X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=151a3e563e8ea94eb33652a09dd3e21dda1d8965;hb=12b27463955ee6d787d5c5e7cfbef303d8327669;hp=b94080f8c617e0e689153caa68785036dfbc2aae;hpb=c6c81526c849833f8691761d10e1c3f79aedd362;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index b94080f..151a3e5 100644
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -34,9 +34,9 @@ import java.awt.GradientPaint;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.Point;
-import java.awt.Polygon;
 import java.awt.Rectangle;
 import java.awt.RenderingHints;
+import java.awt.Stroke;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
@@ -54,6 +54,7 @@ import java.awt.geom.Arc2D;
 import java.awt.geom.CubicCurve2D;
 import java.awt.geom.Ellipse2D;
 import java.awt.geom.Line2D;
+import java.awt.geom.Path2D;
 import java.awt.geom.QuadCurve2D;
 import java.awt.geom.Rectangle2D;
 import java.awt.image.BufferedImage;
@@ -75,9 +76,11 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map.Entry;
 import java.util.Set;
+import java.util.SortedMap;
 import java.util.SortedSet;
-import java.util.regex.Matcher;
+import java.util.TreeMap;
 
 import javax.swing.BorderFactory;
 import javax.swing.JApplet;
@@ -131,6 +134,13 @@ import org.forester.util.SequenceIdParser;
 
 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
 
+    private static final BasicStroke     STROKE_2                                           = new BasicStroke( 2f );
+    private static final BasicStroke     STROKE_1                                           = new BasicStroke( 1f );
+    private static final BasicStroke     STROKE_075                                         = new BasicStroke( 0.75f );
+    private static final BasicStroke     STROKE_05                                          = new BasicStroke( 0.5f );
+    private static final BasicStroke     STROKE_025                                         = new BasicStroke( 0.25f );
+    private static final BasicStroke     STROKE_01                                          = new BasicStroke( 0.1f );
+    private static final BasicStroke     STROKE_005                                         = new BasicStroke( 0.05f );
     private static final float           PI                                                 = ( float ) ( Math.PI );
     private static final double          TWO_PI                                             = 2 * Math.PI;
     private static final float           ONEHALF_PI                                         = ( float ) ( 1.5 * Math.PI );
@@ -152,7 +162,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private final static NumberFormat    FORMATTER_CONFIDENCE;
     private final static NumberFormat    FORMATTER_BRANCH_LENGTH;
     private final static int             WIGGLE                                             = 2;
-    private final static int             LIMIT_FOR_HQ_RENDERING                             = 1000;
+    private final static int             LIMIT_FOR_HQ_RENDERING                             = 2000;
     private final static int             CONFIDENCE_LEFT_MARGIN                             = 4;
     private final RenderingHints         _rendering_hints                                   = new RenderingHints( RenderingHints.KEY_RENDERING,
                                                                                                                   RenderingHints.VALUE_RENDER_DEFAULT );
@@ -181,7 +191,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     private float                        _last_drag_point_y                                 = 0;
     private ControlPanel                 _control_panel                                     = null;
     private int                          _external_node_index                               = 0;
-    private final Polygon                _polygon                                           = new Polygon();
+    private final Path2D.Float           _polygon                                           = new Path2D.Float();
     private final StringBuilder          _sb                                                = new StringBuilder();
     private JColorChooser                _color_chooser                                     = null;
     private double                       _scale_distance                                    = 0.0;
@@ -689,21 +699,25 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
     }
 
     final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
-        String species = tax.getTaxonomyCode();
-        if ( ForesterUtil.isEmpty( species ) ) {
-            species = tax.getScientificName();
-            if ( ForesterUtil.isEmpty( species ) ) {
-                species = tax.getCommonName();
-            }
-        }
-        if ( ForesterUtil.isEmpty( species ) ) {
+        if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             return getTreeColorSet().getTaxonomyColor();
         }
-        // Look in species hash
-        Color c = getControlPanel().getSpeciesColors().get( species );
+        Color c = null;
+        if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+            c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
+        }
+        if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+            c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
+        }
         if ( c == null ) {
-            c = AptxUtil.calculateColorFromString( species );
-            getControlPanel().getSpeciesColors().put( species, c );
+            if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+                c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode() );
+                getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
+            }
+            else {
+                c = AptxUtil.calculateColorFromString( tax.getScientificName() );
+                getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
+            }
         }
         return c;
     }
@@ -1522,7 +1536,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
                 }
             }
-            g.setStroke( new BasicStroke( 1 ) );
+            setupStroke( g );
         }
         else {
             g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
@@ -1875,22 +1889,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
         }
         if ( getMainPanel().getOptions().isAntialiasScreen() ) {
-            if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
-                    && !getMainPanel().getOptions().isShowDefaultNodeShapesInternal()
-                    && !getMainPanel().getOptions().isShowDefaultNodeShapesExternal()
-                    && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
-                _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
-            }
-            else {
-                _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
-            }
-            try {
-                _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
-                                      RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
-            }
-            catch ( final Throwable e ) {
-                _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
-            }
+            _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
+            // try {
+            _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
+            // }
+            // catch ( final Throwable e ) {
+            //    _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
+            //}
         }
         else {
             _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
@@ -2429,7 +2434,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         boolean first = true;
         for( final Annotation a : ann ) {
             if ( !first ) {
-                sb.append( "|" );
+                sb.append( "+" );
             }
             else {
                 first = false;
@@ -2911,18 +2916,27 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         return Blast.isContainsQueryForBlast( node );
     }
 
+    final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
+        String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
+        if ( ForesterUtil.isEmpty( v ) ) {
+            v = ForesterUtil.extractGenbankAccessor( node );
+        }
+        if ( ForesterUtil.isEmpty( v ) ) {
+            v = ForesterUtil.extractRefSeqAccessorAccessor( node );
+        }
+        if ( ForesterUtil.isEmpty( v ) ) {
+            v = ForesterUtil.extractGInumber( node );
+        }
+        return v;
+    }
+
     final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
         if ( node.getNodeData().isHasTaxonomy()
-                && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
-                        && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
-                        && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
-                        .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
-                        || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
+                && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
                         || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
                         || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
-                        .getNodeData().getTaxonomy().getIdentifier() != null )
-                        && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
-                        .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
+                        .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+                        .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
             return true;
         }
         else {
@@ -3142,7 +3156,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             final String title = clickto_names.get( i );
             _node_popup_menu_items[ i ] = new JMenuItem( title );
             if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
-                _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
+                final String id = isCanOpenSeqWeb( node );
+                if ( !ForesterUtil.isEmpty( id ) ) {
+                    _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
+                    _node_popup_menu_items[ i ].setEnabled( true );
+                }
+                else {
+                    _node_popup_menu_items[ i ].setEnabled( false );
+                }
             }
             else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
                 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
@@ -3225,6 +3246,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 return "Scientific Names";
             case TAXONOMY_CODE:
                 return "Taxonomy Codes";
+            case TAXONOMY_COMM0N_NAME:
+                return "Taxonomy Common Names";
             case UNKNOWN:
                 return "User Selected Data";
             default:
@@ -3233,137 +3256,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
-    final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
-        if ( node.getNodeData().isHasSequence()
-                && ( node.getNodeData().getSequence().getAccession() != null )
-                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
-                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
-                && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
-                        .toLowerCase() ) ) {
-            return true;
-        }
-        if ( !ForesterUtil.isEmpty( node.getName() )
-                && ( AptxUtil.UNIPROT_KB_PATTERN_1.matcher( node.getName() ).find() || AptxUtil.UNIPROT_KB_PATTERN_2
-                        .matcher( node.getName() ).find() ) ) {
-            return true;
-        }
-        if ( node.getNodeData().isHasSequence() ) {
-            Sequence seq = node.getNodeData().getSequence();
-            if ( !ForesterUtil.isEmpty( seq.getName() )
-                    && ( AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getName() ).find() || AptxUtil.UNIPROT_KB_PATTERN_2
-                            .matcher( seq.getName() ).find() ) ) {
-                return true;
-            }
-            if ( !ForesterUtil.isEmpty( seq.getSymbol() )
-                    && ( AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getSymbol() ).find() || AptxUtil.UNIPROT_KB_PATTERN_2
-                            .matcher( seq.getSymbol() ).find() ) ) {
-                return true;
-            }
-            if ( ( node.getNodeData().getSequence().getAccession() != null )
-                    && !ForesterUtil.isEmpty( seq.getAccession().getValue() )
-                    && ( AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getAccession().getValue() ).find() || AptxUtil.UNIPROT_KB_PATTERN_2
-                            .matcher( seq.getAccession().getValue() ).find() ) ) {
-                return true;
-            }
-        }
-        return false;
-    }
-
     final private void openSeqWeb( final PhylogenyNode node ) {
-        if ( !isCanOpenSeqWeb( node ) ) {
+        if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
             cannotOpenBrowserWarningMessage( "sequence" );
             return;
         }
-        String uri_str = null;
-        if ( node.getNodeData().isHasSequence()
-                && ( node.getNodeData().getSequence().getAccession() != null )
-                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
-                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
-                && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
-                        .toLowerCase() ) ) {
-            final Sequence seq = node.getNodeData().getSequence();
-            final String source = seq.getAccession().getSource().toLowerCase();
-            String url;
-            if ( source.toLowerCase().equals( "ncbi" ) ) {
-                url = Constants.NCBI_ALL_DATABASE_SEARCH;
-            }
-            else {
-                final WebLink weblink = getConfiguration().getWebLink( source );
-                url = weblink.getUrl().toString();
-            }
-            try {
-                uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
-            }
-            catch ( final UnsupportedEncodingException e ) {
-                AptxUtil.showErrorMessage( this, e.toString() );
-                e.printStackTrace();
-            }
-        }
-        else {
-            String upkb = null;
-            if ( node.getNodeData().isHasSequence() ) {
-                Sequence seq = node.getNodeData().getSequence();
-                Matcher m;
-                if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
-                    m = AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getSymbol() );
-                    if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
-                        if ( m.find() ) {
-                            upkb = m.group( 2 );
-                        }
-                        else {
-                            m = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getSymbol() );
-                            if ( m.find() ) {
-                                upkb = m.group();
-                            }
-                        }
-                    }
-                }
-                if ( ForesterUtil.isEmpty( upkb ) && !ForesterUtil.isEmpty( seq.getName() ) ) {
-                    m = AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getName() );
-                    if ( m.find() ) {
-                        upkb = m.group( 2 );
-                    }
-                    else {
-                        m = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getName() );
-                        if ( m.find() ) {
-                            upkb = m.group();
-                        }
-                    }
-                }
-                if ( ForesterUtil.isEmpty( upkb ) && ( node.getNodeData().getSequence().getAccession() != null )
-                        && !ForesterUtil.isEmpty( seq.getAccession().getValue() ) ) {
-                    m = AptxUtil.UNIPROT_KB_PATTERN_1.matcher( seq.getAccession().getValue() );
-                    if ( m.find() ) {
-                        upkb = m.group( 2 );
-                    }
-                    else {
-                        m = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( seq.getAccession().getValue() );
-                        if ( m.find() ) {
-                            upkb = m.group();
-                        }
-                    }
-                }
-            }
-            if ( ForesterUtil.isEmpty( upkb ) && !ForesterUtil.isEmpty( node.getName() ) ) {
-                final Matcher m1 = AptxUtil.UNIPROT_KB_PATTERN_1.matcher( node.getName() );
-                if ( m1.find() ) {
-                    upkb = m1.group( 2 );
-                }
-                else {
-                    final Matcher m2 = AptxUtil.UNIPROT_KB_PATTERN_2.matcher( node.getName() );
-                    if ( m2.find() ) {
-                        upkb = m2.group();
-                    }
-                }
-            }
-            try {
-                uri_str = AptxUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 );
-            }
-            catch ( final UnsupportedEncodingException e ) {
-                AptxUtil.showErrorMessage( this, e.toString() );
-                e.printStackTrace();
-            }
-        }
+        final String uri_str = AptxUtil.createUriForSeqWeb( node, getConfiguration(), this );
         if ( !ForesterUtil.isEmpty( uri_str ) ) {
             try {
                 AptxUtil.launchWebBrowser( new URI( uri_str ),
@@ -3392,32 +3290,34 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         String uri_str = null;
         final Taxonomy tax = node.getNodeData().getTaxonomy();
-        if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
-                && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
-            final String type = tax.getIdentifier().getProvider().toLowerCase();
-            final WebLink weblink = getConfiguration().getWebLink( type );
+        if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+                && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
             try {
-                uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
+                uri_str = new URI( tax.getIdentifier().getValue() ).toString();
             }
-            catch ( final UnsupportedEncodingException e ) {
+            catch ( final URISyntaxException e ) {
                 AptxUtil.showErrorMessage( this, e.toString() );
+                uri_str = null;
                 e.printStackTrace();
             }
         }
-        else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
-                && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
+        else if ( ( tax.getIdentifier() != null )
+                && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+                && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
+                && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
+                        .equalsIgnoreCase( "uniprot" ) ) ) {
             try {
-                uri_str = new URI( tax.getIdentifier().getValue() ).toString();
+                uri_str = "http://www.uniprot.org/taxonomy/"
+                        + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
             }
-            catch ( final URISyntaxException e ) {
+            catch ( final UnsupportedEncodingException e ) {
                 AptxUtil.showErrorMessage( this, e.toString() );
-                uri_str = null;
                 e.printStackTrace();
             }
         }
         else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             try {
-                uri_str = "http://www.eol.org/search?q="
+                uri_str = "http://www.uniprot.org/taxonomy/?query="
                         + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {
@@ -3437,7 +3337,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
             try {
-                uri_str = "http://www.eol.org/search?q="
+                uri_str = "http://www.uniprot.org/taxonomy/?query="
                         + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {
@@ -3447,11 +3347,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
         if ( !ForesterUtil.isEmpty( uri_str ) ) {
             try {
-                JApplet applet = null;
-                if ( isApplet() ) {
-                    applet = obtainApplet();
-                }
-                AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
+                AptxUtil.launchWebBrowser( new URI( uri_str ),
+                                           isApplet(),
+                                           isApplet() ? obtainApplet() : null,
+                                           "_aptx_tax" );
             }
             catch ( final IOException e ) {
                 AptxUtil.showErrorMessage( this, e.toString() );
@@ -3761,30 +3660,30 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else {
             d = ( Math.log10( d ) * _y_distance ) / 2.5;
         }
-        final int box_size = getOptions().getDefaultNodeShapeSize();
+        final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
         if ( d < box_size ) {
             d = box_size;
         }
+        final float xx = node.getXcoord() - ( 2 * box_size );
+        final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
         _polygon.reset();
-        _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
-                           ForesterUtil.roundToInt( node.getYcoord() ) );
-        _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
-                           ForesterUtil.roundToInt( node.getYcoord() - d ) );
-        _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
-                           ForesterUtil.roundToInt( node.getYcoord() + d ) );
+        _polygon.moveTo( xxx, node.getYcoord() );
+        _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
+        _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
+        _polygon.closePath();
         if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
             g.setColor( c );
-            g.fillPolygon( _polygon );
+            g.fill( _polygon );
         }
         else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
             g.setColor( getBackground() );
-            g.fillPolygon( _polygon );
+            g.fill( _polygon );
             g.setColor( c );
-            g.drawPolygon( _polygon );
+            g.draw( _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.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
+                    .getYcoord() - d ), c, false ) );
             g.fill( _polygon );
             g.setPaint( c );
             g.draw( _polygon );
@@ -4036,6 +3935,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
             return;
         }
+        _sb.setLength( 0 );
         int x = 0;
         final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
         if ( getControlPanel().isShowTaxonomyImages()
@@ -4074,11 +3974,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else {
             g.setColor( getTreeColorSet().getSequenceColor() );
         }
-        _sb.setLength( 0 );
         if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
-            _sb.append( " [" );
-            _sb.append( node.getAllExternalDescendants().size() );
-            _sb.append( "]" );
+            if ( _sb.length() > 0 ) {
+                _sb.setLength( 0 );
+                _sb.append( "(" );
+                _sb.append( node.getAllExternalDescendants().size() );
+                _sb.append( ")" );
+            }
+        }
+        else {
+            _sb.setLength( 0 );
         }
         if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
             if ( _sb.length() > 0 ) {
@@ -4388,7 +4293,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
 
     final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
         if ( node.isCollapse() ) {
-            if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
+            if ( !node.isRoot() && !node.getParent().isCollapse() ) {
                 paintCollapsedNode( g, node, false, false, false );
             }
             return;
@@ -4442,7 +4347,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                              final boolean to_graphics_file ) {
         final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
         if ( node.isCollapse() ) {
-            if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
+            if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
                 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
             }
             return;
@@ -4639,6 +4544,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
         g.setColor( getTreeColorSet().getFoundColor() );
         getOvRectangle().setRect( x, y, width, height );
+        final Stroke s = g.getStroke();
+        g.setStroke( STROKE_1 );
         if ( ( width < 6 ) && ( height < 6 ) ) {
             drawRectFilled( x, y, 6, 6, g );
             getOvVirtualRectangle().setRect( x, y, 6, 6 );
@@ -4658,6 +4565,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             getOvVirtualRectangle().setRect( x, y, width, height );
         }
+        g.setStroke( s );
     }
 
     final private void paintPhylogenyLite( final Graphics2D g ) {
@@ -4666,9 +4574,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
                         .getWidth() ) ) ) );
         _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
+        final Stroke s = g.getStroke();
+        g.setStroke( STROKE_05 );
         for( final PhylogenyNode element : _nodes_in_preorder ) {
             paintNodeLite( g, element );
         }
+        g.setStroke( s );
         paintOvRectangle( g );
     }
 
@@ -4720,12 +4631,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else {
             g.setColor( getTreeColorSet().getBranchLengthColor() );
         }
+        final Stroke s = g.getStroke();
+        g.setStroke( STROKE_1 );
         drawLine( x1, y1, x1, y2, g );
         drawLine( x2, y1, x2, y2, g );
         drawLine( x1, y3, x2, y3, g );
         if ( getScaleLabel() != null ) {
             g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
         }
+        g.setStroke( s );
     }
 
     final private int paintTaxonomy( final Graphics2D g,
@@ -5106,6 +5020,30 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         _scale_label = scale_label;
     }
 
+    private final void setupStroke( final Graphics2D g ) {
+        if ( getYdistance() < 0.001 ) {
+            g.setStroke( STROKE_005 );
+        }
+        else if ( getYdistance() < 0.01 ) {
+            g.setStroke( STROKE_01 );
+        }
+        else if ( getYdistance() < 0.5 ) {
+            g.setStroke( STROKE_025 );
+        }
+        else if ( getYdistance() < 1 ) {
+            g.setStroke( STROKE_05 );
+        }
+        else if ( getYdistance() < 2 ) {
+            g.setStroke( STROKE_075 );
+        }
+        else if ( getYdistance() < 20 ) {
+            g.setStroke( STROKE_1 );
+        }
+        else {
+            g.setStroke( STROKE_2 );
+        }
+    }
+
     final private void setUpUrtFactor() {
         final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
                 : getVisibleRect().height;
@@ -5163,14 +5101,44 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     final StringBuilder sb = new StringBuilder();
                     if ( n.getNodeData().isHasSequence()
                             && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+                        final StringBuilder ann = new StringBuilder();
+                        if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+                            ann.append( n.getName() );
+                            ann.append( "|" );
+                        }
+                        if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+                            ann.append( "SYM=" );
+                            ann.append( n.getNodeData().getSequence().getSymbol() );
+                            ann.append( "|" );
+                        }
                         if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
-                            sb.append( SequenceWriter.toFasta( n.getNodeData().getSequence().getName(), n.getNodeData()
-                                    .getSequence().getMolecularSequence(), 60 ) );
+                            ann.append( "NAME=" );
+                            ann.append( n.getNodeData().getSequence().getName() );
+                            ann.append( "|" );
                         }
-                        else {
-                            sb.append( SequenceWriter.toFasta( n.getName(), n.getNodeData().getSequence()
-                                    .getMolecularSequence(), 60 ) );
+                        if ( n.getNodeData().getSequence().getAccession() != null ) {
+                            ann.append( "ACC=" );
+                            ann.append( n.getNodeData().getSequence().getAccession().asText() );
+                            ann.append( "|" );
                         }
+                        if ( n.getNodeData().isHasTaxonomy() ) {
+                            if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+                                ann.append( "TAXID=" );
+                                ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+                                ann.append( "|" );
+                            }
+                            if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                                ann.append( "SN=" );
+                                ann.append( n.getNodeData().getTaxonomy().getScientificName() );
+                                ann.append( "|" );
+                            }
+                        }
+                        String ann_str = ann.toString().trim();
+                        if ( ann_str.endsWith( "|" ) ) {
+                            ann_str = ann_str.substring( 0, ann_str.length() - 1 );
+                        }
+                        sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
+                                .getMolecularSequence(), 60 ) );
                         data.add( sb.toString() );
                     }
                     break;
@@ -5186,6 +5154,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         data.add( n.getNodeData().getTaxonomy().getScientificName() );
                     }
                     break;
+                case TAXONOMY_COMM0N_NAME:
+                    if ( n.getNodeData().isHasTaxonomy()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+                        data.add( n.getNodeData().getTaxonomy().getCommonName() );
+                    }
+                    break;
                 case TAXONOMY_CODE:
                     if ( n.getNodeData().isHasTaxonomy()
                             && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
@@ -5200,17 +5174,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                             + getOptions().getExtDescNodeDataToReturn() );
             }
         } // for loop
+        final StringBuilder sb = new StringBuilder();
+        final int size = makeSB( data, getOptions(), sb );
         if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
                 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
-            final StringBuilder sb = new StringBuilder();
-            for( final String d : data ) {
-                if ( !ForesterUtil.isEmpty( d ) ) {
-                    if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
-                        System.out.println( d );
-                    }
-                    sb.append( d );
-                    sb.append( ForesterUtil.LINE_SEPARATOR );
-                }
+            if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
+                System.out.println( sb );
             }
             if ( sb.length() < 1 ) {
                 clearCurrentExternalNodesDataBuffer();
@@ -5220,13 +5189,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
         }
         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( ForesterUtil.LINE_SEPARATOR );
-                }
-            }
             if ( sb.length() < 1 ) {
                 AptxUtil.showInformationMessage( this,
                                                  "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
@@ -5235,10 +5197,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             else {
                 setCurrentExternalNodesDataBuffer( sb );
-                final String title = "External Descendants "
-                        + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
-                                : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
-                        + node.getNumberOfExternalNodes() + ") For Node " + node;
+                final String title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
+                        : obtainTitleForExtDescNodeData() )
+                        + " for "
+                        + data.size()
+                        + "/"
+                        + node.getNumberOfExternalNodes()
+                        + " external descendats of node "
+                        + node
+                        + ", unique entries: " + size;
                 final String s = sb.toString().trim();
                 if ( getMainPanel().getMainFrame() == null ) {
                     // Must be "E" applet version.
@@ -5252,6 +5219,46 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
+    private int makeSB( final List<String> data, final Options optz, final StringBuilder sb ) {
+        final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
+        if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+                && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+            for( final String d : data ) {
+                if ( !ForesterUtil.isEmpty( d ) ) {
+                    if ( map.containsKey( d ) ) {
+                        map.put( d, map.get( d ) + 1 );
+                    }
+                    else {
+                        map.put( d, 1 );
+                    }
+                }
+            }
+        }
+        int size = 0;
+        if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+                && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+            for( final Entry<String, Integer> e : map.entrySet() ) {
+                final String v = e.getKey();
+                final Object c = e.getValue();
+                sb.append( v );
+                sb.append( "\t" );
+                sb.append( c );
+                sb.append( ForesterUtil.LINE_SEPARATOR );
+            }
+            size = map.size();
+        }
+        else {
+            for( final String d : data ) {
+                if ( !ForesterUtil.isEmpty( d ) ) {
+                    sb.append( d );
+                    sb.append( ForesterUtil.LINE_SEPARATOR );
+                }
+            }
+            size = data.size();
+        }
+        return size;
+    }
+
     final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
         try {
             if ( ( node.getName().length() > 0 )