X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=3954da02587b4b9c5b90f64c03178729b1ac243e;hb=e6ea1a1dcb0a9b96cad1bc08c3b80a6f876344d2;hp=72bb43f4ad48a5bd4268df8b8915087e0b3f25fd;hpb=d33a5a1d64863f9b0207e1da71151396cea74a38;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 72bb43f..3954da0 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -96,6 +96,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JMenuItem                   _phyloxml_ref_item;
     private JMenuItem                   _aptx_ref_item;
     private JMenuItem                   _remove_branch_color_item;
+    private JMenuItem                   _remove_visual_styles_item;
     private JCheckBoxMenuItem           _show_domain_labels;
     private JCheckBoxMenuItem           _show_annotation_ref_source;
     private JCheckBoxMenuItem           _color_labels_same_as_parent_branch;
@@ -125,7 +126,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
     private JMenuItem                   _cycle_node_shape_mi;
     private JMenuItem                   _cycle_node_fill_mi;
     private JMenuItem                   _choose_node_size_mi;
-    private JCheckBoxMenuItem           _taxonomy_colorize_node_shapes_cbmi;
     private JCheckBoxMenuItem           _show_confidence_stddev_cbmi;
     private final LinkedList<TextFrame> _textframes      = new LinkedList<TextFrame>();
     private JMenu                       _analysis_menu;
@@ -165,6 +165,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( o == _remove_branch_color_item ) {
             removeBranchColors();
         }
+        else if ( o == _remove_visual_styles_item ) {
+            removeVisualStyles();
+        }
         else if ( o == _switch_colors_mi ) {
             switchColors();
         }
@@ -300,9 +303,6 @@ public class ArchaeopteryxE extends JApplet 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 == _about_item ) {
             MainFrame.about();
         }
@@ -450,45 +450,65 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         setConfiguration( configuration );
         setOptions( Options.createInstance( configuration ) );
         setupUI();
-        URL phys_url = null;
-        Phylogeny[] phys = null;
         final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+        if ( ForesterUtil.isEmpty( tree_url_str ) ) {
+            ForesterUtil.printErrorMessage( NAME, "could not get tree URL from "
+                    + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+            JOptionPane.showMessageDialog( this, NAME + ": could not get tree URL from "
+                    + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD, "Failed get URL", JOptionPane.ERROR_MESSAGE );
+            return;
+        }
         AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
         // Get URL to tree file
-        if ( tree_url_str != null ) {
-            try {
-                phys_url = new URL( tree_url_str );
-            }
-            catch ( final Exception e ) {
-                ForesterUtil.printErrorMessage( NAME, "error: " + e );
-                e.printStackTrace();
-                JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
-                        + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
-            }
+        URL phys_url = null;
+        try {
+            phys_url = new URL( tree_url_str );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.printErrorMessage( NAME, "error: " + e );
+            e.printStackTrace();
+            JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
+                    + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
+        }
+        if ( phys_url == null ) {
+            ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from "
+                    + Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+            JOptionPane.showMessageDialog( this,
+                                           NAME + ": Could not create URL from: \"" + tree_url_str,
+                                           "Failed to create URL",
+                                           JOptionPane.ERROR_MESSAGE );
+            return;
         }
         // Load the tree from URL
-        if ( phys_url != null ) {
-            try {
-                phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
-                                                        getConfiguration().isValidatePhyloXmlAgainstSchema(),
-                                                        getConfiguration().isReplaceUnderscoresInNhParsing(),
-                                                        getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
-                                                        getConfiguration().getTaxonomyExtraction(),
-                                                        getConfiguration().isMidpointReroot() );
-            }
-            catch ( final Exception e ) {
-                ForesterUtil.printErrorMessage( NAME, e.toString() );
-                e.printStackTrace();
-                JOptionPane.showMessageDialog( this,
-                                               NAME + ": Failed to read phylogenies: " + "\nException: " + e,
-                                               "Failed to read phylogenies",
-                                               JOptionPane.ERROR_MESSAGE );
-            }
+        Phylogeny[] phys = null;
+        try {
+            phys = AptxUtil.readPhylogeniesFromUrl( phys_url,
+                                                    getConfiguration().isValidatePhyloXmlAgainstSchema(),
+                                                    getConfiguration().isReplaceUnderscoresInNhParsing(),
+                                                    getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
+                                                    getConfiguration().getTaxonomyExtraction(),
+                                                    getConfiguration().isMidpointReroot() );
         }
-        if ( ( phys == null ) || ( phys.length < 1 ) ) {
-            ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null or empty" );
+        catch ( final Exception e ) {
+            ForesterUtil.printErrorMessage( NAME, e.toString() );
+            e.printStackTrace();
+            JOptionPane.showMessageDialog( this,
+                                           NAME + ": Failed to read phylogenies: " + "\nException: " + e,
+                                           "Failed to read phylogenies",
+                                           JOptionPane.ERROR_MESSAGE );
+        }
+        if ( phys == null ) {
+            ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are null" );
             JOptionPane.showMessageDialog( this,
-                                           NAME + ": phylogenies from [" + phys_url + "] are null or empty",
+                                           NAME + ": phylogenies from [" + phys_url + "] are null",
+                                           "Failed to read phylogenies",
+                                           JOptionPane.ERROR_MESSAGE );
+            return;
+        }
+        else if ( phys.length < 1 ) {
+            ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + phys_url + "] are empty" );
+            JOptionPane.showMessageDialog( this,
+                                           NAME + ": phylogenies from [" + phys_url + "] are empty",
                                            "Failed to read phylogenies",
                                            JOptionPane.ERROR_MESSAGE );
             return;
@@ -588,8 +608,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         setName( NAME );
         getMainPanel().getControlPanel().showWholeAll();
         getMainPanel().getControlPanel().showWhole();
-        System.gc();
-        AptxUtil.printAppletMessage( NAME, "successfully initialized" );
         /* GUILHEM_BEG */
         getCurrentTreePanel().getControlPanel().getSequenceRelationTypeBox().removeAllItems();
         for( final SequenceRelation.SEQUENCE_RELATION_TYPE type : getMainPanel().getCurrentPhylogeny()
@@ -605,6 +623,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
         }
         /* GUILHEM_END */
+        System.gc();
+        AptxUtil.printAppletMessage( NAME, "successfully initialized" );
         setVisible( true );
     }
 
@@ -724,8 +744,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         _options_jmenu
                 .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) );
         _options_jmenu
-                .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
-        _options_jmenu
                 .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) );
         _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
         _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) );
@@ -765,7 +783,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
                 .isShowDefaultNodeShapesExternal() );
         customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
                 .isShowDefaultNodeShapesInternal() );
-        customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
         customizeJMenuItem( _choose_node_size_mi );
@@ -792,8 +809,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         customizeJMenuItem( _confcolor_item );
         _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
         customizeJMenuItem( _taxcolor_item );
-        _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
-        _remove_branch_color_item.setToolTipText( "To delete branch color values from the current phylogeny." );
+        _tools_menu.addSeparator();
+        _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
+        _remove_visual_styles_item
+                .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );
+        customizeJMenuItem( _remove_visual_styles_item );
+        _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
+        _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );
         customizeJMenuItem( _remove_branch_color_item );
         _tools_menu.addSeparator();
         _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );
@@ -1305,8 +1327,6 @@ public class ArchaeopteryxE extends JApplet 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 );
         }
@@ -1391,8 +1411,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) {
                 title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
             }
-            showTextFrame( getMainPanel().getCurrentPhylogeny()
-                                   .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
+            showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions()
+                                   .getNhConversionSupportValueStyle() ),
                            title );
         }
     }
@@ -1475,6 +1495,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         }
     }
 
+    private void removeVisualStyles() {
+        if ( getMainPanel().getCurrentPhylogeny() != null ) {
+            AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );
+        }
+    }
+
     private void setMainPanel( final MainPanelApplets main_panel ) {
         _mainpanel = main_panel;
     }