace();
             }
         }

@@ -2126,7 +2403,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         final double root_y = _root.getYcoord();
         final double dx = root_x - p.getXcoord();
         final double dy = root_y - p.getYcoord();
         final double root_y = _root.getYcoord();
         final double dx = root_x - p.getXcoord();
         final double dy = root_y - p.getYcoord();

-        final double parent_radius = Math.sqrt( dx * dx + dy * dy );
+        final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );

         final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
         assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
         if ( ( c.isFirstChildNode() || c.isLastChildNode() )
         final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
         assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
         if ( ( c.isFirstChildNode() || c.isLastChildNode() )

@@ -2143,7 +2420,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( c.isExternal() ) {
             final boolean is_in_found_nodes = isInFoundNodes( c );
             if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
         if ( c.isExternal() ) {
             final boolean is_in_found_nodes = isInFoundNodes( c );
             if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes

-                    && ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor != 1 ) ) {
+                    && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {

                 return;
             }
             paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
                 return;
             }
             paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );

@@ -2157,7 +2434,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         final double dx = root_x - p.getXSecondary();
         final double dy = root_y - p.getYSecondary();
         final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
         final double dx = root_x - p.getXSecondary();
         final double dy = root_y - p.getYSecondary();
         final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;

-        final double parent_radius = Math.sqrt( dx * dx + dy * dy );
+        final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );

         g.setColor( getTreeColorSet().getOvColor() );
         if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
             final double r2 = 2.0 * parent_radius;
         g.setColor( getTreeColorSet().getOvColor() );
         if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
             final double r2 = 2.0 * parent_radius;

@@ -2245,7 +2522,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     final private void paintBranchRectangular( final Graphics2D g,
                                                final float x1,
                                                final float x2,
     final private void paintBranchRectangular( final Graphics2D g,
                                                final float x1,
                                                final float x2,

-                                               float y1,
+                                               final float y1,

                                                final float y2,
                                                final PhylogenyNode node,
                                                final boolean to_pdf,
                                                final float y2,
                                                final PhylogenyNode node,
                                                final boolean to_pdf,

@@ -2266,131 +2543,87 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             g.draw( _cubic_curve );
         }
         else {
             g.draw( _cubic_curve );
         }
         else {

-            float x2a = x2;
-            float x1a = x1;
-            // draw the vertical line
-            boolean draw_horizontal = true;
+            final float x2a = x2;
+            final float x1a = x1;

             float y2_r = 0;
             if ( node.isFirstChildNode() || node.isLastChildNode()
                     || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
                     || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
             float y2_r = 0;
             if ( node.isFirstChildNode() || node.isLastChildNode()
                     || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
                     || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {

-                boolean draw_vertical = true;
-                final PhylogenyNode parent = node.getParent();
-                if ( ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file ) || ( ( getControlPanel()
-                        .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) )
-                        && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) )
-                        && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent
-                                .isDuplication() ) ) {
-                    if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
-                            && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
-                        if ( Math.abs( y2 - y1 ) <= TreePanel.HALF_BOX_SIZE ) {
-                            draw_vertical = false;
-                        }
-                        else {
-                            if ( y1 < y2 ) {
-                                y1 += TreePanel.HALF_BOX_SIZE;
-                            }
-                            else {
-                                if ( !to_pdf ) {
-                                    y1 -= TreePanel.HALF_BOX_SIZE + 1;
-                                }
-                                else {
-                                    y1 -= TreePanel.HALF_BOX_SIZE;
-                                }
-                            }
-                        }
-                    }
-                    if ( ( x2 - x1 ) <= TreePanel.HALF_BOX_SIZE ) {
-                        draw_horizontal = false;
-                    }
-                    else if ( !draw_vertical ) {
-                        x1a += TreePanel.HALF_BOX_SIZE;
-                    }
-                    if ( ( ( x2 - x1a ) > TreePanel.HALF_BOX_SIZE )
-                            && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node
-                                    .isDuplication() ) ) {
-                        x2a -= TreePanel.HALF_BOX_SIZE;
-                    }
+                if ( !to_graphics_file
+                        && !to_pdf
+                        && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect()
+                                .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
+                    // Do nothing.

                 }
                 }

-                if ( draw_vertical ) {
-                    if ( !to_graphics_file
-                            && !to_pdf
-                            && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
-                                    .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
-                        // Do nothing.
-                    }
-                    else {
-                        if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
-                            float x2c = x1 + EURO_D;
-                            if ( x2c > x2a ) {
-                                x2c = x2a;
-                            }
-                            drawLine( x1, y1, x2c, y2, g );
+                else {
+                    if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+                        float x2c = x1 + EURO_D;
+                        if ( x2c > x2a ) {
+                            x2c = x2a;

                         }
                         }

-                        else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
-                            if ( y2 > y1 ) {
-                                y2_r = y2 - ROUNDED_D;
-                                if ( y2_r < y1 ) {
-                                    y2_r = y1;
-                                }
-                                drawLine( x1, y1, x1, y2_r, g );
-                            }
-                            else {
-                                y2_r = y2 + ROUNDED_D;
-                                if ( y2_r > y1 ) {
-                                    y2_r = y1;
-                                }
-                                drawLine( x1, y1, x1, y2_r, g );
+                        drawLine( x1, y1, x2c, y2, g );
+                    }
+                    else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+                        if ( y2 > y1 ) {
+                            y2_r = y2 - ROUNDED_D;
+                            if ( y2_r < y1 ) {
+                                y2_r = y1;

                             }
                             }

+                            drawLine( x1, y1, x1, y2_r, g );

                         }
                         else {
                         }
                         else {

-                            drawLine( x1, y1, x1, y2, g );
+                            y2_r = y2 + ROUNDED_D;
+                            if ( y2_r > y1 ) {
+                                y2_r = y1;
+                            }
+                            drawLine( x1, y1, x1, y2_r, g );

                         }
                     }
                         }
                     }

+                    else {
+                        drawLine( x1, y1, x1, y2, g );
+                    }

                 }
             }
             // draw the horizontal line
             if ( !to_graphics_file && !to_pdf
                 }
             }
             // draw the horizontal line
             if ( !to_graphics_file && !to_pdf

-                    && ( ( y2 < getVisibleRect().getMinY() - 20 ) || ( y2 > getVisibleRect().getMaxY() + 20 ) ) ) {
+                    && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {

                 return;
             }
             float x1_r = 0;
                 return;
             }
             float x1_r = 0;

-            if ( draw_horizontal ) {
-                if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
-                    if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
-                        x1_r = x1a + ROUNDED_D;
-                        if ( x1_r < x2a ) {
-                            drawLine( x1_r, y2, x2a, y2, g );
-                        }
-                    }
-                    else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
-                        final float x1c = x1a + EURO_D;
-                        if ( x1c < x2a ) {
-                            drawLine( x1c, y2, x2a, y2, g );
-                        }
+            if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
+                if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+                    x1_r = x1a + ROUNDED_D;
+                    if ( x1_r < x2a ) {
+                        drawLine( x1_r, y2, x2a, y2, g );

                     }
                     }

-                    else {
-                        drawLine( x1a, y2, x2a, y2, g );
+                }
+                else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+                    final float x1c = x1a + EURO_D;
+                    if ( x1c < x2a ) {
+                        drawLine( x1c, y2, x2a, y2, g );

                     }
                 }
                 else {
                     }
                 }
                 else {

-                    final double w = PhylogenyMethods.getBranchWidthValue( node );
-                    if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
-                        x1_r = x1a + ROUNDED_D;
-                        if ( x1_r < x2a ) {
-                            drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
-                        }
-                    }
-                    else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
-                        final float x1c = x1a + EURO_D;
-                        if ( x1c < x2a ) {
-                            drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
-                        }
+                    drawLine( x1a, y2, x2a, y2, g );
+                }
+            }
+            else {
+                final double w = PhylogenyMethods.getBranchWidthValue( node );
+                if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+                    x1_r = x1a + ROUNDED_D;
+                    if ( x1_r < x2a ) {
+                        drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );

                     }
                     }

-                    else {
-                        drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+                }
+                else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+                    final float x1c = x1a + EURO_D;
+                    if ( x1c < x2a ) {
+                        drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );

                     }
                 }
                     }
                 }

+                else {
+                    drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+                }

             }
             if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
                 if ( x1_r > x2a ) {
             }
             if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
                 if ( x1_r > x2a ) {

@@ -2406,7 +2639,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 g.draw( _arc );
             }
         }
                 g.draw( _arc );
             }
         }

-        paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
+        if ( node.isExternal() ) {
+            paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
+        }

     }
 
     final void paintCircular( final Phylogeny phy,
     }
 
     final void paintCircular( final Phylogeny phy,

@@ -2417,23 +2652,49 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                               final Graphics2D g,
                               final boolean to_pdf,
                               final boolean to_graphics_file ) {
                               final Graphics2D g,
                               final boolean to_pdf,
                               final boolean to_graphics_file ) {

-        _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
+        final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
+        System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );

         _root = phy.getRoot();
         _root.setXcoord( center_x );
         _root.setYcoord( center_y );
         _root = phy.getRoot();
         _root.setXcoord( center_x );
         _root.setYcoord( center_y );

-        paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );

         final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
         double current_angle = starting_angle;
         int i = 0;
         for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
         final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
         double current_angle = starting_angle;
         int i = 0;
         for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();

-            n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
-            n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
-            _urt_nodeid_angle_map.put( n.getId(), current_angle );
-            _urt_nodeid_index_map.put( n.getId(), i++ );
-            current_angle += ( TWO_PI / _circ_num_ext_nodes );
+            if ( !n.isCollapse() ) {
+                n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
+                n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
+                _urt_nodeid_angle_map.put( n.getId(), current_angle );
+                _urt_nodeid_index_map.put( n.getId(), i++ );
+                current_angle += ( TWO_PI / circ_num_ext_nodes );
+            }
+            else {
+                //TODO remove me
+                System.out.println( "is collapse" + n.getName() );
+            }

         }
         paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
         }
         paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );

+        paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
+    }
+
+    void updateSetOfCollapsedExternalNodes() {
+        final Phylogeny phy = getPhylogeny();
+        _collapsed_external_nodeid_set.clear();
+        if ( phy != null ) {
+            E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+                final PhylogenyNode ext_node = it.next();
+                PhylogenyNode n = ext_node;
+                while ( !n.isRoot() ) {
+                    if ( n.isCollapse() ) {
+                        _collapsed_external_nodeid_set.add( ext_node.getId() );
+                        ext_node.setCollapse( true );
+                        continue E;
+                    }
+                    n = n.getParent();
+                }
+            }
+        }

     }
 
     final void paintCircularLite( final Phylogeny phy,
     }
 
     final void paintCircularLite( final Phylogeny phy,

@@ -2442,17 +2703,17 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                   final int center_y,
                                   final int radius,
                                   final Graphics2D g ) {
                                   final int center_y,
                                   final int radius,
                                   final Graphics2D g ) {

-        _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
+        final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();

         _root = phy.getRoot();
         _root.setXSecondary( center_x );
         _root.setYSecondary( center_y );
         double current_angle = starting_angle;
         for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
         _root = phy.getRoot();
         _root.setXSecondary( center_x );
         _root.setYSecondary( center_y );
         double current_angle = starting_angle;
         for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();

-            n.setXSecondary( ( float ) ( center_x + radius * Math.cos( current_angle ) ) );
-            n.setYSecondary( ( float ) ( center_y + radius * Math.sin( current_angle ) ) );
+            n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
+            n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );

             _urt_nodeid_angle_map.put( n.getId(), current_angle );
             _urt_nodeid_angle_map.put( n.getId(), current_angle );

-            current_angle += ( TWO_PI / _circ_num_ext_nodes );
+            current_angle += ( TWO_PI / circ_num_ext_nodes );

         }
         paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
     }
         }
         paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
     }

@@ -2466,9 +2727,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                          final Graphics2D g,
                                          final boolean to_pdf,
                                          final boolean to_graphics_file ) {
                                          final Graphics2D g,
                                          final boolean to_pdf,
                                          final boolean to_graphics_file ) {

-        if ( n.isExternal() ) {
+        if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse

             if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
             if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {

-                System.out.println( "no " + n + ", fucker!" );//TODO
+                System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO

             }
             return _urt_nodeid_angle_map.get( n.getId() );
         }
             }
             return _urt_nodeid_angle_map.get( n.getId() );
         }

@@ -2488,11 +2749,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             double r = 0;
             if ( !n.isRoot() ) {
             }
             double r = 0;
             if ( !n.isRoot() ) {

-                r = 1 - ( ( ( double ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
+                r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );

             }
             final double theta = sum / descs.size();
             }
             final double theta = sum / descs.size();

-            n.setXcoord( ( float ) ( center_x + r * radius * Math.cos( theta ) ) );
-            n.setYcoord( ( float ) ( center_y + r * radius * Math.sin( theta ) ) );
+            n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
+            n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );

             _urt_nodeid_angle_map.put( n.getId(), theta );
             for( final PhylogenyNode desc : descs ) {
                 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
             _urt_nodeid_angle_map.put( n.getId(), theta );
             for( final PhylogenyNode desc : descs ) {
                 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );

@@ -2517,11 +2778,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             float r = 0;
             if ( !n.isRoot() ) {
             }
             float r = 0;
             if ( !n.isRoot() ) {

-                r = 1 - ( ( ( float ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
+                r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );

             }
             final double theta = _urt_nodeid_angle_map.get( n.getId() );
             }
             final double theta = _urt_nodeid_angle_map.get( n.getId() );

-            n.setXSecondary( ( float ) ( center_x + radius * r * Math.cos( theta ) ) );
-            n.setYSecondary( ( float ) ( center_y + radius * r * Math.sin( theta ) ) );
+            n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
+            n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );

             for( final PhylogenyNode desc : descs ) {
                 paintBranchCircularLite( n, desc, g );
             }
             for( final PhylogenyNode desc : descs ) {
                 paintBranchCircularLite( n, desc, g );
             }

@@ -2533,21 +2794,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                            final boolean to_graphics_file,
                                            final boolean to_pdf,
                                            final boolean is_in_found_nodes ) {
                                            final boolean to_graphics_file,
                                            final boolean to_pdf,
                                            final boolean is_in_found_nodes ) {

+        Color c = null;

         if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
         if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {

-            g.setColor( Color.BLACK );
+            c = Color.BLACK;

         }
         else if ( is_in_found_nodes ) {
         }
         else if ( is_in_found_nodes ) {

-            g.setColor( getTreeColorSet().getFoundColor() );
+            c = getTreeColorSet().getFoundColor();

         }
         else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
         }
         else if ( getControlPanel().isColorAccordingToTaxonomy() ) {

-            g.setColor( getTaxonomyBasedColor( node ) );
+            c = getTaxonomyBasedColor( node );

         }
         else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
                 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
         }
         else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
                 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {

-            g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+            c = PhylogenyMethods.getBranchColorValue( node );

         }
         else {
         }
         else {

-            g.setColor( getTreeColorSet().getCollapseFillColor() );
+            c = getTreeColorSet().getCollapseFillColor();

         }
         double d = node.getAllExternalDescendants().size();
         if ( d > 1000 ) {
         }
         double d = node.getAllExternalDescendants().size();
         if ( d > 1000 ) {

@@ -2556,17 +2818,34 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else {
             d = ( Math.log10( d ) * _y_distance ) / 2.5;
         }
         else {
             d = ( Math.log10( d ) * _y_distance ) / 2.5;
         }

-        if ( d < BOX_SIZE ) {
-            d = BOX_SIZE;
+        final int box_size = getOptions().getDefaultNodeShapeSize();
+        if ( d < box_size ) {
+            d = box_size;

         }
         _polygon.reset();
         }
         _polygon.reset();

-        _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - TreePanel.BOX_SIZE ),
+        _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),

                            ForesterUtil.roundToInt( node.getYcoord() ) );
                            ForesterUtil.roundToInt( node.getYcoord() ) );

-        _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ),
+        _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),

                            ForesterUtil.roundToInt( node.getYcoord() - d ) );
                            ForesterUtil.roundToInt( node.getYcoord() - d ) );

-        _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ),
+        _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),

                            ForesterUtil.roundToInt( node.getYcoord() + d ) );
                            ForesterUtil.roundToInt( node.getYcoord() + d ) );

-        g.fillPolygon( _polygon );
+        if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+            g.setColor( c );
+            g.fillPolygon( _polygon );
+        }
+        else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
+            g.setColor( getBackground() );
+            g.fillPolygon( _polygon );
+            g.setColor( c );
+            g.drawPolygon( _polygon );
+        }
+        else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+            g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
+                    .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
+            g.fill( _polygon );
+            g.setPaint( c );
+            g.draw( _polygon );
+        }

         paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
     }
 
         paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
     }
 

@@ -2597,36 +2876,45 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                               final PhylogenyNode node,
                                               final boolean to_pdf,
                                               final boolean to_graphics_file ) {
                                               final PhylogenyNode node,
                                               final boolean to_pdf,
                                               final boolean to_graphics_file ) {

-        String conf_str = "";

         final List<Confidence> confidences = node.getBranchData().getConfidences();
         final List<Confidence> confidences = node.getBranchData().getConfidences();

-        if ( confidences.size() == 1 ) {
-            final double value = node.getBranchData().getConfidence( 0 ).getValue();
-            if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
-                return;
-            }
-            conf_str = FORMATTER_CONFIDENCE.format( value );
-        }
-        else if ( confidences.size() > 1 ) {
-            boolean one_ok = false;
-            boolean not_first = false;
-            Collections.sort( confidences );
-            final StringBuilder sb = new StringBuilder();
-            for( final Confidence confidence : confidences ) {
-                final double value = confidence.getValue();
-                if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
-                    if ( value >= getOptions().getMinConfidenceValue() ) {
-                        one_ok = true;
-                    }
-                    if ( not_first ) {
-                        sb.append( "/" );
-                    }
-                    else {
-                        not_first = true;
+        //        if ( confidences.size() == 1 ) {
+        //            final double value = node.getBranchData().getConfidence( 0 ).getValue();
+        //            if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
+        //                return;
+        //            }
+        //            conf_str = FORMATTER_CONFIDENCE.format( value );
+        //        }
+        //        else if ( confidences.size() > 1 ) {
+        boolean one_ok = false;
+        boolean not_first = false;
+        Collections.sort( confidences );
+        final StringBuilder sb = new StringBuilder();
+        String conf_str = "";
+        for( final Confidence confidence : confidences ) {
+            final double value = confidence.getValue();
+            if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+                if ( value >= getOptions().getMinConfidenceValue() ) {
+                    one_ok = true;
+                }
+                if ( not_first ) {
+                    sb.append( "/" );
+                }
+                else {
+                    not_first = true;
+                }
+                sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
+                        .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+                if ( getOptions().isShowConfidenceStddev() ) {
+                    if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+                        sb.append( "(" );
+                        sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
+                                                                                    getOptions()
+                                                                                            .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+                        sb.append( ")" );

                     }
                     }

-                    sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
-                            .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );

                 }
             }
                 }
             }

+            //}

             if ( one_ok ) {
                 conf_str = sb.toString();
             }
             if ( one_ok ) {
                 conf_str = sb.toString();
             }

@@ -2657,8 +2945,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
     }
 
     final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {

+        final int box_size = getOptions().getDefaultNodeShapeSize();
+        final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;

         g.setColor( getTreeColorSet().getFoundColor() );
         g.setColor( getTreeColorSet().getFoundColor() );

-        g.fillRect( x - TreePanel.HALF_BOX_SIZE, y - TreePanel.HALF_BOX_SIZE, TreePanel.BOX_SIZE, TreePanel.BOX_SIZE );
+        g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );

     }
 
     final private void paintGainedAndLostCharacters( final Graphics2D g,
     }
 
     final private void paintGainedAndLostCharacters( final Graphics2D g,

@@ -2715,33 +3005,93 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
         }
         else {
             paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
         }
         else {

+            Color outline_color = null;

             if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
             if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {

-                g.setColor( Color.BLACK );
+                outline_color = Color.BLACK;

             }
             }

-            else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) {
+            else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {

                 final Event event = node.getNodeData().getEvent();
                 if ( event.isDuplication() ) {
                 final Event event = node.getNodeData().getEvent();
                 if ( event.isDuplication() ) {

-                    g.setColor( getTreeColorSet().getDuplicationBoxColor() );
+                    outline_color = getTreeColorSet().getDuplicationBoxColor();

                 }
                 else if ( event.isSpeciation() ) {
                 }
                 else if ( event.isSpeciation() ) {

-                    g.setColor( getTreeColorSet().getSpecBoxColor() );
+                    outline_color = getTreeColorSet().getSpecBoxColor();

                 }
                 else if ( event.isSpeciationOrDuplication() ) {
                 }
                 else if ( event.isSpeciationOrDuplication() ) {

-                    g.setColor( getTreeColorSet().getDuplicationOrSpeciationColor() );
+                    outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();

                 }
             }
                 }
             }

-            else {
-                assignGraphicsForNodeBoxWithColorForParentBranch( node, g );
+            else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
+                outline_color = getTaxonomyBasedColor( node );

             }
             }

-            if ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file )
-                    || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
-                if ( to_pdf || to_graphics_file ) {
-                    if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) {
-                        drawOvalFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
+            else {
+                outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
+                if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
+                    outline_color = getTreeColorSet().getBranchColorForPdf();
+                }
+            }
+            final int box_size = getOptions().getDefaultNodeShapeSize();
+            final int half_box_size = box_size / 2;
+            if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
+                if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
+                    if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+                        drawOvalGradient( x - half_box_size,
+                                          y - half_box_size,
+                                          box_size,
+                                          box_size,
+                                          g,
+                                          to_pdf ? Color.WHITE : outline_color,
+                                          to_pdf ? outline_color : getBackground(),
+                                          outline_color );
+                    }
+                    else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+                        Color background = getBackground();
+                        if ( to_pdf ) {
+                            background = Color.WHITE;
+                        }
+                        drawOvalGradient( x - half_box_size,
+                                          y - half_box_size,
+                                          box_size,
+                                          box_size,
+                                          g,
+                                          background,
+                                          background,
+                                          outline_color );
+                    }
+                    else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+                        g.setColor( outline_color );
+                        drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );

                     }
                 }
                     }
                 }

-                else {
-                    drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
+                else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
+                    if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
+                        drawRectGradient( x - half_box_size,
+                                          y - half_box_size,
+                                          box_size,
+                                          box_size,
+                                          g,
+                                          to_pdf ? Color.WHITE : outline_color,
+                                          to_pdf ? outline_color : getBackground(),
+                                          outline_color );
+                    }
+                    else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
+                        Color background = getBackground();
+                        if ( to_pdf ) {
+                            background = Color.WHITE;
+                        }
+                        drawRectGradient( x - half_box_size,
+                                          y - half_box_size,
+                                          box_size,
+                                          box_size,
+                                          g,
+                                          background,
+                                          background,
+                                          outline_color );
+                    }
+                    else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+                        g.setColor( outline_color );
+                        drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+                    }

                 }
             }
         }
                 }
             }
         }

@@ -2758,20 +3108,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( getOptions().isShowBranchLengthValues()
                 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
                         || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
         if ( getOptions().isShowBranchLengthValues()
                 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
                         || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )

-                && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) ) {
+                && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {

             paintBranchLength( g, node, to_pdf, to_graphics_file );
         }
         if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
             return;
         }
         int x = 0;
             paintBranchLength( g, node, to_pdf, to_graphics_file );
         }
         if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
             return;
         }
         int x = 0;

+        final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;

         if ( getControlPanel().isShowTaxonomyImages()
                 && ( getImageMap() != null )
                 && !getImageMap().isEmpty()
                 && node.getNodeData().isHasTaxonomy()
                 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
                         .getUris().isEmpty() ) ) {
         if ( getControlPanel().isShowTaxonomyImages()
                 && ( getImageMap() != null )
                 && !getImageMap().isEmpty()
                 && node.getNodeData().isHasTaxonomy()
                 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
                         .getUris().isEmpty() ) ) {

-            x += drawTaxonomyImage( node.getXcoord() + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord(), node, g );
+            x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );

         }
         if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
                 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
         }
         if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
                 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {

@@ -2832,6 +3183,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
             }
         }
                 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
             }
         }

+        if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+            if ( _sb.length() > 0 ) {
+                _sb.append( " " );
+            }
+            _sb.append( propertiesToString( node ) );
+        }

         g.setFont( getTreeFontSet().getLargeFont() );
         if ( is_in_found_nodes ) {
             g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
         g.setFont( getTreeFontSet().getLargeFont() );
         if ( is_in_found_nodes ) {
             g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );

@@ -2840,7 +3197,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
             down_shift_factor = 1;
         }
         if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
             down_shift_factor = 1;
         }

-        final double pos_x = node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE;
+        final double pos_x = node.getXcoord() + x + 2 + half_box_size;

         final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
         final String sb_str = _sb.toString();
         // GUILHEM_BEG ______________
         final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
         final String sb_str = _sb.toString();
         // GUILHEM_BEG ______________

@@ -2865,7 +3222,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                             && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
                                     .getSelectedItem() );
                     if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
                             && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
                                     .getSelectedItem() );
                     if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query

-                        final double linePosX = node.getXcoord() + 2 + TreePanel.HALF_BOX_SIZE;
+                        final double linePosX = node.getXcoord() + 2 + half_box_size;

                         final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
                                 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
                                 + ")";
                         final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
                                 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
                                 + ")";

@@ -2882,7 +3239,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
                             }
                         }
                                 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
                             }
                         }

-                        if ( x + nodeTextBoundsWidth > 0 ) /* we only underline if there is something displayed */
+                        if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */

                         {
                             if ( nodeTextBoundsWidth == 0 ) {
                                 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
                         {
                             if ( nodeTextBoundsWidth == 0 ) {
                                 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */

@@ -2923,7 +3280,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 g.setColor( calculateColorForAnnotation( ann ) );
             }
             final String ann_str = ann.asSimpleText().toString();
                 g.setColor( calculateColorForAnnotation( ann ) );
             }
             final String ann_str = ann.asSimpleText().toString();

-            TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+            TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()

                     + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
             _sb.setLength( 0 );
             _sb.append( ann_str );
                     + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
             _sb.setLength( 0 );
             _sb.append( ann_str );

@@ -2944,35 +3301,18 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 }
                 if ( getControlPanel().isShowBinaryCharacters() ) {
                     TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
                 }
                 if ( getControlPanel().isShowBinaryCharacters() ) {
                     TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()

-                            .toString(), node.getXcoord() + x + 1 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
+                            .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()

                             + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
                     paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
                             .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
                             .getLostCharactersAsStringBuffer().toString() );
                 }
                 else {
                             + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
                     paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
                             .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
                             .getLostCharactersAsStringBuffer().toString() );
                 }
                 else {

-                    if ( DRAW_MEAN_COUNTS && node.isInternal() ) {
-                        final List<PhylogenyNode> ec = node.getAllExternalDescendants();
-                        double sum = 0;
-                        int count = 0;
-                        for( final PhylogenyNode phylogenyNode : ec ) {
-                            count++;
-                            if ( phylogenyNode.getNodeData().getBinaryCharacters() != null ) {
-                                sum += phylogenyNode.getNodeData().getBinaryCharacters().getPresentCount();
-                            }
-                        }
-                        final double mean = ForesterUtil.round( sum / count, 1 );
-                        TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " ["
-                                + mean + "]", node.getXcoord() + x + 4 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
-                                + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
-                    }
-                    else {
-                        TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
-                                              node.getXcoord() + x + 4 + TreePanel.HALF_BOX_SIZE,
-                                              node.getYcoord()
-                                                      + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
-                                              g );
-                    }
+                    TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
+                                          node.getXcoord() + x + 4 + half_box_size,
+                                          node.getYcoord()
+                                                  + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
+                                          g );

                     paintGainedAndLostCharacters( g, node, "+"
                             + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
                             + node.getNodeData().getBinaryCharacters().getLostCount() );
                     paintGainedAndLostCharacters( g, node, "+"
                             + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
                             + node.getNodeData().getBinaryCharacters().getLostCount() );

@@ -2981,6 +3321,36 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
         }
     }
 

+    private StringBuffer propertiesToString( final PhylogenyNode node ) {
+        final PropertiesMap properties = node.getNodeData().getProperties();
+        final StringBuffer sb = new StringBuffer();
+        boolean first = true;
+        for( final String ref : properties.getPropertyRefs() ) {
+            if ( first ) {
+                first = false;
+            }
+            else {
+                sb.append( " " );
+            }
+            final Property p = properties.getProperty( ref );
+            sb.append( getPartAfterColon( p.getRef() ) );
+            sb.append( "=" );
+            sb.append( p.getValue() );
+            if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
+                sb.append( getPartAfterColon( p.getUnit() ) );
+            }
+        }
+        return sb;
+    }
+
+    final private static String getPartAfterColon( final String s ) {
+        final int i = s.indexOf( ':' );
+        if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
+            return s;
+        }
+        return s.substring( i + 1, s.length() );
+    }
+

     private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
         final List<Uri> us = new ArrayList<Uri>();
         for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
     private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
         final List<Uri> us = new ArrayList<Uri>();
         for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {

@@ -3002,11 +3372,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         }
                         // y = y - ( 0.9 * getYdistance() );
                         final double hs = bi.getHeight() * scaling_factor;
                         }
                         // y = y - ( 0.9 * getYdistance() );
                         final double hs = bi.getHeight() * scaling_factor;

-                        double ws = bi.getWidth() * scaling_factor + offset;
+                        double ws = ( bi.getWidth() * scaling_factor ) + offset;

                         final double my_y = y - ( 0.5 * hs );
                         final int x_w = ( int ) ( x + ws + 0.5 );
                         final int y_h = ( int ) ( my_y + hs + 0.5 );
                         final double my_y = y - ( 0.5 * hs );
                         final int x_w = ( int ) ( x + ws + 0.5 );
                         final int y_h = ( int ) ( my_y + hs + 0.5 );

-                        if ( ( x_w - x > 7 ) && ( y_h - my_y > 7 ) ) {
+                        if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {

                             g.drawImage( bi,
                                          ( int ) ( x + 0.5 + offset ),
                                          ( int ) ( my_y + 0.5 ),
                             g.drawImage( bi,
                                          ( int ) ( x + 0.5 + offset ),
                                          ( int ) ( my_y + 0.5 ),

@@ -3228,7 +3598,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             ++_external_node_index;
         }
         // Confidence values
             ++_external_node_index;
         }
         // Confidence values

-        if ( getControlPanel().isShowBootstrapValues()
+        if ( getControlPanel().isShowConfidenceValues()

                 && !node.isExternal()
                 && !node.isRoot()
                 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
                 && !node.isExternal()
                 && !node.isRoot()
                 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )

@@ -3299,11 +3669,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 child_node.setYcoord( y2 );
                 y2 += _y_distance * child_node.getNumberOfExternalNodes();
             }
                 child_node.setYcoord( y2 );
                 y2 += _y_distance * child_node.getNumberOfExternalNodes();
             }

+            paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );

         }
         if ( dynamically_hide
                 && !is_in_found_nodes
         }
         if ( dynamically_hide
                 && !is_in_found_nodes

-                && ( ( node.isExternal() && ( _external_node_index % dynamic_hiding_factor != 1 ) ) || ( !node
-                        .isExternal() && ( ( new_x_min < 20 ) || ( _y_distance * node.getNumberOfExternalNodes() < getTreeFontSet()._fm_large
+                && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
+                        .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large

                         .getHeight() ) ) ) ) ) {
             return;
         }
                         .getHeight() ) ) ) ) ) {
             return;
         }

@@ -3330,17 +3701,53 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 }
                 catch ( final ClassCastException cce ) {
                     cce.printStackTrace();
                 }
                 catch ( final ClassCastException cce ) {
                     cce.printStackTrace();

-                    return;

                 }
                 }

-                rds.setRenderingHeight( 6 );
-                int x = 0;
-                if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) {
-                    x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " );
-                }
-                if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
-                    x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
+                if ( rds != null ) {
+                    rds.setRenderingHeight( 6 );
+                    int x = 0;
+                    if ( node.getNodeData().isHasTaxonomy() ) {
+                        if ( getControlPanel().isShowTaxonomyCode()
+                                && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                            x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
+                                    .getTaxonomyCode()
+                                    + " " );
+                        }
+                        if ( getControlPanel().isShowTaxonomyScientificNames()
+                                && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
+                            x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
+                                    .getScientificName()
+                                    + " " );
+                        }
+                        if ( getControlPanel().isShowTaxonomyCommonNames()
+                                && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                            x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
+                                    .getCommonName()
+                                    + " " );
+                        }
+                    }
+                    if ( node.getNodeData().isHasSequence() ) {
+                        if ( getControlPanel().isShowGeneNames()
+                                && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
+                            x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
+                                    + " " );
+                        }
+                        if ( getControlPanel().isShowGeneSymbols()
+                                && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
+                            x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
+                                    + " " );
+                        }
+                        if ( getControlPanel().isShowSequenceAcc()
+                                && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+                            x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
+                                    .getAccession().toString()
+                                    + " " );
+                        }
+                    }
+                    if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
+                        x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
+                    }
+                    rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );

                 }
                 }

-                rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );

             }
         }
         //////////////
             }
         }
         //////////////

@@ -3349,18 +3756,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
                                                                          getStatisticsForExpressionValues(),
                                                                          getConfiguration() );
             final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
                                                                          getStatisticsForExpressionValues(),
                                                                          getConfiguration() );

-            int x = 0;
-            PhylogenyNode my_node = node;
-            if ( !getControlPanel().isDrawPhylogram() ) {
-                my_node = getPhylogeny().getFirstExternalNode();
-            }
-            if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
-                x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
-            }
-            if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
-                x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
+            if ( rv != null ) {
+                int x = 0;
+                PhylogenyNode my_node = node;
+                if ( !getControlPanel().isDrawPhylogram() ) {
+                    my_node = getPhylogeny().getFirstExternalNode();
+                }
+                if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
+                    x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
+                }
+                if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
+                    x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
+                }
+                rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );

             }
             }

-            rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );

         }
         //////////////
     }
         }
         //////////////
     }

@@ -3372,8 +3781,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
         final float width = getOvMaxWidth() / w_ratio;
         final float height = getOvMaxHeight() / h_ratio;
         final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
         final float width = getOvMaxWidth() / w_ratio;
         final float height = getOvMaxHeight() / h_ratio;

-        final float x = getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / x_ratio;
-        final float y = getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / y_ratio;
+        final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
+        final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );

         g.setColor( getTreeColorSet().getFoundColor() );
         getOvRectangle().setRect( x, y, width, height );
         if ( ( width < 6 ) && ( height < 6 ) ) {
         g.setColor( getTreeColorSet().getFoundColor() );
         getOvRectangle().setRect( x, y, width, height );
         if ( ( width < 6 ) && ( height < 6 ) ) {

@@ -3404,6 +3813,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                final int graphics_file_height,
                                final int graphics_file_x,
                                final int graphics_file_y ) {
                                final int graphics_file_height,
                                final int graphics_file_x,
                                final int graphics_file_y ) {

+        if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
+            return;
+        }

         if ( _control_panel.isShowSequenceRelations() ) {
             _query_sequence = _control_panel.getSelectedQuerySequence();
         }
         if ( _control_panel.isShowSequenceRelations() ) {
             _query_sequence = _control_panel.getSelectedQuerySequence();
         }

@@ -3471,7 +3883,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             if ( _nodes_in_preorder == null ) {
                 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
             }
             if ( _nodes_in_preorder == null ) {
                 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];

-                System.out.println( "total nodes: " + _nodes_in_preorder.length );

                 int i = 0;
                 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
                     _nodes_in_preorder[ i++ ] = it.next();
                 int i = 0;
                 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
                     _nodes_in_preorder[ i++ ] = it.next();

@@ -3482,8 +3893,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             //    paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
             //            && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
             //}
             //    paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
             //            && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
             //}

-            for( int i = 0; i < _nodes_in_preorder.length; ++i ) {
-                paintNodeRectangular( g, _nodes_in_preorder[ i ], to_pdf, getControlPanel().isDynamicallyHideData()
+            for( final PhylogenyNode element : _nodes_in_preorder ) {
+                paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData()

                         && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
             }
             if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
                         && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
             }
             if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {

@@ -3523,7 +3934,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             paintUnrooted( _phylogeny.getRoot(),
                            angle,
             }
             paintUnrooted( _phylogeny.getRoot(),
                            angle,

-                           ( float ) ( angle + 2 * Math.PI ),
+                           ( float ) ( angle + ( 2 * Math.PI ) ),

                            radial_labels,
                            g,
                            to_pdf,
                            radial_labels,
                            g,
                            to_pdf,

@@ -3544,7 +3955,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 g.setColor( getTreeColorSet().getOvColor() );
                 paintUnrootedLite( _phylogeny.getRoot(),
                                    angle,
                 g.setColor( getTreeColorSet().getOvColor() );
                 paintUnrootedLite( _phylogeny.getRoot(),
                                    angle,

-                                   angle + 2 * Math.PI,
+                                   angle + ( 2 * Math.PI ),

                                    g,
                                    ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
                 paintOvRectangle( g );
                                    g,
                                    ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
                 paintOvRectangle( g );

@@ -3608,8 +4019,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
         //    paintNodeLite( g, it.next() );
         //}
         //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
         //    paintNodeLite( g, it.next() );
         //}

-        for( int i = 0; i < _nodes_in_preorder.length; ++i ) {
-            paintNodeLite( g, _nodes_in_preorder[ i ] );
+        for( final PhylogenyNode element : _nodes_in_preorder ) {
+            paintNodeLite( g, element );

         }
         paintOvRectangle( g );
     }
         }
         paintOvRectangle( g );
     }

@@ -3698,7 +4109,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else {
             g.setColor( getTreeColorSet().getTaxonomyColor() );
         }
         else {
             g.setColor( getTreeColorSet().getTaxonomyColor() );
         }

-        final double start_x = node.getXcoord() + 3 + TreePanel.HALF_BOX_SIZE + x_shift;
+        final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;

         final double start_y = node.getYcoord()
                 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
         _sb.setLength( 0 );
         final double start_y = node.getYcoord()
                 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
         _sb.setLength( 0 );

@@ -3797,7 +4208,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( n.isRoot() ) {
             n.setXcoord( getWidth() / 2 );
             n.setYcoord( getHeight() / 2 );
         if ( n.isRoot() ) {
             n.setXcoord( getWidth() / 2 );
             n.setYcoord( getHeight() / 2 );

-            paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );

         }
         if ( n.isExternal() ) {
             paintNodeDataUnrootedCirc( g,
         }
         if ( n.isExternal() ) {
             paintNodeDataUnrootedCirc( g,

@@ -3845,16 +4255,19 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             else {
                 length = getUrtFactor();
             }
             else {
                 length = getUrtFactor();
             }

-            final double mid_angle = current_angle + arc_size / 2;
-            final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
-            final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
+            final double mid_angle = current_angle + ( arc_size / 2 );
+            final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
+            final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );

             desc.setXcoord( new_x );
             desc.setYcoord( new_y );
             desc.setXcoord( new_x );
             desc.setYcoord( new_y );

-            paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );

             paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
             current_angle += arc_size;
             assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
             drawLine( x, y, new_x, new_y, g );
             paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
             current_angle += arc_size;
             assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
             drawLine( x, y, new_x, new_y, g );

+            paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
+        }
+        if ( n.isRoot() ) {
+            paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );

         }
     }
 
         }
     }
 

@@ -3864,8 +4277,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                           final Graphics2D g,
                                           final float urt_ov_factor ) {
         if ( n.isRoot() ) {
                                           final Graphics2D g,
                                           final float urt_ov_factor ) {
         if ( n.isRoot() ) {

-            final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / 2 );
-            final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / 2 );
+            final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
+            final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );

             n.setXSecondary( x_pos );
             n.setYSecondary( y_pos );
         }
             n.setXSecondary( x_pos );
             n.setYSecondary( y_pos );
         }

@@ -3892,9 +4305,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             else {
                 length = urt_ov_factor;
             }
             else {
                 length = urt_ov_factor;
             }

-            final double mid_angle = current_angle + arc_size / 2;
-            final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
-            final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
+            final double mid_angle = current_angle + ( arc_size / 2 );
+            final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
+            final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );

             desc.setXSecondary( new_x );
             desc.setYSecondary( new_y );
             if ( isInFoundNodes( desc ) ) {
             desc.setXSecondary( new_x );
             desc.setYSecondary( new_y );
             if ( isInFoundNodes( desc ) ) {

@@ -3920,7 +4333,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                            JOptionPane.ERROR_MESSAGE );
             return;
         }
                                            JOptionPane.ERROR_MESSAGE );
             return;
         }

-        final String label = getASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
+        final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );

         final Object[] options = { "As sibling", "As descendant", "Cancel" };
         final int r = JOptionPane.showOptionDialog( this,
                                                     "How to paste subtree" + label + "?",
         final Object[] options = { "As sibling", "As descendant", "Cancel" };
         final int r = JOptionPane.showOptionDialog( this,
                                                     "How to paste subtree" + label + "?",

@@ -3939,7 +4352,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
         buffer_phy.setAllNodesToNotCollapse();
         }
         final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
         buffer_phy.setAllNodesToNotCollapse();

-        buffer_phy.preOrderReId();
+        PhylogenyMethods.preOrderReId( buffer_phy );

         buffer_phy.setRooted( true );
         boolean need_to_show_whole = false;
         if ( paste_as_sibling ) {
         buffer_phy.setRooted( true );
         boolean need_to_show_whole = false;
         if ( paste_as_sibling ) {

@@ -3971,8 +4384,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         node_ids.add( node.getId() );
         getCopiedAndPastedNodes().addAll( node_ids );
         }
         node_ids.add( node.getId() );
         getCopiedAndPastedNodes().addAll( node_ids );

+        setNodeInPreorderToNull();

         _phylogeny.externalNodesHaveChanged();
         _phylogeny.externalNodesHaveChanged();

-        _phylogeny.hashIDs();
+        _phylogeny.clearHashIdToNodeMap();

         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         setEdited( true );
         _phylogeny.recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         setEdited( true );

@@ -3982,6 +4396,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         repaint();
     }
 
         repaint();
     }
 

+    @Override

     final public int print( final Graphics g, final PageFormat page_format, final int page_index )
             throws PrinterException {
         if ( page_index > 0 ) {
     final public int print( final Graphics g, final PageFormat page_format, final int page_index )
             throws PrinterException {
         if ( page_index > 0 ) {

@@ -4021,7 +4436,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         _node_frame_index--;
         _node_frames[ i ] = null;
         if ( i < _node_frame_index ) {
         _node_frame_index--;
         _node_frames[ i ] = null;
         if ( i < _node_frame_index ) {

-            for( int j = 0; j < _node_frame_index - 1; j++ ) {
+            for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {

                 _node_frames[ j ] = _node_frames[ j + 1 ];
             }
             _node_frames[ _node_frame_index ] = null;
                 _node_frames[ j ] = _node_frames[ j + 1 ];
             }
             _node_frames[ _node_frame_index ] = null;

@@ -4046,6 +4461,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         getPhylogeny().reRoot( node );
         getPhylogeny().recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();
         getPhylogeny().reRoot( node );
         getPhylogeny().recalculateNumberOfExternalDescendants( true );
         resetNodeIdToDistToLeafMap();

+        setNodeInPreorderToNull();

         resetPreferredSize();
         getMainPanel().adjustJScrollPane();
         repaint();
         resetPreferredSize();
         getMainPanel().adjustJScrollPane();
         repaint();

@@ -4089,7 +4505,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         setPreferredSize( new Dimension( x, y ) );
     }
 
         setPreferredSize( new Dimension( x, y ) );
     }
 

-    final void setArrowCursor() {
+    public final void setArrowCursor() {

         setCursor( ARROW_CURSOR );
         repaint();
     }
         setCursor( ARROW_CURSOR );
         repaint();
     }

@@ -4106,7 +4522,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
     }
 
         getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
     }
 

-    final void setEdited( final boolean edited ) {
+    public final void setEdited( final boolean edited ) {

         _edited = edited;
     }
 
         _edited = edited;
     }
 

@@ -4184,7 +4600,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
      * @param x
      * @param y
      */
      * @param x
      * @param y
      */

-    final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
+    public final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {

         // updateStyle(); not needed?
         if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
             initNodeData();
         // updateStyle(); not needed?
         if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
             initNodeData();

@@ -4274,7 +4690,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
         }
         if ( getMainPanel().getOptions().isAntialiasScreen() ) {
             }
         }
         if ( getMainPanel().getOptions().isAntialiasScreen() ) {

-            if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) {
+            if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
+                    && !getMainPanel().getOptions().isShowDefaultNodeShapes()
+                    && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {

                 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
             }
             else {
                 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
             }
             else {

@@ -4304,10 +4722,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
      * @param t
      *            an instance of a Phylogeny
      */
      * @param t
      *            an instance of a Phylogeny
      */

-    final void setTree( final Phylogeny t ) {
+    public final void setTree( final Phylogeny t ) {
+        setNodeInPreorderToNull();

         _phylogeny = t;
     }
 
         _phylogeny = t;
     }
 

+    final void setNodeInPreorderToNull() {
+        _nodes_in_preorder = null;
+    }
+

     final void setTreeFile( final File treefile ) {
         _treefile = treefile;
     }
     final void setTreeFile( final File treefile ) {
         _treefile = treefile;
     }

@@ -4338,7 +4761,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         _urt_factor_ov = urt_factor_ov;
     }
 
         _urt_factor_ov = urt_factor_ov;
     }
 

-    final void setWaitCursor() {
+    public final void setWaitCursor() {

         setCursor( WAIT_CURSOR );
         repaint();
     }
         setCursor( WAIT_CURSOR );
         repaint();
     }

@@ -4515,6 +4938,26 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
                                                                                           getOptions()
                                                                                                   .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
                                 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
                                                                                           getOptions()
                                                                                                   .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );

+                        if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+                            _popup_buffer.append( " (sd=" );
+                            _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
+                                    .getStandardDeviation(), getOptions()
+                                    .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+                            _popup_buffer.append( ")" );
+                        }
+                    }
+                }
+                if ( node.getNodeData().isHasProperties() ) {
+                    final PropertiesMap properties = node.getNodeData().getProperties();
+                    for( final String ref : properties.getPropertyRefs() ) {
+                        _popup_buffer.append( "\n" );
+                        final Property p = properties.getProperty( ref );
+                        _popup_buffer.append( getPartAfterColon( p.getRef() ) );
+                        _popup_buffer.append( "=" );
+                        _popup_buffer.append( p.getValue() );
+                        if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
+                            _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
+                        }

                     }
                 }
                 if ( _popup_buffer.length() > 0 ) {
                     }
                 }
                 if ( _popup_buffer.length() > 0 ) {

@@ -4594,6 +5037,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                            JOptionPane.WARNING_MESSAGE );
             return;
         }
                                            JOptionPane.WARNING_MESSAGE );
             return;
         }

+        setNodeInPreorderToNull();

         if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
             _sub_phylogenies[ _subtree_index ] = _phylogeny;
             _sub_phylogenies_temp_roots[ _subtree_index ] = node;
         if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
             _sub_phylogenies[ _subtree_index ] = _phylogeny;
             _sub_phylogenies_temp_roots[ _subtree_index ] = node;

@@ -4630,6 +5074,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final void superTree() {
     }
 
     final void superTree() {

+        setNodeInPreorderToNull();

         final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
         for( final PhylogenyNode n : temp_root.getDescendants() ) {
             n.setParent( temp_root );
         final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
         for( final PhylogenyNode n : temp_root.getDescendants() ) {
             n.setParent( temp_root );

@@ -4641,8 +5086,48 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final void swap( final PhylogenyNode node ) {
     }
 
     final void swap( final PhylogenyNode node ) {

+        if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
+            return;
+        }
+        if ( node.getNumberOfDescendants() > 2 ) {
+            JOptionPane.showMessageDialog( this,
+                                           "Cannot swap descendants of nodes with more than 2 descendants",
+                                           "Cannot swap descendants",
+                                           JOptionPane.ERROR_MESSAGE );
+            return;
+        }
+        if ( !node.isExternal() ) {
+            node.swapChildren();
+            setNodeInPreorderToNull();
+            _phylogeny.externalNodesHaveChanged();
+            _phylogeny.clearHashIdToNodeMap();
+            _phylogeny.recalculateNumberOfExternalDescendants( true );
+            resetNodeIdToDistToLeafMap();
+            setEdited( true );
+        }
+        repaint();
+    }
+
+    final void sortDescendants( final PhylogenyNode node ) {

         if ( !node.isExternal() ) {
         if ( !node.isExternal() ) {

-            _phylogeny.swapChildren( node );
+            DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
+            if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
+                    .isShowTaxonomyCommonNames() ) ) {
+                if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
+                        .isShowGeneSymbols() ) ) {
+                    pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
+                }
+                else if ( getControlPanel().isShowNodeNames() ) {
+                    pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+                }
+            }
+            PhylogenyMethods.sortNodeDescendents( node, pri );
+            setNodeInPreorderToNull();
+            _phylogeny.externalNodesHaveChanged();
+            _phylogeny.clearHashIdToNodeMap();
+            _phylogeny.recalculateNumberOfExternalDescendants( true );
+            resetNodeIdToDistToLeafMap();
+            setEdited( true );

         }
         repaint();
     }
         }
         repaint();
     }

@@ -4713,7 +5198,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return;
         }
         setWaitCursor();
             return;
         }
         setWaitCursor();

-        Util.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+        AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );

         _control_panel.setColorBranches( true );
         if ( _control_panel.getColorBranchesCb() != null ) {
             _control_panel.getColorBranchesCb().setSelected( true );
         _control_panel.setColorBranches( true );
         if ( _control_panel.getColorBranchesCb() != null ) {
             _control_panel.getColorBranchesCb().setSelected( true );

@@ -4748,7 +5233,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final void updateOvSizes() {
     }
 
     final void updateOvSizes() {

-        if ( ( getWidth() > 1.05 * getVisibleRect().width ) || ( getHeight() > 1.05 * getVisibleRect().height ) ) {
+        if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {

             setOvOn( true );
             float l = getLongestExtNodeInfo();
             final float w_ratio = getOvMaxWidth() / getWidth();
             setOvOn( true );
             float l = getLongestExtNodeInfo();
             final float w_ratio = getOvMaxWidth() / getWidth();

@@ -4856,11 +5341,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
         }
     }
 

-    synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
+    public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {

         getMainPanel().setImageMap( image_map );
     }
 
         getMainPanel().setImageMap( image_map );
     }
 

-    synchronized Hashtable<String, BufferedImage> getImageMap() {
+    public synchronized Hashtable<String, BufferedImage> getImageMap() {

         return getMainPanel().getImageMap();
     }
 }
         return getMainPanel().getImageMap();
     }
 }