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[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrame.java
diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 0f7fd20..4bac494 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -65,8 +65,8 @@ import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Annotation;
-import org.forester.phylogeny.data.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
 import org.forester.sdi.GSDI;
 import org.forester.sdi.GSDIR;
 import org.forester.sdi.SDIException;
@@ -140,7 +140,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _lineage_inference;
     // file menu:
     JMenuItem                   _open_item;
-    JMenuItem                   _open_url_item;
     JMenuItem                   _save_item;
     JMenuItem                   _save_all_item;
     JMenuItem                   _close_item;
@@ -160,6 +159,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _move_node_names_to_seq_names_jmi;
     JMenuItem                   _extract_tax_code_from_node_names_jmi;
     JMenuItem                   _annotate_item;
+    JMenuItem                   _remove_branch_color_item;
+    JMenuItem                   _remove_visual_styles_item;
     // font size menu:
     JMenuItem                   _super_tiny_fonts_item;
     JMenuItem                   _tiny_fonts_item;
@@ -192,7 +193,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _cycle_node_shape_mi;
     JMenuItem                   _cycle_node_fill_mi;
     JMenuItem                   _choose_node_size_mi;
-    JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
     JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
     // _  print
     JCheckBoxMenuItem           _graphics_export_visible_only_cbmi;
@@ -209,6 +209,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JRadioButtonMenuItem        _extract_taxonomy_pfam_strict_rbmi;
     JRadioButtonMenuItem        _extract_taxonomy_pfam_relaxed_rbmi;
     JCheckBoxMenuItem           _replace_underscores_cbmi;
+    JCheckBoxMenuItem           _allow_errors_in_distance_to_parent_cbmi;
     JCheckBoxMenuItem           _use_brackets_for_conf_in_nh_export_cbmi;
     JCheckBoxMenuItem           _use_internal_names_for_conf_in_nh_export_cbmi;
     // _  search
@@ -244,7 +245,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     Container                   _contentpane;
     final LinkedList<TextFrame> _textframes                             = new LinkedList<TextFrame>();                                                                                                                                         ;
     Configuration               _configuration;
-    JMenuItem                   _remove_branch_color_item;
     Options                     _options;
     private Phylogeny           _species_tree;
     InferenceManager            _inference_manager;
@@ -269,10 +269,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 applet = getCurrentTreePanel().obtainApplet();
             }
         }
-        if ( o == _open_url_item ) {
-            readPhylogeniesFromURL();
-        }
-        else if ( o == _exit_item ) {
+        if ( o == _exit_item ) {
             close();
         }
         else if ( o == _gsdi_item ) {
@@ -310,6 +307,12 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             }
             removeBranchColors();
         }
+        else if ( o == _remove_visual_styles_item ) {
+            if ( isSubtreeDisplayed() ) {
+                return;
+            }
+            removeVisualStyles();
+        }
         else if ( o == _midpoint_root_item ) {
             if ( isSubtreeDisplayed() ) {
                 return;
@@ -407,9 +410,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         else if ( o == _show_default_node_shapes_external_cbmi ) {
             updateOptions( getOptions() );
         }
-        else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
-            updateOptions( getOptions() );
-        }
         else if ( o == _non_lined_up_cladograms_rbmi ) {
             updateOptions( getOptions() );
             showWhole();
@@ -424,15 +424,18 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
         else if ( o == _search_case_senstive_cbmi ) {
             updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
         }
         else if ( o == _search_whole_words_only_cbmi ) {
             updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
         }
         else if ( o == _inverse_search_result_cbmi ) {
             updateOptions( getOptions() );
-            getMainPanel().getControlPanel().search();
+            getMainPanel().getControlPanel().search0();
+            getMainPanel().getControlPanel().search1();
         }
         else if ( o == _show_scale_cbmi ) {
             updateOptions( getOptions() );
@@ -594,10 +597,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 
     void buildFileMenu() {
         _file_jmenu = createMenu( "File", getConfiguration() );
-        _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
-        _file_jmenu.addSeparator();
         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
-        customizeJMenuItem( _open_url_item );
         customizeJMenuItem( _exit_item );
         _jmenubar.add( _file_jmenu );
     }
@@ -1147,8 +1147,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
     }
 
-    abstract void readPhylogeniesFromURL();
-
     void readPhylogeniesFromWebservice( final int i ) {
         final UrlTreeReader reader = new UrlTreeReader( this, i );
         new Thread( reader ).start();
@@ -1280,8 +1278,6 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 && _show_default_node_shapes_internal_cbmi.isSelected() );
         options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
                 && _show_default_node_shapes_external_cbmi.isSelected() );
-        options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
-                && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
         if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
             options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
         }
@@ -1347,6 +1343,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
         options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
                 && _replace_underscores_cbmi.isSelected() );
+        options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
+                && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
         options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
                 && _search_whole_words_only_cbmi.isSelected() );
         options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
@@ -1409,8 +1407,8 @@ public abstract class MainFrame extends JFrame implements ActionListener {
             if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
             }
-            showTextFrame( _mainpanel.getCurrentPhylogeny()
-                                   .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
+            showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
+                                   .getNhConversionSupportValueStyle() ),
                            title );
         }
     }
@@ -1427,7 +1425,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 
     private void annotateSequences() {
         if ( getCurrentTreePanel() != null ) {
-            final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
+            final Set<Long> nodes = getCurrentTreePanel().getFoundNodes0();
             if ( ( nodes == null ) || nodes.isEmpty() ) {
                 JOptionPane
                         .showMessageDialog( this,
@@ -1567,6 +1565,12 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }
     }
 
+    private void removeVisualStyles() {
+        if ( getMainPanel().getCurrentPhylogeny() != null ) {
+            AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
+        }
+    }
+
     private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
         _previous_node_annotation_ref = previous_node_annotation_ref;
     }
@@ -1746,15 +1750,16 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 
     static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
         if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
-            mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
+            mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
+                    + ")" );
         }
         else {
-            mi.setText( "Select Colors..." );
+            mi.setText( "Select Color Scheme..." );
         }
     }
 
     static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
-        mi.setText( "Select Font... (current: " + font_desc + ")" );
+        mi.setText( "Select Default Font... (current: " + font_desc + ")" );
     }
 
     static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {