inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 89a0cda..35b0e2b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -795,9 +795,8 @@ public final class AptxUtil {
                 desc.append( "\n" );
                 desc.append( "    Median: " + ForesterUtil.round( bs.median(), 6 ) );
                 desc.append( "\n" );
-                desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) );
-                desc.append( "\n" );
-                desc.append( "    SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) );
+                desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (±"
+                        + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
                 desc.append( "\n" );
                 desc.append( "    Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
                 desc.append( "\n" );
@@ -816,9 +815,8 @@ public final class AptxUtil {
                 desc.append( "\n" );
                 desc.append( "    Median: " + ForesterUtil.round( ds.median(), 2 ) );
                 desc.append( "\n" );
-                desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
-                desc.append( "\n" );
-                desc.append( "    SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
+                desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) + " (±"
+                        + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) + ")" );
                 desc.append( "\n" );
                 desc.append( "    Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
                 desc.append( "\n" );

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index a855d90..aab7b78 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -262,6 +262,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
         else if ( o == _label_direction_cbmi ) {
             updateOptions( getOptions() );
         }
+        else if ( o == _abbreviate_scientific_names ) {
+            updateOptions( getOptions() );
+        }
         else if ( o == _show_overview_cbmi ) {
             updateOptions( getOptions() );
             if ( getCurrentTreePanel() != null ) {
@@ -812,7 +815,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
 
     void buildViewMenu() {
         _view_jmenu = MainFrame.createMenu( "View", getConfiguration() );
-        _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+        _view_jmenu
+                .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) );
         _view_jmenu.addSeparator();
         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );

diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 8c80f0c..d1c071c 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -470,11 +470,11 @@ final class ControlPanel extends JPanel implements ActionListener {
         _zoom_in_y = new JButton( "Y+" );
         _zoom_out_y = new JButton( "Y-" );
         _show_whole = new JButton( "F" );
-        _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [Backspace]" );
-        _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+Right]" );
-        _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+Up]" );
-        _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+Left]" );
-        _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+Down]" );
+        _show_whole.setToolTipText( "To fit the complete phylogeny to the current display size [F or Home]" );
+        _zoom_in_x.setToolTipText( "To zoom in horizontally [Shift+cursor-right]" );
+        _zoom_in_y.setToolTipText( "To zoom in vertically [Shift+cursor-up]" );
+        _zoom_out_x.setToolTipText( "To zoom out horizontally [Shift+cursor-left]" );
+        _zoom_out_y.setToolTipText( "To zoom out vertically [Shift+cursor-down]" );
         if ( getConfiguration().isUseNativeUI() && AptxUtil.isMac() ) {
             _zoom_out_x.setPreferredSize( new Dimension( 55, 10 ) );
             _zoom_in_x.setPreferredSize( new Dimension( 55, 10 ) );

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index c26c630..e4bd6f1 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -120,6 +120,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     static final String         SHOW_CONF_STDDEV_LABEL                  = "Show Confidence Standard Deviations";
     static final String         USE_BRACKETS_FOR_CONF_IN_NH_LABEL       = "Use Brackets for Confidence Values";
     static final String         USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
+    static final String         SHOW_BASIC_TREE_INFORMATION_LABEL       = "Show Basic Tree Information";
     JMenuBar                    _jmenubar;
     JMenu                       _file_jmenu;
     JMenu                       _tools_menu;
@@ -651,7 +652,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 
     void buildViewMenu() {
         _view_jmenu = createMenu( "View", getConfiguration() );
-        _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+        _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
         _view_jmenu.addSeparator();
         _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
         _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );

diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
index 454ca74..e4b7dc7 100644 (file)
--- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
+++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
@@ -622,44 +622,24 @@ public final class PhylogenyWriter {
         }
         if ( tree != null ) {
             reset( writer, tree );
-            boolean rerootable = true;
             String unit = "";
             String type = "";
-            String rooted = "false";
-            if ( tree.isRooted() ) {
-                rooted = "true";
-            }
-            if ( !tree.isRerootable() ) {
-                rerootable = false;
-            }
             if ( !ForesterUtil.isEmpty( tree.getDistanceUnit() ) ) {
                 unit = tree.getDistanceUnit();
             }
             if ( !ForesterUtil.isEmpty( tree.getType() ) ) {
                 type = tree.getType();
             }
-            if ( rerootable ) {
-                PhylogenyDataUtil.appendOpen( writer,
-                                              PhyloXmlMapping.PHYLOGENY,
-                                              PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR,
-                                              rooted,
-                                              PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR,
-                                              unit,
-                                              PhyloXmlMapping.PHYLOGENY_TYPE_ATTR,
-                                              type );
-            }
-            else {
-                PhylogenyDataUtil.appendOpen( writer,
-                                              PhyloXmlMapping.PHYLOGENY,
-                                              PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR,
-                                              rooted,
-                                              PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR,
-                                              unit,
-                                              PhyloXmlMapping.PHYLOGENY_TYPE_ATTR,
-                                              type,
-                                              PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR,
-                                              "false" );
-            }
+            PhylogenyDataUtil.appendOpen( writer,
+                                          PhyloXmlMapping.PHYLOGENY,
+                                          PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR,
+                                          tree.isRooted() + "",
+                                          PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR,
+                                          unit,
+                                          PhyloXmlMapping.PHYLOGENY_TYPE_ATTR,
+                                          type,
+                                          PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR,
+                                          tree.isRerootable() + "" );
             appendPhylogenyLevelPhyloXml( writer, tree );
             while ( isHasNext() ) {
                 next();