X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=9488a1c9a188327ed4ab8687b9eaa819f0606c17;hb=cb49ee5684c6907b3161db82ff9aea72961b8548;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..9488a1c 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -77,7 +77,6 @@ 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 +102,8 @@ 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;
@@ -761,10 +760,7 @@ 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 +1349,9 @@ 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();
     }
@@ -1834,6 +1825,11 @@ 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 +1937,8 @@ 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,