X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=dc9306377ab70c810cb7b1474806eed767d0c93f;hb=5642da5f473ab9ae57fee86c0cb3b33525a2e916;hp=3baabd1da0857ed4c2a5fc5d4e63290c2e9bdc71;hpb=4a71774e563925de62c37378a6c32c3275f2e287;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 3baabd1..dc93063 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -57,6 +57,8 @@ import javax.swing.UnsupportedLookAndFeelException;
 import javax.swing.WindowConstants;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
 
 import org.forester.analysis.TaxonomyDataManager;
 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
@@ -77,7 +79,6 @@ import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.io.parsers.tol.TolParser;
 import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.SequenceWriter;
@@ -103,8 +104,8 @@ import org.forester.util.ForesterUtil;
 
 public final class MainFrameApplication extends MainFrame {
 
-    private final static int             FRAME_X_SIZE                    = 800;
-    private final static int             FRAME_Y_SIZE                    = 800;
+    private final static int             FRAME_X_SIZE                    = 900;
+    private final static int             FRAME_Y_SIZE                    = 900;
     // Filters for the file-open dialog (classes defined in this file)
     private static final long            serialVersionUID                = -799735726778865234L;
     private static final boolean         PREPROCESS_TREES                = false;
@@ -162,10 +163,10 @@ public final class MainFrameApplication extends MainFrame {
         setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
         // The window listener
         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
-        addWindowListener( new WindowAdapter() {
+        addInternalFrameListener( new InternalFrameAdapter() {
 
             @Override
-            public void windowClosing( final WindowEvent e ) {
+            public void internalFrameClosing (final InternalFrameEvent e ) {
                 exit();
             }
         } );
@@ -303,14 +304,16 @@ public final class MainFrameApplication extends MainFrame {
         //        } );
         // The window listener
         setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
-        addWindowListener( new WindowAdapter() {
+ 
+        addInternalFrameListener( new InternalFrameAdapter() {
 
             @Override
-            public void windowClosing( final WindowEvent e ) {
+            public void internalFrameClosing( final InternalFrameEvent e ) {
+                if (MainFrameApplication.this.getParent() == null) {
                 if ( isUnsavedDataPresent() ) {
-                    final int r = JOptionPane.showConfirmDialog( null,
-                                                                 "Exit despite potentially unsaved changes?",
-                                                                 "Exit?",
+                    final int r = JOptionPane.showConfirmDialog( _mainpanel,
+                                                                 "Close Archaeopteryx despite potentially unsaved changes?",
+                                                                 "Close viewer?",
                                                                  JOptionPane.YES_NO_OPTION );
                     if ( r != JOptionPane.YES_OPTION ) {
                         return;
@@ -322,10 +325,10 @@ public final class MainFrameApplication extends MainFrame {
                     if ( r != JOptionPane.YES_OPTION ) {
                         return;
                     }
-                }
+                }}
                 exit();
-            }
-        } );
+            
+        } });
         // The component listener
         addComponentListener( new ComponentAdapter() {
 
@@ -516,7 +519,7 @@ public final class MainFrameApplication extends MainFrame {
                     msa = FastaParser.parseMsa( is );
                 }
                 else {
-                    msa = GeneralMsaParser.parse( is );
+                    msa = GeneralMsaParser.parseMsa( is );
                 }
             }
             catch ( final MsaFormatException e ) {
@@ -761,10 +764,7 @@ public final class MainFrameApplication extends MainFrame {
                         l.add( d );
                     }
                     if ( !l.isEmpty() ) {
-                        if ( node.getNodeData().getProperties() != null ) {
-                            node.getNodeData().getProperties()
-                                    .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
-                        }
+                       
                         node.getNodeData().setVector( l );
                     }
                 }
@@ -1353,14 +1353,9 @@ public final class MainFrameApplication extends MainFrame {
         _mainpanel.getControlPanel().showWhole();
         _mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
         _mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
-        if ( getMainPanel().getMainFrame() == null ) {
-            // Must be "E" applet version.
-            ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
-                    .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
-        }
-        else {
-            getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
-        }
+       
+        getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+       
         activateSaveAllIfNeeded();
         System.gc();
     }
@@ -1751,6 +1746,7 @@ public final class MainFrameApplication extends MainFrame {
         if ( AptxUtil.canWriteFormat( "bmp" ) ) {
             _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
         }
+        _file_jmenu.add( _write_to_eps_item = new JMenuItem("Export to EPS file...") );
         _file_jmenu.addSeparator();
         _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
         _file_jmenu.addSeparator();
@@ -1779,6 +1775,7 @@ public final class MainFrameApplication extends MainFrame {
         customizeJMenuItem( _write_to_gif_item );
         customizeJMenuItem( _write_to_tif_item );
         customizeJMenuItem( _write_to_bmp_item );
+        customizeJMenuItem( _write_to_eps_item );
         customizeJMenuItem( _print_item );
         customizeJMenuItem( _exit_item );
         _jmenubar.add( _file_jmenu );
@@ -1834,6 +1831,11 @@ public final class MainFrameApplication extends MainFrame {
 
         
         _options_jmenu
+        .add( _show_abbreviated_labels_for_collapsed_nodes_cbmi = new JCheckBoxMenuItem( "Add Abbreviated Labels to Collapsed Subtrees" ) );
+
+     
+        
+        _options_jmenu
                 .add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
         
        
@@ -1941,6 +1943,8 @@ public final class MainFrameApplication extends MainFrame {
         customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
         customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
         customizeCheckBoxMenuItem( _collapsed_with_average_height_cbmi, getOptions().isCollapsedWithAverageHeigh() );
+        customizeCheckBoxMenuItem( _show_abbreviated_labels_for_collapsed_nodes_cbmi, getOptions().isShowAbbreviatedLabelsForCollapsedNodes() );
+        
         customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
                                       getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
         customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,