work on data buffer for aLeaves MAFFT suite + clean up

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 03af1c1..deaaec8 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -57,7 +57,7 @@ import org.forester.util.ForesterUtil;
 public final class Configuration {
 
     public enum EXT_NODE_DATA_RETURN_ON {
-        CONSOLE, WINODW;
+        CONSOLE, WINODW, BUFFER_ONLY;
     }
     static final String                     VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA                   = "validate_against_phyloxml_xsd_schema";
     private static final String             WEB_LINK_KEY                                           = "web_link";
@@ -1356,6 +1356,9 @@ public final class Configuration {
             else if ( s.equals( "window" ) ) {
                 setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
             }
+            else if ( s.equals( "buffer_only" ) ) {
+                setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY );
+            }
             else {
                 ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
                         + "] for [ext_descendents_data_to_return_on]" );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index e9c0405..12710c0 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -231,6 +231,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     InferenceManager            _inference_manager;
     final ProcessPool           _process_pool;
     private String              _previous_node_annotation_ref;
+    private String              _ext_node_data_buffer                   = "";
 
     MainFrame() {
         _process_pool = ProcessPool.createInstance();
@@ -489,6 +490,18 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         return _configuration;
     }
 
+    /**
+     * This method returns the current external node data which
+     * has been selected by the user by clicking the "Return ..."
+     * menu item. This method is expected to be called from Javascript or
+     * something like it.
+     * 
+     * @return current external node data as String
+     */
+    public String getCurrentExternalNodesDataBuffer() {
+        return _ext_node_data_buffer;
+    }
+
     public InferenceManager getInferenceManager() {
         return _inference_manager;
     }
@@ -944,6 +957,15 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         _configuration = configuration;
     }
 
+    void setCurrentExternalNodesDataBuffer( final String s ) {
+        if ( !ForesterUtil.isEmpty( s ) ) {
+            _ext_node_data_buffer = s.trim();
+        }
+        else {
+            _ext_node_data_buffer = "";
+        }
+    }
+
     void setInferenceManager( final InferenceManager i ) {
         _inference_manager = i;
     }
@@ -1266,14 +1288,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
     }
 
-    private String getPreviousNodeAnnotationReference() {
-        return _previous_node_annotation_ref;
-    }
-
-    private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
-        _previous_node_annotation_ref = previous_node_annotation_ref;
-    }
-
     private void chooseFont() {
         final FontChooser fc = new FontChooser();
         fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
@@ -1338,12 +1352,20 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         repaint();
     }
 
+    private String getPreviousNodeAnnotationReference() {
+        return _previous_node_annotation_ref;
+    }
+
     private void removeBranchColors() {
         if ( getMainPanel().getCurrentPhylogeny() != null ) {
             AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
         }
     }
 
+    private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
+        _previous_node_annotation_ref = previous_node_annotation_ref;
+    }
+
     /**
      * Display the about box.
      */

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 0ff8a49..77f0364 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -663,7 +663,6 @@ public final class MainFrameApplication extends MainFrame {
         _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
         _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
         _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (re-rooting)" ) );
-        
         _analysis_menu.addSeparator();
         _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
         _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
@@ -1242,7 +1241,7 @@ public final class MainFrameApplication extends MainFrame {
         }
         catch ( final Exception e ) {
             JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
-            return; 
+            return;
         }
         gene_tree.setRerootable( false );
         _mainpanel.getCurrentTreePanel().setTree( gene_tree );
@@ -1267,13 +1266,12 @@ public final class MainFrameApplication extends MainFrame {
         if ( !isOKforSDI( false, true ) ) {
             return;
         }
-      
         final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
         gene_tree.setAllNodesToNotCollapse();
         gene_tree.recalculateNumberOfExternalDescendants( false );
         GSDIR gsdir = null;
         try {
-            gsdir = new GSDIR( gene_tree, _species_tree.copy(),  true, 1 );
+            gsdir = new GSDIR( gene_tree, _species_tree.copy(), true, 1 );
         }
         catch ( final Exception e ) {
             JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDIR", JOptionPane.ERROR_MESSAGE );
@@ -1283,13 +1281,9 @@ public final class MainFrameApplication extends MainFrame {
         result_gene_tree.setRerootable( false );
         result_gene_tree.clearHashIdToNodeMap();
         result_gene_tree.recalculateNumberOfExternalDescendants( true );
-        
-        
-        _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree" , null );
-        
+        _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
         //_mainpanel.getCurrentTreePanel().setTree( gene_tree );
-        
-       // _mainpanel.getCurrentTreePanel().setEdited( true );
+        // _mainpanel.getCurrentTreePanel().setEdited( true );
         getControlPanel().setShowEvents( true );
         showWhole();
         final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
@@ -1302,7 +1296,7 @@ public final class MainFrameApplication extends MainFrame {
                 + "Potential duplications: " + gsdir.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
                 + gsdir.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
     }
-    
+
     void executeFunctionAnalysis() {
         if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
             return;

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 907a20f..fcb1580 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -2339,6 +2339,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         repaint();
     }
 
+    private String createAnnotationString( final SortedSet<Annotation> ann ) {
+        final StringBuilder sb = new StringBuilder();
+        boolean first = true;
+        for( final Annotation a : ann ) {
+            if ( !first ) {
+                sb.append( "|" );
+            }
+            else {
+                first = false;
+            }
+            sb.append( a.asSimpleText() );
+        }
+        final String ann_str = sb.toString();
+        return ann_str;
+    }
+
     final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
         final String tax = PhylogenyMethods.getSpecies( node );
         String label = node.getName();
@@ -4035,22 +4051,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
-    private String createAnnotationString( final SortedSet<Annotation> ann ) {
-        final StringBuilder sb = new StringBuilder();
-        boolean first = true;
-        for( final Annotation a : ann ) {
-            if ( !first ) {
-                sb.append( "|" );
-            }
-            else {
-                first = false;
-            }
-            sb.append( a.asSimpleText() );
-        }
-        final String ann_str = sb.toString();
-        return ann_str;
-    }
-
     final private void paintNodeDataUnrootedCirc( final Graphics2D g,
                                                   final PhylogenyNode node,
                                                   final boolean to_pdf,
@@ -4991,10 +4991,37 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                             + getOptions().getExtDescNodeDataToReturn() );
             }
         } // for loop
-        if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
+        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 ) ) {
-                    System.out.println( d );
+                    if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
+                        System.out.println( d );
+                    }
+                    sb.append( d );
+                    sb.append( ForesterUtil.LINE_SEPARATOR );
+                }
+            }
+            if ( sb.length() < 1 ) {
+                if ( getMainPanel().getMainFrame() == null ) {
+                    // Must be "E" applet version.
+                    ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
+                            .setCurrentExternalNodesDataBuffer( "" );
+                }
+                else {
+                    getMainPanel().getMainFrame().setCurrentExternalNodesDataBuffer( "" );
+                }
+            }
+            else {
+                final String s = sb.toString().trim();
+                if ( getMainPanel().getMainFrame() == null ) {
+                    // Must be "E" applet version.
+                    ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
+                            .setCurrentExternalNodesDataBuffer( s );
+                }
+                else {
+                    getMainPanel().getMainFrame().setCurrentExternalNodesDataBuffer( s );
                 }
             }
         }
@@ -5003,28 +5030,37 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             for( final String d : data ) {
                 if ( !ForesterUtil.isEmpty( d ) ) {
                     sb.append( d );
-                    sb.append( "\n" );
+                    sb.append( ForesterUtil.LINE_SEPARATOR );
                 }
             }
             if ( sb.length() < 1 ) {
                 AptxUtil.showInformationMessage( this,
                                                  "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
                                                  "Descendants of selected node do not contain selected data" );
+                if ( getMainPanel().getMainFrame() == null ) {
+                    // Must be "E" applet version.
+                    ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
+                            .setCurrentExternalNodesDataBuffer( "" );
+                }
+                else {
+                    getMainPanel().getMainFrame().setCurrentExternalNodesDataBuffer( "" );
+                }
             }
             else {
                 final String title = "External Descendants "
                         + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
                                 : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
                         + node.getNumberOfExternalNodes() + ") For Node " + node;
+                final String s = sb.toString().trim();
                 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 );
+                    getMainPanel().getMainFrame().showTextFrame( s, title );
+                    getMainPanel().getMainFrame().setCurrentExternalNodesDataBuffer( s );
                 }
             }
         }

diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java
index c2cea38..5a9be41 100644 (file)
--- a/forester/java/src/org/forester/rio/RIO.java
+++ b/forester/java/src/org/forester/rio/RIO.java
@@ -395,7 +395,7 @@ public final class RIO {
         }
         final Phylogeny[] gene_trees = factory.create( gene_trees_file, p );
         // Removes from species_tree all species not found in gene_tree.
-        List<PhylogenyNode> _removed_gene_tree_nodes = PhylogenyMethods
+        final List<PhylogenyNode> _removed_gene_tree_nodes = PhylogenyMethods
                 .taxonomyBasedDeletionOfExternalNodes( gene_trees[ 0 ], species_tree );
         if ( species_tree.isEmpty() ) {
             throw new RIOException( "failed to establish species based mapping between gene and species trees" );

diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java
index 71f4e45..bfdd14f 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDI.java
+++ b/forester/java/src/org/forester/sdi/GSDI.java
@@ -69,8 +69,8 @@ public class GSDI extends SDI {
     private final boolean             _most_parsimonious_duplication_model;
     private final boolean             _strip_gene_tree;
     private final boolean             _strip_species_tree;
-    protected int                       _speciation_or_duplication_events_sum;
-    protected int                       _speciations_sum;
+    protected int                     _speciation_or_duplication_events_sum;
+    protected int                     _speciations_sum;
     private final List<PhylogenyNode> _stripped_gene_tree_nodes;
     private final List<PhylogenyNode> _stripped_species_tree_nodes;
     private final Set<PhylogenyNode>  _mapped_species_tree_nodes;
@@ -102,13 +102,13 @@ public class GSDI extends SDI {
             throws SDIException {
         this( gene_tree, species_tree, most_parsimonious_duplication_model, false, false );
     }
-    
+
     public GSDI( final Phylogeny gene_tree,
                  final Phylogeny species_tree,
                  final boolean most_parsimonious_duplication_model,
                  final boolean strip_gene_tree,
                  final boolean strip_species_tree,
-                 int x ) throws SDIException {
+                 final int x ) throws SDIException {
         super( gene_tree, species_tree );
         _speciation_or_duplication_events_sum = 0;
         _speciations_sum = 0;
@@ -120,7 +120,6 @@ public class GSDI extends SDI {
         _stripped_species_tree_nodes = new ArrayList<PhylogenyNode>();
         _mapped_species_tree_nodes = new HashSet<PhylogenyNode>();
         _scientific_names_mapped_to_reduced_specificity = new TreeSet<String>();
-       
     }
 
     // s is the node on the species tree g maps to.

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index 34efda2..dc3fcae 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -54,7 +54,6 @@ public class GSDIR extends GSDI {
             _duplications_sum = 0;\r
             _speciation_or_duplication_events_sum = 0;\r
             _speciations_sum = 0;\r
-          \r
             _gene_tree.reRoot( root.getId() ); //TODO reRoot( root )\r
             PhylogenyMethods.preOrderReId( getSpeciesTree() );\r
             //TEST, remove later\r
@@ -65,23 +64,19 @@ public class GSDIR extends GSDI {
                 }\r
             }\r
             geneTreePostOrderTraversal();\r
-           \r
-            if (  _duplications_sum < _min_duplications_sum ) {\r
+            if ( _duplications_sum < _min_duplications_sum ) {\r
                 _min_duplications_sum = _duplications_sum;\r
                 _min_duplications_sum_gene_trees.clear();\r
                 _min_duplications_sum_gene_trees.add( getGeneTree().copy() );\r
             }\r
-            else if (  _duplications_sum == _min_duplications_sum ) {\r
+            else if ( _duplications_sum == _min_duplications_sum ) {\r
                 _min_duplications_sum_gene_trees.add( getGeneTree().copy() );\r
             }\r
             System.out.println( getDuplicationsSum() );\r
-            _duplications_sum_stats.addValue(  _duplications_sum );\r
+            _duplications_sum_stats.addValue( _duplications_sum );\r
         }\r
     }\r
 \r
-   \r
-   \r
-\r
     public int getMinDuplicationsSum() {\r
         return _min_duplications_sum;\r
     }\r

diff --git a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
index 538f6a1..0818951 100644 (file)
--- a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
+++ b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
@@ -146,7 +146,6 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return _sum;
     }
 
-  
     @Override
     public String getSummaryAsString() {
         validate();
@@ -155,7 +154,6 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return "" + mean + ( ( char ) 177 ) + sd + " [" + getMin() + "..." + getMax() + "]";
     }
 
-   
     @Override
     public double getValue( final int index ) {
         validate();