Applet is going more functions.

diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java
index c78bde4..d204f5f 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java
@@ -60,6 +60,8 @@ public class ArchaeopteryxA extends JApplet {
             getMainFrameApplet().close();
         }
     }
+    
+    
 
     /**
      * This method returns the current external node data which

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index 3a83b40..ba09c6a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,8 +42,8 @@ public final class Constants {
     public final static boolean __SYNTH_LF                                                    = false;                                                                             // TODO remove me
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9904 beta";
-    final static String         PRG_DATE                                                      = "150218";
+    final static String         VERSION                                                       = "0.9905 experimental";
+    final static String         PRG_DATE                                                      = "150304";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Arial", "Helvetica",
             "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans"  };

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index 505918e..e8d28e0 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -41,6 +41,7 @@ import java.util.NoSuchElementException;
 import javax.swing.Box;\r
 import javax.swing.JApplet;\r
 import javax.swing.JCheckBoxMenuItem;\r
+import javax.swing.JFileChooser;\r
 import javax.swing.JFrame;\r
 import javax.swing.JLabel;\r
 import javax.swing.JMenu;\r
@@ -58,6 +59,8 @@ import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
 import org.forester.archaeopteryx.tools.InferenceManager;\r
 import org.forester.archaeopteryx.tools.ProcessPool;\r
 import org.forester.archaeopteryx.tools.ProcessRunning;\r
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;\r
+import org.forester.archaeopteryx.webservices.WebservicesManager;\r
 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
 import org.forester.phylogeny.Phylogeny;\r
 import org.forester.phylogeny.PhylogenyMethods;\r
@@ -74,6 +77,7 @@ import org.forester.sdi.GSDIR;
 import org.forester.sdi.SDIException;\r
 import org.forester.util.ForesterConstants;\r
 import org.forester.util.ForesterUtil;\r
+import org.forester.util.WindowsUtils;\r
 \r
 public abstract class MainFrame extends JFrame implements ActionListener {\r
 \r
@@ -152,6 +156,13 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _close_item;\r
     JMenuItem                   _exit_item;\r
     JMenuItem                   _new_item;\r
+   JMenuItem                        _print_item;\r
+    JMenuItem                        _write_to_pdf_item;\r
+    JMenuItem                        _write_to_jpg_item;\r
+    JMenuItem                        _write_to_gif_item;\r
+    JMenuItem                        _write_to_tif_item;\r
+   JMenuItem                        _write_to_png_item;\r
+    JMenuItem                        _write_to_bmp_item;\r
     // tools menu:\r
     JMenuItem                   _midpoint_root_item;\r
     JMenuItem                   _taxcolor_item;\r
@@ -250,6 +261,10 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                   _phyloxml_website_item;\r
     JMenuItem                   _phyloxml_ref_item;\r
     JMenuItem                   _aptx_ref_item;\r
+    //\r
+    JFileChooser               _writetopdf_filechooser;\r
+    File                             _current_dir;\r
+    \r
     // process menu:\r
     JMenu                       _process_menu;\r
     // Handy pointers to child components:\r
@@ -265,6 +280,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
 \r
     MainFrame() {\r
         _process_pool = ProcessPool.createInstance();\r
+        _writetopdf_filechooser = new JFileChooser();\r
     }\r
 \r
     /**\r
@@ -573,6 +589,9 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
             }\r
         }\r
+        else if ( o == _write_to_pdf_item ) {\r
+            writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
+        }\r
         else {\r
             if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
                 for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
@@ -585,6 +604,122 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         _contentpane.repaint();\r
     }\r
 \r
+    \r
+    void setCurrentDir( final File current_dir ) {\r
+        _current_dir = current_dir;\r
+    } \r
+    \r
+   void writeToPdf( final Phylogeny t ) {\r
+        if ( ( t == null ) || t.isEmpty() ) {\r
+            return;\r
+        }\r
+        String initial_filename = "";\r
+        if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+            initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+        }\r
+        if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+            initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+        }\r
+        initial_filename = initial_filename + ".pdf";\r
+        _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
+        final File my_dir = getCurrentDir();\r
+        if ( my_dir != null ) {\r
+            _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
+        }\r
+        final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
+        File file = _writetopdf_filechooser.getSelectedFile();\r
+        setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
+        if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+            if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
+                file = new File( file.toString() + ".pdf" );\r
+            }\r
+            if ( file.exists() ) {\r
+                final int i = JOptionPane.showConfirmDialog( this,\r
+                                                             file + " already exists. Overwrite?",\r
+                                                             "WARNING",\r
+                                                             JOptionPane.OK_CANCEL_OPTION,\r
+                                                             JOptionPane.WARNING_MESSAGE );\r
+                if ( i != JOptionPane.OK_OPTION ) {\r
+                    return;\r
+                }\r
+            }\r
+            printPhylogenyToPdf( file.toString() );\r
+        }\r
+    }\r
+\r
+   \r
+    void printPhylogenyToPdf( final String file_name ) {\r
+       if ( !getOptions().isPrintUsingActualSize() ) {\r
+           getCurrentTreePanel()\r
+           .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
+           getCurrentTreePanel().resetPreferredSize();\r
+           getCurrentTreePanel().repaint();\r
+       }\r
+       String pdf_written_to = "";\r
+       boolean error = false;\r
+       try {\r
+           if ( getOptions().isPrintUsingActualSize() ) {\r
+               pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
+                                                                 getCurrentTreePanel(),\r
+                                                                 getCurrentTreePanel().getWidth(),\r
+                                                                 getCurrentTreePanel().getHeight() );\r
+           }\r
+           else {\r
+               pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
+                       .getPrintSizeX(), getOptions().getPrintSizeY() );\r
+           }\r
+       }\r
+       catch ( final IOException e ) {\r
+           error = true;\r
+           JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+       }\r
+       if ( !error ) {\r
+           if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
+               JOptionPane.showMessageDialog( this,\r
+                                              "Wrote PDF to: " + pdf_written_to,\r
+                                              "Information",\r
+                                              JOptionPane.INFORMATION_MESSAGE );\r
+           }\r
+           else {\r
+               JOptionPane.showMessageDialog( this,\r
+                                              "There was an unknown problem when attempting to write to PDF file: \""\r
+                                                      + file_name + "\"",\r
+                                              "Error",\r
+                                              JOptionPane.ERROR_MESSAGE );\r
+           }\r
+       }\r
+       if ( !getOptions().isPrintUsingActualSize() ) {\r
+           getControlPanel().showWhole();\r
+       }\r
+   }\r
+   \r
+    ControlPanel getControlPanel() {\r
+        return getMainPanel().getControlPanel();\r
+    }\r
+\r
+    \r
+    File getCurrentDir() {\r
+       if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+           if ( ForesterUtil.isWindows() ) {\r
+               try {\r
+                   _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
+               }\r
+               catch ( final Exception e ) {\r
+                   _current_dir = null;\r
+               }\r
+           }\r
+       }\r
+       if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+           if ( System.getProperty( "user.home" ) != null ) {\r
+               _current_dir = new File( System.getProperty( "user.home" ) );\r
+           }\r
+           else if ( System.getProperty( "user.dir" ) != null ) {\r
+               _current_dir = new File( System.getProperty( "user.dir" ) );\r
+           }\r
+       }\r
+       return _current_dir;\r
+   }\r
+    \r
     private void deleteSelectedNodes( final boolean delete ) {\r
         final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
         if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
@@ -741,9 +876,50 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         }\r
     }\r
 \r
+//    void buildFileMenu() {\r
+//        _file_jmenu = createMenu( "File", getConfiguration() );\r
+//        _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+//        customizeJMenuItem( _exit_item );\r
+//        _jmenubar.add( _file_jmenu );\r
+//    }\r
+    \r
     void buildFileMenu() {\r
-        _file_jmenu = createMenu( "File", getConfiguration() );\r
+        _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+        \r
+       // _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+       // _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
+       // _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
+       // _save_all_item.setEnabled( false );\r
+       // _file_jmenu.addSeparator();\r
+        _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
+//        if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+//            _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
+//        }\r
+//        _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+//        _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+//        if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+//            _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
+//        }\r
+//        if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+//            _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+//        }\r
+     //   _file_jmenu.addSeparator();\r
+      //  _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+        _file_jmenu.addSeparator();\r
+\r
         _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+       \r
+       customizeJMenuItem( _save_item );\r
+\r
+// customizeJMenuItem( _close_item );\r
+ //customizeJMenuItem( _save_all_item );\r
+        customizeJMenuItem( _write_to_pdf_item );\r
+//        customizeJMenuItem( _write_to_png_item );\r
+//        customizeJMenuItem( _write_to_jpg_item );\r
+//        customizeJMenuItem( _write_to_gif_item );\r
+//        customizeJMenuItem( _write_to_tif_item );\r
+//        customizeJMenuItem( _write_to_bmp_item );\r
+//        customizeJMenuItem( _print_item );\r
         customizeJMenuItem( _exit_item );\r
         _jmenubar.add( _file_jmenu );\r
     }\r

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index 2c0398b..f5bfd5c 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -87,6 +87,7 @@ public final class MainFrameApplet extends MainFrame {
         if ( getSpeciesTree() != null ) {
             buildAnalysisMenu();
         }
+        buildFileMenu();
         buildToolsMenu();
         buildViewMenu();
         buildFontSizeMenu();

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index fd49edc..dcf7818 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -133,19 +133,13 @@ public final class MainFrameApplication extends MainFrame {
     private final JFileChooser               _seqs_pi_filechooser;\r
     private final JFileChooser               _open_filechooser_for_species_tree;\r
     private final JFileChooser               _save_filechooser;\r
-    private final JFileChooser               _writetopdf_filechooser;\r
+   \r
     private final JFileChooser               _writetographics_filechooser;\r
     // Application-only print menu items\r
-    private JMenuItem                        _print_item;\r
-    private JMenuItem                        _write_to_pdf_item;\r
-    private JMenuItem                        _write_to_jpg_item;\r
-    private JMenuItem                        _write_to_gif_item;\r
-    private JMenuItem                        _write_to_tif_item;\r
-    private JMenuItem                        _write_to_png_item;\r
-    private JMenuItem                        _write_to_bmp_item;\r
+   \r
     private JMenuItem                        _collapse_below_threshold;\r
     private JMenuItem                        _collapse_below_branch_length;\r
-    private File                             _current_dir;\r
+   \r
     private ButtonGroup                      _radio_group_1;\r
     private ButtonGroup                      _radio_group_2;\r
     // Others:\r
@@ -439,9 +433,6 @@ public final class MainFrameApplication extends MainFrame {
             else if ( o == _close_item ) {\r
                 closeCurrentPane();\r
             }\r
-            else if ( o == _write_to_pdf_item ) {\r
-                writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
-            }\r
             else if ( o == _write_to_jpg_item ) {\r
                 writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );\r
             }\r
@@ -2007,31 +1998,8 @@ public final class MainFrameApplication extends MainFrame {
         }\r
     }\r
 \r
-    private ControlPanel getControlPanel() {\r
-        return getMainPanel().getControlPanel();\r
-    }\r
-\r
-    private File getCurrentDir() {\r
-        if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
-            if ( ForesterUtil.isWindows() ) {\r
-                try {\r
-                    _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
-                }\r
-                catch ( final Exception e ) {\r
-                    _current_dir = null;\r
-                }\r
-            }\r
-        }\r
-        if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
-            if ( System.getProperty( "user.home" ) != null ) {\r
-                _current_dir = new File( System.getProperty( "user.home" ) );\r
-            }\r
-            else if ( System.getProperty( "user.dir" ) != null ) {\r
-                _current_dir = new File( System.getProperty( "user.dir" ) );\r
-            }\r
-        }\r
-        return _current_dir;\r
-    }\r
+   \r
+   \r
 \r
     private double getMinNotCollapseConfidenceValue() {\r
         return _min_not_collapse;\r
@@ -2175,50 +2143,7 @@ public final class MainFrameApplication extends MainFrame {
         }\r
     }\r
 \r
-    private void printPhylogenyToPdf( final String file_name ) {\r
-        if ( !getOptions().isPrintUsingActualSize() ) {\r
-            getCurrentTreePanel()\r
-            .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
-            getCurrentTreePanel().resetPreferredSize();\r
-            getCurrentTreePanel().repaint();\r
-        }\r
-        String pdf_written_to = "";\r
-        boolean error = false;\r
-        try {\r
-            if ( getOptions().isPrintUsingActualSize() ) {\r
-                pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
-                                                                  getCurrentTreePanel(),\r
-                                                                  getCurrentTreePanel().getWidth(),\r
-                                                                  getCurrentTreePanel().getHeight() );\r
-            }\r
-            else {\r
-                pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
-                        .getPrintSizeX(), getOptions().getPrintSizeY() );\r
-            }\r
-        }\r
-        catch ( final IOException e ) {\r
-            error = true;\r
-            JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
-        }\r
-        if ( !error ) {\r
-            if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
-                JOptionPane.showMessageDialog( this,\r
-                                               "Wrote PDF to: " + pdf_written_to,\r
-                                               "Information",\r
-                                               JOptionPane.INFORMATION_MESSAGE );\r
-            }\r
-            else {\r
-                JOptionPane.showMessageDialog( this,\r
-                                               "There was an unknown problem when attempting to write to PDF file: \""\r
-                                                       + file_name + "\"",\r
-                                               "Error",\r
-                                               JOptionPane.ERROR_MESSAGE );\r
-            }\r
-        }\r
-        if ( !getOptions().isPrintUsingActualSize() ) {\r
-            getControlPanel().showWhole();\r
-        }\r
-    }\r
+   \r
 \r
     private void readPhylogeniesFromFile() {\r
         boolean exception = false;\r
@@ -2489,9 +2414,7 @@ public final class MainFrameApplication extends MainFrame {
         }\r
     }\r
 \r
-    private void setCurrentDir( final File current_dir ) {\r
-        _current_dir = current_dir;\r
-    }\r
+   \r
 \r
     private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
         _min_not_collapse = min_not_collapse;\r
@@ -2750,44 +2673,7 @@ public final class MainFrameApplication extends MainFrame {
         }\r
     }\r
 \r
-    private void writeToPdf( final Phylogeny t ) {\r
-        if ( ( t == null ) || t.isEmpty() ) {\r
-            return;\r
-        }\r
-        String initial_filename = "";\r
-        if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
-            initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
-        }\r
-        if ( initial_filename.indexOf( '.' ) > 0 ) {\r
-            initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
-        }\r
-        initial_filename = initial_filename + ".pdf";\r
-        _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
-        final File my_dir = getCurrentDir();\r
-        if ( my_dir != null ) {\r
-            _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
-        }\r
-        final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
-        File file = _writetopdf_filechooser.getSelectedFile();\r
-        setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
-        if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
-            if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
-                file = new File( file.toString() + ".pdf" );\r
-            }\r
-            if ( file.exists() ) {\r
-                final int i = JOptionPane.showConfirmDialog( this,\r
-                                                             file + " already exists. Overwrite?",\r
-                                                             "WARNING",\r
-                                                             JOptionPane.OK_CANCEL_OPTION,\r
-                                                             JOptionPane.WARNING_MESSAGE );\r
-                if ( i != JOptionPane.OK_OPTION ) {\r
-                    return;\r
-                }\r
-            }\r
-            printPhylogenyToPdf( file.toString() );\r
-        }\r
-    }\r
-\r
+    \r
     public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
         return new MainFrameApplication( phys, config );\r
     }\r