make PH, aPH, CL selection

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
index 2e0f76f..775f5e6 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
@@ -38,8 +38,8 @@ public final class AptxConstants {
 
     final static boolean        __ALLOW_PHYLOGENETIC_INFERENCE                                = true;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9917 beta";
-    final static String         PRG_DATE                                                      = "161018";
+    final static String         VERSION                                                       = "0.9918 beta";
+    final static String         PRG_DATE                                                      = "161019";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { 
             "Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" };

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 41aac93..d683f29 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -63,6 +63,7 @@ import javax.swing.JApplet;
 import javax.swing.JOptionPane;
 import javax.swing.text.MaskFormatter;
 
+import org.forester.archaeopteryx.ControlPanel.TreeDisplayType;
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
 import org.forester.io.parsers.nhx.NHXParser;
@@ -805,13 +806,16 @@ public final class AptxUtil {
             final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t );
              
             if ( !has_bl ) {
-                cp.setDrawPhylogram( false );
+                cp.setTreeDisplayType( TreeDisplayType.CLADOGRAM );
                 cp.setDrawPhylogramEnabled( false );
             }
             else {
                 final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t );
-                cp.setDrawPhylogram(  has_all_bl );
-                if ( cp.getDisplayAsPhylogramCb() != null ) {
+                if (has_all_bl) {
+                    cp.setTreeDisplayType( TreeDisplayType.UNALIGNED_PHYLOGRAM );
+                }
+               
+                if ( cp.getDisplayAsUnalignedPhylogramRb() != null ) {
                     cp.setDrawPhylogramEnabled( true );
                 }
             }
@@ -823,7 +827,7 @@ public final class AptxUtil {
         if ( ( t != null ) && !t.isEmpty() ) {
             final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t );
             if ( !has_bl ) {
-                atv_control.setDrawPhylogram( false );
+                atv_control.setTreeDisplayType( TreeDisplayType.CLADOGRAM );
                 atv_control.setDrawPhylogramEnabled( false );
             }
             if ( t.getFirstExternalNode().getBranchData().getBranchColor() != null
@@ -839,15 +843,17 @@ public final class AptxUtil {
             
             
             if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
-                if ( atv_control.getDisplayAsPhylogramCb() != null ) {
+                if ( atv_control.getDisplayAsAlignedPhylogramRb() != null ) {
                     if ( has_bl ) {
                         final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t );
-                        
-                        atv_control.setDrawPhylogram( has_all_bl );
+                        if (has_all_bl) {
+                            atv_control.setTreeDisplayType( TreeDisplayType.UNALIGNED_PHYLOGRAM );
+                        }
+                       
                         atv_control.setDrawPhylogramEnabled( true );
                     }
                     else {
-                        atv_control.setDrawPhylogram( false );
+                        atv_control.setTreeDisplayType( TreeDisplayType.CLADOGRAM );
                     }
                 }
             }

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 501877f..4e5e29b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -47,6 +47,7 @@ import java.util.Map;
 import java.util.Set;
 
 import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
 import javax.swing.DefaultListCellRenderer;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
@@ -54,10 +55,12 @@ import javax.swing.JComboBox;
 import javax.swing.JLabel;
 import javax.swing.JList;
 import javax.swing.JPanel;
+import javax.swing.JRadioButton;
 import javax.swing.JScrollBar;
 import javax.swing.JTextField;
 import javax.swing.ListCellRenderer;
 
+import org.forester.archaeopteryx.ControlPanel.TreeDisplayType;
 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.archaeopteryx.util.TypomaticJButton;
@@ -71,8 +74,15 @@ import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
 
+
 final class ControlPanel extends JPanel implements ActionListener {
 
+    enum TreeDisplayType {
+                          CLADOGRAM,
+                          ALIGNED_PHYLOGRAM,
+                          UNALIGNED_PHYLOGRAM
+    };
+
     enum NodeClickAction {
                           ADD_NEW_NODE,
                           BLAST,
@@ -131,14 +141,17 @@ final class ControlPanel extends JPanel implements ActionListener {
     private int                               _cut_subtree_item;
     private JButton                           _decr_domain_structure_evalue_thr;
     private int                               _delete_node_or_subtree_item;
-    private JCheckBox                         _display_as_phylogram_cb;
+    private JRadioButton                      _display_as_unaligned_phylogram_rb;
+    private JRadioButton                      _display_as_aligned_phylogram_rb;
+    private JRadioButton                      _display_as_cladogram_rb;
+    private ButtonGroup                       _display_as_buttongroup;
     // Tree checkboxes
     private JCheckBox                         _display_internal_data;
     private JLabel                            _domain_display_label;
     private JTextField                        _domain_structure_evalue_thr_tf;
     private JTextField                        _depth_collapse_depth_tf;
     private JTextField                        _rank_collapse_depth_tf;
-    private List<Boolean>                     _draw_phylogram;
+    private List<TreeDisplayType>             _tree_display_types;
     private JCheckBox                         _dynamically_hide_data;
     private int                               _edit_node_data_item;
     private int                               _get_ext_desc_data;
@@ -208,7 +221,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     private JButton                           _decr_rank_collapse_level;
     private JButton                           _incr_rank_collapse_level;
     private JLabel                            _rank_collapse_label;
-
+    
     ControlPanel( final MainPanel ap, final Configuration configuration ) {
         init();
         _mainpanel = ap;
@@ -263,8 +276,16 @@ final class ControlPanel extends JPanel implements ActionListener {
                 displayedPhylogenyMightHaveChanged( true );
             }
             else if ( ( tp != null ) && ( tp.getPhylogeny() != null ) ) {
-                if ( e.getSource() == getDisplayAsPhylogramCb() ) {
-                    setDrawPhylogram( getDisplayAsPhylogramCb().isSelected() );
+                if ( e.getSource() == getDisplayAsUnalignedPhylogramRb() ) {
+                    setTreeDisplayType( TreeDisplayType.UNALIGNED_PHYLOGRAM );
+                    showWhole();
+                }
+                if ( e.getSource() == getDisplayAsAlignedPhylogramRb() ) {
+                    setTreeDisplayType( TreeDisplayType.ALIGNED_PHYLOGRAM );
+                    showWhole();
+                }
+                if ( e.getSource() == getDisplayAsCladogramRb() ) {
+                    setTreeDisplayType( TreeDisplayType.CLADOGRAM );
                     showWhole();
                 }
                 // Zoom buttons
@@ -424,8 +445,16 @@ final class ControlPanel extends JPanel implements ActionListener {
         return _color_acc_species;
     }
 
-    public JCheckBox getDisplayAsPhylogramCb() {
-        return _display_as_phylogram_cb;
+    public JRadioButton getDisplayAsCladogramRb() {
+        return _display_as_cladogram_rb;
+    }
+
+    public JRadioButton getDisplayAsAlignedPhylogramRb() {
+        return _display_as_aligned_phylogram_rb;
+    }
+
+    public JRadioButton getDisplayAsUnalignedPhylogramRb() {
+        return _display_as_unaligned_phylogram_rb;
     }
 
     public JCheckBox getDynamicallyHideData() {
@@ -611,8 +640,8 @@ final class ControlPanel extends JPanel implements ActionListener {
     }// addSequenceRelationBlock
 
     /* GUILHEM_END */
-    private List<Boolean> getIsDrawPhylogramList() {
-        return _draw_phylogram;
+    private List<TreeDisplayType> getTreeDisplayTypes() {
+        return _tree_display_types;
     }
 
     // This takes care of ArchaeopteryxE-issue.
@@ -631,14 +660,14 @@ final class ControlPanel extends JPanel implements ActionListener {
     }
 
     private void init() {
-        _draw_phylogram = new ArrayList<Boolean>();
+        _tree_display_types = new ArrayList<TreeDisplayType>();
         setSpeciesColors( new HashMap<String, Color>() );
         setSequenceColors( new HashMap<String, Color>() );
         setAnnotationColors( new HashMap<String, Color>() );
     }
 
-    private boolean isDrawPhylogram( final int index ) {
-        return getIsDrawPhylogramList().get( index );
+    private TreeDisplayType getTreeDisplayType( final int index ) {
+        return getTreeDisplayTypes().get( index );
     }
 
     private void search0( final MainPanel main_panel, final Phylogeny tree, String query_str ) {
@@ -777,8 +806,8 @@ final class ControlPanel extends JPanel implements ActionListener {
         }
     }
 
-    private void setDrawPhylogram( final int index, final boolean b ) {
-        getIsDrawPhylogramList().set( index, b );
+    private void setTreeDisplayType( final int index, final TreeDisplayType t ) {
+        getTreeDisplayTypes().set( index, t );
     }
 
     private void setupClickToOptions() {
@@ -1002,12 +1031,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     }
 
     private void setupDisplayCheckboxes() {
-        if ( _configuration.doDisplayOption( Configuration.display_as_phylogram ) ) {
-            addCheckbox( Configuration.display_as_phylogram,
-                         _configuration.getDisplayTitle( Configuration.display_as_phylogram ) );
-            setCheckbox( Configuration.display_as_phylogram,
-                         _configuration.doCheckOption( Configuration.display_as_phylogram ) );
-        }
+        
         if ( _configuration.doDisplayOption( Configuration.dynamically_hide_data ) ) {
             addCheckbox( Configuration.dynamically_hide_data,
                          _configuration.getDisplayTitle( Configuration.dynamically_hide_data ) );
@@ -1302,12 +1326,6 @@ final class ControlPanel extends JPanel implements ActionListener {
     void addCheckbox( final int which, final String title ) {
         final JPanel ch_panel = new JPanel( new BorderLayout( 0, 0 ) );
         switch ( which ) {
-            case Configuration.display_as_phylogram:
-                _display_as_phylogram_cb = new JCheckBox( title );
-                getDisplayAsPhylogramCb().setToolTipText( "To switch between phylogram and cladogram display" );
-                addJCheckBox( getDisplayAsPhylogramCb(), ch_panel );
-                add( ch_panel );
-                break;
             case Configuration.display_internal_data:
                 _display_internal_data = new JCheckBox( title );
                 _display_internal_data.setToolTipText( "To allow or disallow display of internal labels" );
@@ -1491,6 +1509,16 @@ final class ControlPanel extends JPanel implements ActionListener {
         jcb.addActionListener( this );
     }
 
+    private final void setupJRadioButton( final JRadioButton rb ) {
+        rb.setFocusPainted( false );
+        rb.setFont( ControlPanel.jcb_font );
+        if ( !_configuration.isUseNativeUI() ) {
+            rb.setBackground( getConfiguration().getGuiBackgroundColor() );
+            rb.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+        }
+        rb.addActionListener( this );
+    }
+
     void addJTextField( final JTextField tf, final JPanel p ) {
         if ( !_configuration.isUseNativeUI() ) {
             tf.setForeground( getConfiguration().getGuiBackgroundColor() );
@@ -1626,7 +1654,8 @@ final class ControlPanel extends JPanel implements ActionListener {
     }
 
     boolean isDrawPhylogram() {
-        return isDrawPhylogram( getMainPanel().getCurrentTabIndex() );
+        final TreeDisplayType t = getTreeDisplayType( getMainPanel().getCurrentTabIndex() );
+        return ((t == TreeDisplayType.ALIGNED_PHYLOGRAM) ||( t == TreeDisplayType.UNALIGNED_PHYLOGRAM));
     }
 
     boolean isDynamicallyHideData() {
@@ -1723,11 +1752,16 @@ final class ControlPanel extends JPanel implements ActionListener {
     }
 
     void phylogenyAdded( final Configuration configuration ) {
-        getIsDrawPhylogramList().add( configuration.isDrawAsPhylogram() );
+        if (configuration.isDrawAsPhylogram()) {
+            getTreeDisplayTypes().add( TreeDisplayType.UNALIGNED_PHYLOGRAM);
+        }
+        else {
+            getTreeDisplayTypes().add( TreeDisplayType.CLADOGRAM);
+        }
     }
 
     void phylogenyRemoved( final int index ) {
-        getIsDrawPhylogramList().remove( index );
+        getTreeDisplayTypes().remove( index );
     }
 
     void search0() {
@@ -1795,8 +1829,10 @@ final class ControlPanel extends JPanel implements ActionListener {
     void setCheckbox( final int which, final boolean state ) {
         switch ( which ) {
             case Configuration.display_as_phylogram:
-                if ( getDisplayAsPhylogramCb() != null ) {
-                    getDisplayAsPhylogramCb().setSelected( state );
+                if ( getDisplayAsUnalignedPhylogramRb() != null ) {
+                    getDisplayAsUnalignedPhylogramRb().setSelected( state );
+                    getDisplayAsAlignedPhylogramRb().setSelected( !state );
+                    getDisplayAsCladogramRb().setSelected( !state );
                 }
                 break;
             case Configuration.display_internal_data:
@@ -2044,13 +2080,31 @@ final class ControlPanel extends JPanel implements ActionListener {
         _color_branches = color_branches;
     }
 
-    void setDrawPhylogram( final boolean b ) {
-        getDisplayAsPhylogramCb().setSelected( b );
-        setDrawPhylogram( getMainPanel().getCurrentTabIndex(), b );
+    void setTreeDisplayType( final TreeDisplayType t ) {
+        switch (t) {
+            case UNALIGNED_PHYLOGRAM:
+                getDisplayAsUnalignedPhylogramRb().setSelected( true );
+                break;
+            case ALIGNED_PHYLOGRAM:
+                getDisplayAsAlignedPhylogramRb().setSelected( true );
+                break;
+           case CLADOGRAM:
+                getDisplayAsCladogramRb().setSelected( true );
+                break;
+        }
+        setTreeDisplayType(  getMainPanel().getCurrentTabIndex(), t );
     }
 
     void setDrawPhylogramEnabled( final boolean b ) {
-        getDisplayAsPhylogramCb().setEnabled( b );
+        if ( getDisplayAsAlignedPhylogramRb() != null &&
+                getDisplayAsUnalignedPhylogramRb() != null &&
+                getDisplayAsCladogramRb() != null
+                ) {
+    
+        getDisplayAsAlignedPhylogramRb().setEnabled( b );
+        getDisplayAsUnalignedPhylogramRb().setEnabled( b );
+        getDisplayAsCladogramRb().setEnabled( b );
+    }
     }
 
     void setDynamicHidingIsOn( final boolean is_on ) {
@@ -2091,7 +2145,8 @@ final class ControlPanel extends JPanel implements ActionListener {
     }
 
     void setupControls() {
-        // The tree display options:
+       
+        setupTreeDisplayTypeOptions();
         setupDisplayCheckboxes();
         /* GUILHEM_BEG */
         // The sequence relation query selection combo-box
@@ -2109,6 +2164,33 @@ final class ControlPanel extends JPanel implements ActionListener {
         setupSearchTools1();
     }
 
+    void setupTreeDisplayTypeOptions() {
+        _display_as_unaligned_phylogram_rb = new JRadioButton( "PH" );
+        _display_as_aligned_phylogram_rb = new JRadioButton( "aPH" );
+        _display_as_cladogram_rb = new JRadioButton( "CL" );
+        _display_as_buttongroup = new ButtonGroup();
+        _display_as_buttongroup.add( _display_as_unaligned_phylogram_rb );
+        _display_as_buttongroup.add( _display_as_aligned_phylogram_rb );
+        _display_as_buttongroup.add( _display_as_cladogram_rb );
+        getDisplayAsUnalignedPhylogramRb().setToolTipText( "(unaligned) phylogram" );
+        getDisplayAsAlignedPhylogramRb().setToolTipText( "aligned phylogram" );
+        getDisplayAsCladogramRb().setToolTipText( "cladogram" );
+        setupJRadioButton( getDisplayAsUnalignedPhylogramRb() );
+        setupJRadioButton( getDisplayAsAlignedPhylogramRb() );
+        setupJRadioButton( getDisplayAsCladogramRb() );
+        final JPanel p = new JPanel(new GridLayout( 1, 3, 0, 0 ));
+        p.setFont( ControlPanel.jcb_font );
+        if ( !_configuration.isUseNativeUI() ) {
+            p.setBackground( getConfiguration().getGuiBackgroundColor() );
+            p.setForeground( getConfiguration().getGuiCheckboxTextColor() );
+        }
+        p.add(  _display_as_unaligned_phylogram_rb );
+        p.add( _display_as_aligned_phylogram_rb );
+        p.add( _display_as_cladogram_rb );
+        add( p );
+    }
+    
+    
     void setUpControlsForDomainStrucures() {
         _domain_display_label = new JLabel( "Domain Architectures:" );
         add( customizeLabel( _domain_display_label, getConfiguration() ) );
@@ -2522,11 +2604,12 @@ final class ControlPanel extends JPanel implements ActionListener {
             if ( getCurrentTreePanel().isPhyHasBranchLengths()
                     && ( getCurrentTreePanel().getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
                 setDrawPhylogramEnabled( true );
-                setDrawPhylogram( isDrawPhylogram() );
+              
+                setTreeDisplayType( getTreeDisplayType(  getMainPanel().getCurrentTabIndex() ) );
             }
             else {
                 setDrawPhylogramEnabled( false );
-                setDrawPhylogram( false );
+                setTreeDisplayType( TreeDisplayType.CLADOGRAM );
             }
             if ( getMainPanel().getMainFrame() == null ) {
                 // Must be "E" applet version.
@@ -2735,6 +2818,12 @@ final class ControlPanel extends JPanel implements ActionListener {
         }
     }
 
+    private final boolean isDrawPhylogram( int currentTabIndex ) {
+        TreeDisplayType t = getTreeDisplayType( currentTabIndex );
+        return ((t==TreeDisplayType.ALIGNED_PHYLOGRAM)|(t==TreeDisplayType.UNALIGNED_PHYLOGRAM));
+        
+    }
+
     final void zoomOutY( final float factor ) {
         final TreePanel treepanel = getMainPanel().getCurrentTreePanel();
         treepanel.multiplyUrtFactor( 0.9f );
@@ -2765,4 +2854,14 @@ final class ControlPanel extends JPanel implements ActionListener {
     final public JCheckBox getUseBranchWidthsCb() {
         return _width_branches;
     }
+
+    public TreeDisplayType getTreeDisplayType() {
+        if (_display_as_unaligned_phylogram_rb.isSelected() ) {
+            return TreeDisplayType.UNALIGNED_PHYLOGRAM;
+        }
+        else if (_display_as_aligned_phylogram_rb.isSelected() ) {
+            return TreeDisplayType.ALIGNED_PHYLOGRAM;
+        }
+        return TreeDisplayType.CLADOGRAM;
+    }
 }

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 0aecc53..184e795 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -122,7 +122,6 @@ final public class Options {
     private boolean                           _parse_beast_style_extended_nexus_tags;
     private boolean                           _collapsed_with_average_height;
     private boolean                           _show_abbreviated_labels_for_collapsed_nodes;
-    private boolean                           _align_ext_labels_in_phylogram;
     
     private Options() {
         init();
@@ -229,7 +228,6 @@ final public class Options {
         _right_align_domains = false;
         _collapsed_with_average_height = true;
         _show_abbreviated_labels_for_collapsed_nodes = true;
-        _align_ext_labels_in_phylogram = true;
     }
 
     final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) {
@@ -624,13 +622,6 @@ final public class Options {
         _show_abbreviated_labels_for_collapsed_nodes =  show_abbreviated_labels_for_collapsed_nodes;
     }
     
-    final boolean isAlignExtLabelsInPhylogram() {
-        return _align_ext_labels_in_phylogram;
-    }
-
-    final void setAlignExtLabelsInPhylogram( final boolean align_ext_labels_in_phylogram ) {
-        _align_ext_labels_in_phylogram = align_ext_labels_in_phylogram;
-    }
-    
+   
     
 }

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index a07d472..6d0c4ae 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -97,6 +97,7 @@ import javax.swing.PopupFactory;
 
 import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON;
 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
+import org.forester.archaeopteryx.ControlPanel.TreeDisplayType;
 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
@@ -2926,7 +2927,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             down_shift_factor = 1;
         }
         float pos_x;
-        if ( getControlPanel().isDrawPhylogram() && getOptions().isAlignExtLabelsInPhylogram()
+        if ( getControlPanel().getTreeDisplayType() == TreeDisplayType.ALIGNED_PHYLOGRAM
                 && ( node.isExternal() || node.isCollapse() ) ) {
             pos_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
                     + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x + ( 2 * TreePanel.MOVE ) + getXdistance()
@@ -2942,7 +2943,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else {
             pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) );
         }
-        if ( getControlPanel().isDrawPhylogram() && getOptions().isAlignExtLabelsInPhylogram()
+        if ( getControlPanel().getTreeDisplayType() == TreeDisplayType.ALIGNED_PHYLOGRAM
                 && ( node.isExternal() || node.isCollapse() ) ) {
             drawConnection( node.getXcoord(), pos_x - x, node.getYcoord(), 5, 20, g, to_pdf );
             if ( node.isCollapse() ) {
@@ -3649,7 +3650,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
         setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() );
         float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
-        if ( getControlPanel().isDrawPhylogram() && getOptions().isAlignExtLabelsInPhylogram() && node.isExternal() ) {
+        if ( getControlPanel().getTreeDisplayType() == TreeDisplayType.ALIGNED_PHYLOGRAM && node.isExternal() ) {
             start_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
                     + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift + ( 2 * TreePanel.MOVE ) + getXdistance()
                     + 3 );

diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index 0c7a916..2a19ee8 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -27,8 +27,8 @@ package org.forester.util;
 
 public final class ForesterConstants {
 
-    public final static String  FORESTER_VERSION            = "1.044";
-    public final static String  FORESTER_DATE               = "161018";
+    public final static String  FORESTER_VERSION            = "1.045";
+    public final static String  FORESTER_DATE               = "161019";
     public final static String  PHYLO_XML_VERSION           = "1.20";
     public final static String  PHYLO_XML_LOCATION          = "http://www.phyloxml.org";
     public final static String  PHYLO_XML_XSD               = "phyloxml.xsd";