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[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 fce060b..151a3e5 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -76,8 +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.TreeMap;
 
 import javax.swing.BorderFactory;
 import javax.swing.JApplet;
@@ -3243,6 +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:
@@ -4539,6 +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 );
@@ -4558,6 +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 ) {
@@ -4623,12 +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,
@@ -5090,14 +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;
@@ -5113,6 +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() ) ) {
@@ -5127,17 +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();
@@ -5147,13 +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() + ")",
@@ -5162,10 +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.
@@ -5179,6 +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 )