in progress

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index fb37c4f..7f22501 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -117,7 +117,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JCheckBoxMenuItem           _inverse_search_result_cbmi;
     private JCheckBoxMenuItem           _show_overview_cbmi;
     private JMenuItem                   _choose_minimal_confidence_mi;
-    private JCheckBoxMenuItem           _show_branch_length_values_cbmi;
     private JMenuItem                   _collapse_species_specific_subtrees;
     private JMenuItem                   _overview_placment_mi;
     private ButtonGroup                 _radio_group_1;
@@ -263,9 +262,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( o == _show_scale_cbmi ) {
             updateOptions( getOptions() );
         }
-        else if ( o == _show_branch_length_values_cbmi ) {
-            updateOptions( getOptions() );
-        }
         else if ( o == _show_confidence_stddev_cbmi ) {
             updateOptions( getOptions() );
         }
@@ -763,8 +759,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
         _options_jmenu
-                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-        _options_jmenu
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
@@ -829,7 +823,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
-        customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
         customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
         customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
@@ -1344,9 +1337,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
                 && _show_confidence_stddev_cbmi.isSelected() );
-        if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
-            options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
-        }
         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
                 && _search_whole_words_only_cbmi.isSelected() );
         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 5df336a..e642d8e 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -101,7 +101,8 @@ public final class Configuration {
             { "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", "display", "no" }, { "Gene Name", "display", "yes" }                  };
+            { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
+            { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };
     final static int                        display_as_phylogram                                   = 0;
     final static int                        show_node_names                                        = 1;
     final static int                        show_tax_code                                          = 2;
@@ -129,6 +130,8 @@ public final class Configuration {
     final static int                        show_taxonomy_images                                   = 24;
     final static int                        show_properties                                        = 25;
     final static int                        show_gene_names                                        = 26;
+    final static int                        show_mol_seqs                                          = 27;
+    final static int                        write_branch_length_values                             = 28;
     static final String                     VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA                   = "validate_against_phyloxml_xsd_schema";
     private static Hashtable<String, Color> _sequence_colors;
     private static Hashtable<String, Color> _annotation_colors;
@@ -205,7 +208,6 @@ public final class Configuration {
     private PHYLOGENY_GRAPHICS_TYPE         _phylogeny_graphics_type                               = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
     private float                           _print_line_width                                      = Constants.PDF_LINE_WIDTH_DEFAULT;
     private boolean                         _show_annotation_ref_source                            = true;
-    private boolean                         _show_branch_length_values                             = false;
     private boolean                         _show_default_node_shapes_external                     = false;
     private boolean                         _show_default_node_shapes_internal                     = false;
     private boolean                         _show_domain_labels                                    = true;
@@ -538,10 +540,6 @@ public final class Configuration {
         _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
     }
 
-    public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
-        _show_branch_length_values = show_branch_length_values;
-    }
-
     public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
         _show_default_node_shapes_external = show_default_node_shapes_external;
     }
@@ -765,10 +763,6 @@ public final class Configuration {
         return _nh_parsing_replace_underscores;
     }
 
-    boolean isShowBranchLengthValues() {
-        return _show_branch_length_values;
-    }
-
     boolean isShowOverview() {
         return _show_overview;
     }
@@ -1199,9 +1193,6 @@ public final class Configuration {
         else if ( key.equals( "show_overview" ) ) {
             setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
         }
-        else if ( key.equals( "show_branch_length_values" ) ) {
-            setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
-        }
         else if ( key.equals( "background_gradient" ) ) {
             setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
         }
@@ -1544,6 +1535,9 @@ public final class Configuration {
             else if ( key.equals( "write_confidence_values" ) ) {
                 key_index = Configuration.write_confidence_values;
             }
+            else if ( key.equals( "write_branch_length_values" ) ) {
+                key_index = Configuration.write_branch_length_values;
+            }
             else if ( key.equals( "write_events" ) ) {
                 key_index = Configuration.write_events;
             }
@@ -1562,6 +1556,9 @@ public final class Configuration {
             else if ( key.equals( "show_domain_architectures" ) ) {
                 key_index = Configuration.show_domain_architectures;
             }
+            else if ( key.equals( "show_msa" ) ) {
+                key_index = Configuration.show_mol_seqs;
+            }
             else if ( key.equals( "show_annotations" ) ) {
                 key_index = Configuration.show_annotation;
             }

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index bafb79d..789edcc 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -142,6 +142,8 @@ final class ControlPanel extends JPanel implements ActionListener {
     // Indices for the click-to options in the combo box
     private int                               _show_data_item;
     private JCheckBox                         _show_domain_architectures;
+    private JCheckBox                         _show_mol_seqs;
+    private JCheckBox                         _write_branch_length_values;
     private JCheckBox                         _show_events;
     private JCheckBox                         _show_gene_names;
     private JCheckBox                         _show_node_names;
@@ -632,11 +634,21 @@ final class ControlPanel extends JPanel implements ActionListener {
                 addJCheckBox( _width_branches, ch_panel );
                 add( ch_panel );
                 break;
+            case Configuration.write_branch_length_values:
+                _write_branch_length_values = new JCheckBox( title );
+                addJCheckBox( _write_branch_length_values, ch_panel );
+                add( ch_panel );
+                break;
             case Configuration.show_domain_architectures:
                 _show_domain_architectures = new JCheckBox( title );
                 addJCheckBox( _show_domain_architectures, ch_panel );
                 add( ch_panel );
                 break;
+            case Configuration.show_mol_seqs:
+                _show_mol_seqs = new JCheckBox( title );
+                addJCheckBox( _show_mol_seqs, ch_panel );
+                add( ch_panel );
+                break;
             case Configuration.show_seq_names:
                 _show_seq_names = new JCheckBox( title );
                 addJCheckBox( _show_seq_names, ch_panel );
@@ -873,10 +885,18 @@ final class ControlPanel extends JPanel implements ActionListener {
         return ( ( getWriteConfidenceCb() != null ) && getWriteConfidenceCb().isSelected() );
     }
 
+    boolean isWriteBranchLengthValues() {
+        return ( ( _write_branch_length_values != null ) && _write_branch_length_values.isSelected() );
+    }
+
     boolean isShowDomainArchitectures() {
         return ( ( _show_domain_architectures != null ) && _show_domain_architectures.isSelected() );
     }
 
+    public boolean isShowMolSequences() {
+        return ( ( _show_mol_seqs != null ) && _show_mol_seqs.isSelected() );
+    }
+
     boolean isShowGeneNames() {
         return ( ( _show_gene_names != null ) && _show_gene_names.isSelected() );
     }
@@ -1087,6 +1107,16 @@ final class ControlPanel extends JPanel implements ActionListener {
                     _show_domain_architectures.setSelected( state );
                 }
                 break;
+            case Configuration.write_branch_length_values:
+                if ( _write_branch_length_values != null ) {
+                    _write_branch_length_values.setSelected( state );
+                }
+                break;
+            case Configuration.show_mol_seqs:
+                if ( _show_mol_seqs != null ) {
+                    _show_mol_seqs.setSelected( state );
+                }
+                break;
             case Configuration.show_seq_names:
                 if ( _show_seq_names != null ) {
                     _show_seq_names.setSelected( state );
@@ -2218,6 +2248,18 @@ final class ControlPanel extends JPanel implements ActionListener {
             addCheckbox( Configuration.show_annotation, _configuration.getDisplayTitle( Configuration.show_annotation ) );
             setCheckbox( Configuration.show_annotation, _configuration.doCheckOption( Configuration.show_annotation ) );
         }
+        if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
+            addCheckbox( Configuration.write_confidence_values,
+                         _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
+            setCheckbox( Configuration.write_confidence_values,
+                         _configuration.doCheckOption( Configuration.write_confidence_values ) );
+        }
+        if ( _configuration.doDisplayOption( Configuration.write_branch_length_values ) ) {
+            addCheckbox( Configuration.write_branch_length_values,
+                         _configuration.getDisplayTitle( Configuration.write_branch_length_values ) );
+            setCheckbox( Configuration.write_branch_length_values,
+                         _configuration.doCheckOption( Configuration.write_branch_length_values ) );
+        }
         if ( _configuration.doDisplayOption( Configuration.show_binary_characters ) ) {
             addCheckbox( Configuration.show_binary_characters,
                          _configuration.getDisplayTitle( Configuration.show_binary_characters ) );
@@ -2236,11 +2278,9 @@ final class ControlPanel extends JPanel implements ActionListener {
             setCheckbox( Configuration.show_domain_architectures,
                          _configuration.doCheckOption( Configuration.show_domain_architectures ) );
         }
-        if ( _configuration.doDisplayOption( Configuration.write_confidence_values ) ) {
-            addCheckbox( Configuration.write_confidence_values,
-                         _configuration.getDisplayTitle( Configuration.write_confidence_values ) );
-            setCheckbox( Configuration.write_confidence_values,
-                         _configuration.doCheckOption( Configuration.write_confidence_values ) );
+        if ( _configuration.doDisplayOption( Configuration.show_mol_seqs ) ) {
+            addCheckbox( Configuration.show_mol_seqs, _configuration.getDisplayTitle( Configuration.show_mol_seqs ) );
+            setCheckbox( Configuration.show_mol_seqs, _configuration.doCheckOption( Configuration.show_mol_seqs ) );
         }
         if ( _configuration.doDisplayOption( Configuration.write_events ) ) {
             addCheckbox( Configuration.write_events, _configuration.getDisplayTitle( Configuration.write_events ) );
@@ -2370,17 +2410,11 @@ final class ControlPanel extends JPanel implements ActionListener {
                     if ( getMainPanel().getMainFrame()._label_direction_cbmi != null ) {
                         getMainPanel().getMainFrame()._label_direction_cbmi.setVisible( true );
                     }
-                    if ( getMainPanel().getMainFrame()._show_branch_length_values_cbmi != null ) {
-                        getMainPanel().getMainFrame()._show_branch_length_values_cbmi.setVisible( false );
-                    }
                 }
                 else {
                     if ( getMainPanel().getMainFrame()._label_direction_cbmi != null ) {
                         getMainPanel().getMainFrame()._label_direction_cbmi.setVisible( false );
                     }
-                    if ( getMainPanel().getMainFrame()._show_branch_length_values_cbmi != null ) {
-                        getMainPanel().getMainFrame()._show_branch_length_values_cbmi.setVisible( true );
-                    }
                 }
             }
         }
@@ -2455,9 +2489,4 @@ final class ControlPanel extends JPanel implements ActionListener {
         CHANGE_NODE_FONT,
         COLOR_NODE_FONT;
     }
-
-    public boolean isShowMolSequences() {
-        // TODO Auto-generated method stub
-        return true;
-    }
 }

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 1cf79b0..fb23501 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -98,7 +98,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         SEARCH_TERMS_ONLY_LABEL                 = "Match Complete Terms Only";\r
     static final String         SEARCH_CASE_SENSITIVE_LABEL             = "Case Sensitive";\r
     static final String         INVERSE_SEARCH_RESULT_LABEL             = "Negate Result";\r
-    static final String         DISPLAY_BRANCH_LENGTH_VALUES_LABEL      = "Branch Length Values";\r
     static final String         COLOR_BY_TAXONOMIC_GROUP                = "Colorize by Taxonomic Group";\r
     static final String         DISPLAY_SCALE_LABEL                     = "Scale";\r
     static final String         NON_LINED_UP_CLADOGRAMS_LABEL           = "Non-Lined Up Cladograms";\r
@@ -184,7 +183,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JRadioButtonMenuItem        _non_lined_up_cladograms_rbmi;\r
     JRadioButtonMenuItem        _uniform_cladograms_rbmi;\r
     JRadioButtonMenuItem        _ext_node_dependent_cladogram_rbmi;\r
-    JCheckBoxMenuItem           _show_branch_length_values_cbmi;\r
     JCheckBoxMenuItem           _color_by_taxonomic_group_cbmi;\r
     JCheckBoxMenuItem           _show_scale_cbmi;                                                                                                                                                                                             //TODO fix me\r
     JCheckBoxMenuItem           _show_overview_cbmi;\r
@@ -460,9 +458,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _show_scale_cbmi ) {\r
             updateOptions( getOptions() );\r
         }\r
-        else if ( o == _show_branch_length_values_cbmi ) {\r
-            updateOptions( getOptions() );\r
-        }\r
         else if ( o == _color_by_taxonomic_group_cbmi ) {\r
             updateOptions( getOptions() );\r
         }\r
@@ -1337,9 +1332,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
         options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
                 && _show_confidence_stddev_cbmi.isSelected() );\r
-        if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {\r
-            options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );\r
-        }\r
         if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
             options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
         }\r

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index 9713b4f..b804681 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -212,8 +212,6 @@ public final class MainFrameApplet extends MainFrame {
         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) );
         _options_jmenu
-                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-        _options_jmenu
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) );
         _options_jmenu
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) );
@@ -275,7 +273,6 @@ public final class MainFrameApplet extends MainFrame {
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
-        customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );
         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
         customizeCheckBoxMenuItem( _label_direction_cbmi,
                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 30721ca..40d9581 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -893,8 +893,6 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
         _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
         _options_jmenu\r
-                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );\r
-        _options_jmenu\r
                 .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
         _options_jmenu\r
                 .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
@@ -1001,7 +999,6 @@ public final class MainFrameApplication extends MainFrame {
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
-        customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );\r
         customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
         customizeCheckBoxMenuItem( _label_direction_cbmi,\r
                                    getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r

diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java
index 2bf8471..727838a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Options.java
+++ b/forester/java/src/org/forester/archaeopteryx/Options.java
@@ -77,7 +77,6 @@ final public class Options {
     private double                            _scale_bar_length;
     private boolean                           _search_case_sensitive;
     private boolean                           _show_annotation_ref_source;
-    private boolean                           _show_branch_length_values;
     private boolean                           _show_confidence_stddev;
     private boolean                           _show_default_node_shapes_external;
     private boolean                           _show_default_node_shapes_internal;
@@ -272,10 +271,6 @@ final public class Options {
         return _search_case_sensitive;
     }
 
-    final boolean isShowBranchLengthValues() {
-        return _show_branch_length_values;
-    }
-
     boolean isShowConfidenceStddev() {
         return _show_confidence_stddev;
     }
@@ -414,10 +409,6 @@ final public class Options {
         _search_case_sensitive = search_case_sensitive;
     }
 
-    final void setShowBranchLengthValues( final boolean show_branch_length_values ) {
-        _show_branch_length_values = show_branch_length_values;
-    }
-
     void setShowConfidenceStddev( final boolean show_confidence_stddev ) {
         _show_confidence_stddev = show_confidence_stddev;
     }
@@ -446,7 +437,6 @@ final public class Options {
         _default_node_shape = NodeShape.CIRCLE;
         _default_node_fill = NodeFill.GRADIENT;
         _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
-        _show_branch_length_values = false;
         _internal_number_are_confidence_for_nh_parsing = false;
         _show_scale = false;
         _antialias_screen = true;
@@ -507,7 +497,6 @@ final public class Options {
         if ( configuration != null ) {
             instance.setAntialiasScreen( configuration.isAntialiasScreen() );
             instance.setShowScale( configuration.isShowScale() );
-            instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() );
             instance.setShowOverview( configuration.isShowOverview() );
             instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() );
             instance.setCladogramType( configuration.getCladogramType() );

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 3f6496b..e96c197 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -4312,7 +4312,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
             return 0;
         }
-        if ( getOptions().isShowBranchLengthValues()
+        if ( getControlPanel().isWriteBranchLengthValues()
                 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
                         || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
                 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
@@ -4883,14 +4883,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height;
                 rs.setRenderingHeight( h > 1 ? h : 2 );
                 if ( getControlPanel().isDrawPhylogram() ) {
-                   
-                        rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
-                                   node.getYcoord() - ( h / 2 ),
-                                   g,
-                                   this,
-                                   to_pdf );
-                    
-                    
+                    rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
+                               node.getYcoord() - ( h / 2 ),
+                               g,
+                               this,
+                               to_pdf );
                 }
                 else {
                     rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,

diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java
index d70eb12..1fe52bc 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java
+++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java
@@ -43,7 +43,6 @@ import org.forester.archaeopteryx.Constants;
 import org.forester.archaeopteryx.TreePanel;
 import org.forester.phylogeny.data.DomainArchitecture;
 import org.forester.phylogeny.data.PhylogenyData;
-import org.forester.phylogeny.data.PhylogenyDataUtil;
 import org.forester.phylogeny.data.ProteinDomain;
 import org.forester.util.ForesterUtil;
 
@@ -56,8 +55,8 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple
     private final DomainArchitecture  _domain_structure;
     private int                       _e_value_threshold_exp        = E_VALUE_THRESHOLD_EXP_DEFAULT;
     private final Rectangle2D         _rectangle                    = new Rectangle2D.Float();
-    private float                    _rendering_factor_width       = 1;
-    private float                    _rendering_height             = 0;
+    private float                     _rendering_factor_width       = 1;
+    private float                     _rendering_height             = 0;
 
     public RenderableDomainArchitecture( final DomainArchitecture domain_structure ) {
         _domain_structure = domain_structure;
@@ -201,13 +200,9 @@ public final class RenderableDomainArchitecture extends DomainArchitecture imple
                     else {
                         g.setColor( Constants.DOMAIN_LABEL_COLOR_FOR_PDF );
                     }
-                    g.drawString( d.getName(),
-                                  xa,
-                                  y1
-                                  + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent()
-                                  + _rendering_height  );
-                    
-                    
+                    g.drawString( d.getName(), xa, y1
+                            + tree_panel.getMainPanel().getTreeFontSet().getFontMetricsSmall().getAscent()
+                            + _rendering_height );
                 }
                 drawDomain( xa, y1, xb - xa, _rendering_height, d.getName(), g, to_pdf );
             }

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
index 57d9c3c..8b89646 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java
@@ -146,7 +146,6 @@ public class PhylogeneticInferrer extends RunnableProcess {
         final Phylogeny phy = nj.execute( m );
         PhylogenyMethods.addMolecularSeqsToTree( phy, msa );
         PhylogenyMethods.extractFastaInformation( phy );
-        
         return phy;
     }
 

diff --git a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java
index 5718086..76d60b7 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java
+++ b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java
@@ -371,8 +371,6 @@ public final class PhylogenyDataUtil {
                     org.forester.util.ForesterUtil.roundToInt( y2 ) );
     }
 
-   
-
     public static String replaceIllegalXmlCharacters( final String value ) {
         String v = value.replaceAll( "&", "&" );
         v = v.replaceAll( "<", "&lt;" );