inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 3ad3935..32dd030 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -76,11 +76,8 @@ 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;
@@ -2404,10 +2401,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         _color_chooser.setPreviewPanel( new JPanel() );
         SubtreeColorizationActionListener al;
         if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
-            final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
-            for( final Long id : getFoundNodes() ) {
-                additional_nodes.add( _phylogeny.getNode( id ) );
-            }
+            final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
             al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
         }
         else {
@@ -2418,6 +2412,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         dialog.setVisible( true );
     }
 
+    private List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
+        final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+        for( final Long id : getFoundNodes() ) {
+            additional_nodes.add( _phylogeny.getNode( id ) );
+        }
+        return additional_nodes;
+    }
+
     final private void copySubtree( final PhylogenyNode node ) {
         if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
             errorMessageNoCutCopyPasteInUnrootedDisplay();
@@ -5070,7 +5072,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
 
     private void showExtDescNodeData( final PhylogenyNode node ) {
         final List<String> data = new ArrayList<String>();
-        for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
+        final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
+        if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
+            for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
+                if ( !nodes.contains( n ) ) {
+                    nodes.add( n );
+                }
+            }
+        }
+        for( final PhylogenyNode n : nodes ) {
             switch ( getOptions().getExtDescNodeDataToReturn() ) {
                 case NODE_NAME:
                     if ( !ForesterUtil.isEmpty( n.getName() ) ) {
@@ -5131,9 +5141,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                                 ann.append( "|" );
                             }
                         }
-                        String ann_str = ann.toString().trim();
-                        if ( ann_str.endsWith( "|" ) ) {
-                            ann_str = ann_str.substring( 0, ann_str.length() - 1 );
+                        String ann_str;
+                        if ( ann.charAt( ann.length() - 1 ) == '|' ) {
+                            ann_str = ann.substring( 0, ann.length() - 1 );
+                        }
+                        else {
+                            ann_str = ann.toString();
                         }
                         sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
                                 .getMolecularSequence(), 60 ) );
@@ -5173,7 +5186,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
         } // for loop
         final StringBuilder sb = new StringBuilder();
-        final int size = makeSB( data, getOptions(), sb );
+        final int size = TreePanelUtil.makeSB( data, getOptions(), sb );
         if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
                 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
             if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
@@ -5194,15 +5207,26 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             }
             else {
                 setCurrentExternalNodesDataBuffer( sb );
-                final String title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
-                        : obtainTitleForExtDescNodeData() )
-                        + " for "
-                        + data.size()
-                        + "/"
-                        + node.getNumberOfExternalNodes()
-                        + " external descendats of node "
-                        + node
-                        + ", unique entries: " + size;
+                String title;
+                if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
+                    title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
+                            : obtainTitleForExtDescNodeData() )
+                            + " for "
+                            + data.size()
+                            + " nodes, unique entries: "
+                            + size;
+                }
+                else {
+                    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.
@@ -5216,46 +5240,6 @@ 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 )

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
index 082efa9..322199e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
@@ -24,6 +24,7 @@ import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.BranchColor;
+import org.forester.phylogeny.data.NodeData.NODE_DATA;
 import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
@@ -35,6 +36,46 @@ import org.forester.ws.seqdb.UniProtTaxonomy;
 
 public class TreePanelUtil {
 
+    static 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;
+    }
+
     public final static String createUriForSeqWeb( final PhylogenyNode node,
                                                    final Configuration conf,
                                                    final TreePanel tp ) {