in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 1914d76..5ae230f 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -90,17 +90,18 @@ public final class Configuration {
     // ------------------
     final static String                     display_options[][]                                    = {
             { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
-            { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
+            { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
             { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
+            { "Colorize by Sequence", "display", "no" },
             { "Visual Styles/Branch Colors", "display", "no" }, { "Branch Widths", "display", "no" },
-            { "Protein Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
+            { "Protein Domains", "display", "no" }, { "Binary Characters", "nodisplay", "no" },
             { "Binary Char Counts", "nodisplay", "no" }, { "Seq Name", "display", "yes" },
             { "Seq Accession", "display", "no" }, { "Show Internal Data", "display", "yes" },
             { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
-            { "Taxonomy Common", "display", "no" }, { "Colorize by Annotation", "nodisplay", "no" },
+            { "Taxonomy Common", "display", "no" }, { "Colorize by Annotation", "display", "no" },
             { "Seq Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
             { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" },
-            { "Taxonomy Images", "display", "no" }, { "Properties", "nodisplay", "no" },
+            { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" },
             { "Gene Name", "display", "yes" }                                                     };
     final static int                        display_as_phylogram                                   = 0;
     final static int                        show_node_names                                        = 1;
@@ -109,37 +110,32 @@ public final class Configuration {
     final static int                        write_confidence_values                                = 4;
     final static int                        write_events                                           = 5;
     final static int                        color_according_to_species                             = 6;
-    final static int                        use_style                                              = 7;
-    final static int                        width_branches                                         = 8;
-    final static int                        show_domain_architectures                              = 9;
-    final static int                        show_binary_characters                                 = 10;
-    final static int                        show_binary_character_counts                           = 11;
-    final static int                        show_seq_names                                         = 12;
-    final static int                        show_sequence_acc                                      = 13;
-    final static int                        display_internal_data                                  = 14;
-    final static int                        dynamically_hide_data                                  = 15;
-    final static int                        show_taxonomy_scientific_names                         = 16;
-    final static int                        show_taxonomy_common_names                             = 17;
-    final static int                        color_according_to_annotation                          = 18;
-    final static int                        show_seq_symbols                                       = 19;
-    final static int                        node_data_popup                                        = 20;
-    final static int                        show_relation_confidence                               = 21;
-    final static int                        show_vector_data                                       = 22;
-    final static int                        show_taxonomy_images                                   = 23;
-    final static int                        show_properties                                        = 24;
-    final static int                        show_gene_names                                        = 25;
+    final static int                        color_according_to_sequence                            = 7;
+    final static int                        use_style                                              = 8;
+    final static int                        width_branches                                         = 9;
+    final static int                        show_domain_architectures                              = 10;
+    final static int                        show_binary_characters                                 = 11;
+    final static int                        show_binary_character_counts                           = 12;
+    final static int                        show_seq_names                                         = 13;
+    final static int                        show_sequence_acc                                      = 14;
+    final static int                        display_internal_data                                  = 15;
+    final static int                        dynamically_hide_data                                  = 16;
+    final static int                        show_taxonomy_scientific_names                         = 17;
+    final static int                        show_taxonomy_common_names                             = 18;
+    final static int                        color_according_to_annotation                          = 19;
+    final static int                        show_seq_symbols                                       = 20;
+    final static int                        node_data_popup                                        = 21;
+    final static int                        show_relation_confidence                               = 22;
+    final static int                        show_vector_data                                       = 23;
+    final static int                        show_taxonomy_images                                   = 24;
+    final static int                        show_properties                                        = 25;
+    final static int                        show_gene_names                                        = 26;
     static final String                     VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA                   = "validate_against_phyloxml_xsd_schema";
-    // ----------------
-    // Function colors
-    // ----------------
+     private static Hashtable<String, Color> _sequence_colors;
+    
+    
     private static Hashtable<String, Color> _annotation_colors;
-    // ----------------
-    // Domain colors
-    // ----------------
     private static Hashtable<String, Color> _domain_colors;
-    // ----------------
-    // Species colors
-    // ----------------
     private static Hashtable<String, Color> _species_colors;
     private static String                   DEFAULT_FONT_FAMILY                                    = "";
     private static final int                DEPRECATED                                             = -2;
@@ -567,15 +563,7 @@ public final class Configuration {
     public void setShowScale( final boolean show_scale ) {
         _show_scale = show_scale;
     }
-
-    public void setTaxonomyColorize( final boolean b ) {
-        display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no";
-    }
-
-    public void setUseBranchesWidths( final boolean b ) {
-        display_options[ width_branches ][ 2 ] = b ? "yes" : "no";
-    }
-
+  
     boolean displaySequenceRelations() {
         return _display_sequence_relations;
     }
@@ -734,6 +722,13 @@ public final class Configuration {
         }
         return _species_colors;
     }
+    
+    Hashtable<String, Color> getSequenceColors() {
+        if ( _sequence_colors == null ) {
+            _sequence_colors = new Hashtable<String, Color>();
+        }
+        return _sequence_colors;
+    }
 
     final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
         return _taxonomy_extraction;
@@ -1522,6 +1517,9 @@ public final class Configuration {
             else if ( key.equals( "color_according_to_species" ) ) {
                 key_index = Configuration.color_according_to_species;
             }
+            else if ( key.equals( "color_according_to_sequence" ) ) {
+                key_index = Configuration.color_according_to_sequence;
+            }
             else if ( key.equals( "show_node_names" ) ) {
                 key_index = Configuration.show_node_names;
             }
@@ -1625,6 +1623,10 @@ public final class Configuration {
                     getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
                                             Color.decode( ( String ) st.nextElement() ) );
                 }
+                else if ( key.equals( "sequence_color" ) ) {
+                    getSequenceColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
+                                            Color.decode( ( String ) st.nextElement() ) );
+                }
                 else if ( key.equals( "domain_color" ) ) {
                     getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
                 }

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 6172d3e..1f8e21e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,8 +42,8 @@ public final class Constants {
     public final static boolean __SYNTH_LF                                                    = false;                                                               // TODO remove me
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9891 beta";
-    final static String         PRG_DATE                                                      = "140605";
+    final static String         VERSION                                                       = "0.9892 beta";
+    final static String         PRG_DATE                                                      = "140623";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
             "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index a398560..509e24d 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -91,6 +91,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     private List<String>         _click_to_names;
     private int                  _collapse_cb_item;
     private JCheckBox            _color_acc_species;
+    private JCheckBox            _color_acc_sequence;
     private JCheckBox            _color_according_to_annotation;
     private boolean              _color_branches;
     private JCheckBox            _use_visual_styles_cb;
@@ -156,6 +157,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     private JButton              _show_whole;
     private int                  _sort_descendents_item;
     private Map<String, Color>   _species_colors;
+    private Map<String, Color>   _sequence_colors;
     private int                  _subtree_cb_item;
     private int                  _swap_cb_item;
     private JButton              _uncollapse_all;
@@ -189,6 +191,19 @@ final class ControlPanel extends JPanel implements ActionListener {
     @Override
     public void actionPerformed( final ActionEvent e ) {
         try {
+            if ( e.getSource() == _color_acc_sequence ) {
+                if ( _color_acc_species != null  ) {
+                    _color_acc_species.setSelected( false );
+                }
+             }
+            else if ( e.getSource() == _color_acc_species ) {
+                if ( _color_acc_sequence != null  ) {
+                    _color_acc_sequence.setSelected( false );
+                }
+                
+            }
+            
+            
             final TreePanel tp = getMainPanel().getCurrentTreePanel();
             if ( tp == null ) {
                 return;
@@ -291,6 +306,10 @@ final class ControlPanel extends JPanel implements ActionListener {
                     search1();
                     displayedPhylogenyMightHaveChanged( true );
                 }
+                
+              
+                
+                
                 else {
                     displayedPhylogenyMightHaveChanged( true );
                 }
@@ -310,6 +329,10 @@ final class ControlPanel extends JPanel implements ActionListener {
     public JCheckBox getColorAccSpeciesCb() {
         return _color_acc_species;
     }
+    
+    public JCheckBox getColorAccSequenceCb() {
+        return _color_acc_sequence;
+    }
 
     public JCheckBox getUseVisualStylesCb() {
         return _use_visual_styles_cb;
@@ -532,10 +555,17 @@ final class ControlPanel extends JPanel implements ActionListener {
             case Configuration.color_according_to_species:
                 _color_acc_species = new JCheckBox( title );
                 _color_acc_species
-                        .setToolTipText( "To colorize taxonomy and sequence labels as a function of taxonomy" );
+                        .setToolTipText( "To colorize node labels as a function of taxonomy" );
                 addJCheckBox( _color_acc_species, ch_panel );
                 add( ch_panel );
                 break;
+            case Configuration.color_according_to_sequence:
+                _color_acc_sequence = new JCheckBox( title );
+                _color_acc_sequence
+                        .setToolTipText( "To colorize node labels as a function of sequence name" );
+                addJCheckBox( _color_acc_sequence, ch_panel );
+                add( ch_panel );
+                break;
             case Configuration.color_according_to_annotation:
                 _color_according_to_annotation = new JCheckBox( title );
                 _color_according_to_annotation
@@ -790,6 +820,10 @@ final class ControlPanel extends JPanel implements ActionListener {
     Map<String, Color> getSpeciesColors() {
         return _species_colors;
     }
+    
+    Map<String, Color> getSequenceColors() {
+        return _sequence_colors;
+    }
 
     boolean isAntialiasScreenText() {
         return true;
@@ -802,6 +836,10 @@ final class ControlPanel extends JPanel implements ActionListener {
     boolean isColorAccordingToTaxonomy() {
         return ( ( _color_acc_species != null ) && _color_acc_species.isSelected() );
     }
+    
+    boolean isColorAccordingToSequence() {
+        return ( ( _color_acc_sequence != null ) && _color_acc_sequence.isSelected() );
+    }
 
     boolean isUseVisualStyles() {
         return ( ( ( getUseVisualStylesCb() != null ) && getUseVisualStylesCb().isSelected() ) || ( ( getUseVisualStylesCb() == null ) && _color_branches ) );
@@ -978,6 +1016,11 @@ final class ControlPanel extends JPanel implements ActionListener {
                     _color_acc_species.setSelected( state );
                 }
                 break;
+            case Configuration.color_according_to_sequence:
+                if ( _color_acc_sequence != null ) {
+                    _color_acc_sequence.setSelected( state );
+                }
+                break;
             case Configuration.color_according_to_annotation:
                 if ( _color_according_to_annotation != null ) {
                     _color_according_to_annotation.setSelected( state );
@@ -1230,6 +1273,10 @@ final class ControlPanel extends JPanel implements ActionListener {
     void setSpeciesColors( final Map<String, Color> species_colors ) {
         _species_colors = species_colors;
     }
+    
+    void setSequenceColors( final Map<String, Color> sequence_colors ) {
+        _sequence_colors = sequence_colors;
+    }
 
     /* GUILHEM_END */
     /*
@@ -1422,6 +1469,9 @@ final class ControlPanel extends JPanel implements ActionListener {
         if ( _color_acc_species != null ) {
             _color_acc_species.setSelected( false );
         }
+        if ( _color_acc_sequence != null ) {
+            _color_acc_sequence.setSelected( false );
+        }
         _mainpanel.getCurrentTreePanel().repaint();
     }
 
@@ -1721,6 +1771,7 @@ final class ControlPanel extends JPanel implements ActionListener {
     private void init() {
         _draw_phylogram = new ArrayList<Boolean>();
         setSpeciesColors( new HashMap<String, Color>() );
+        setSequenceColors( new HashMap<String, Color>() );
         setAnnotationColors( new HashMap<String, Color>() );
     }
 
@@ -2095,6 +2146,18 @@ final class ControlPanel extends JPanel implements ActionListener {
             setCheckbox( Configuration.display_internal_data,
                          _configuration.doCheckOption( Configuration.display_internal_data ) );
         }
+        
+        
+        if ( _configuration.doDisplayOption( Configuration.color_according_to_sequence ) ) {
+            addCheckbox( Configuration.color_according_to_sequence,
+                         _configuration.getDisplayTitle( Configuration.color_according_to_sequence ) );
+            setCheckbox( Configuration.color_according_to_sequence,
+                         _configuration.doCheckOption( Configuration.color_according_to_sequence ) );
+        }
+        
+        
+        
+        
         if ( _configuration.doDisplayOption( Configuration.color_according_to_species ) ) {
             addCheckbox( Configuration.color_according_to_species,
                          _configuration.getDisplayTitle( Configuration.color_according_to_species ) );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainPanel.java b/forester/java/src/org/forester/archaeopteryx/MainPanel.java
index 24fc5f7..6551f1b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainPanel.java
@@ -409,6 +409,7 @@ public class MainPanel extends JPanel implements ComponentListener {
 
     void setupTreeGraphic( final Configuration config_settings, final ControlPanel control ) {
         control.setSpeciesColors( config_settings.getSpeciesColors() );
+        control.setSequenceColors( config_settings.getSequenceColors() );
         control.setAnnotationColors( config_settings.getAnnotationColors() );
         RenderableDomainArchitecture.setColorMap( config_settings.getDomainColors() );
     }

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index b8905f2..019eaea 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -715,6 +715,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return c;
         }
     }
+    
+    final Color calculateSequenceBasedColor( final Sequence seq ) {
+            if ( ForesterUtil.isEmpty( seq.getName() ) ) {
+                return getTreeColorSet().getSequenceColor();
+            }
+            Color c = null;
+            final String seq_name = seq.getName();
+            c = getControlPanel().getSequenceColors().get( seq_name  );
+            if ( c == null ) {
+                    c = TreePanelUtil.calculateColorFromString( seq_name, false );
+                    getControlPanel().getSequenceColors().put( seq_name, c );
+            }
+            return c;
+    }
 
     void checkForVectorProperties( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
@@ -841,6 +855,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             if ( _control_panel.getColorAccSpeciesCb() != null ) {
                 _control_panel.getColorAccSpeciesCb().setSelected( false );
             }
+           
             _options.setColorLabelsSameAsParentBranch( true );
             _control_panel.repaint();
         }
@@ -986,12 +1001,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         return _statistics_for_vector_data;
     }
 
-    /**
-     * Find a color for this species name.
-     * 
-     * @param species
-     * @return the species color
-     */
+  
     final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
         if ( node.getNodeData().isHasTaxonomy() ) {
             return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
@@ -999,6 +1009,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         // return non-colorized color
         return getTreeColorSet().getTaxonomyColor();
     }
+    
+
+    final Color getSequenceBasedColor( final PhylogenyNode node ) {
+        if ( node.getNodeData().isHasSequence() ) {
+            return calculateSequenceBasedColor( node.getNodeData().getSequence() );
+        }
+        // return non-colorized color
+        return getTreeColorSet().getSequenceColor();
+    }
+    
 
     /**
      * @return pointer to colorset for tree drawing
@@ -3924,6 +3944,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         else if ( is_in_found_nodes ) {
             c = getColorForFoundNode( node );
         }
+        else if ( getControlPanel().isColorAccordingToSequence() ) {
+            c = getSequenceBasedColor( node );
+        }
         else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
             c = getTaxonomyBasedColor( node );
         }
@@ -5161,6 +5184,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
             g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
         }
+        else if ( getControlPanel().isColorAccordingToSequence() ) {
+            g.setColor( getSequenceBasedColor( node ) );
+        }
         else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
             g.setColor( getTaxonomyBasedColor( node ) );
         }
@@ -5689,9 +5715,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                         else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
                             _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
                         }
-                        else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
-                            _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
-                        }
                         else {
                             _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
                         }