inprogress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / MainFrameApplet.java

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
index 8df235b..4a5c932 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java
@@ -24,7 +24,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -52,8 +52,9 @@ import org.forester.util.ForesterUtil;
 
 public final class MainFrameApplet extends MainFrame {
 
-    private static final long    serialVersionUID = 1941019292746717053L;
-    private final static int     FRAME_X_SIZE     = 640, FRAME_Y_SIZE = 580;
+    private static final long    serialVersionUID     = 1941019292746717053L;
+    private final static int     DEFAULT_FRAME_X_SIZE = 640;
+    private final static int     DEFAULT_FRAME_Y_SIZE = 580;
     private final ArchaeopteryxA _applet;
     private ButtonGroup          _radio_group_1;
 
@@ -66,16 +67,16 @@ public final class MainFrameApplet extends MainFrame {
         URL url = null;
         Phylogeny[] phys = null;
         // Get URL to tree file
-        if ( _applet.getUrlString() != null ) {
+        if ( _applet.getTreeUrlStr() != null ) {
             try {
-                url = new URL( _applet.getUrlString() );
+                url = new URL( _applet.getTreeUrlStr() );
             }
             catch ( final Exception e ) {
                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
                 e.printStackTrace();
                 JOptionPane.showMessageDialog( this,
                                                ArchaeopteryxA.NAME + ": Could not create URL from: \""
-                                                       + _applet.getUrlString() + "\"\nError: " + e,
+                                                       + _applet.getTreeUrlStr() + "\"\nError: " + e,
                                                "Failed to create URL",
                                                JOptionPane.ERROR_MESSAGE );
                 close();
@@ -84,7 +85,11 @@ public final class MainFrameApplet extends MainFrame {
         // Load the tree from URL
         if ( url != null ) {
             try {
-                phys = AptxUtil.readPhylogeniesFromUrl( url, getConfiguration().isValidatePhyloXmlAgainstSchema() );
+                phys = AptxUtil.readPhylogeniesFromUrl( url,
+                                                        configuration.isValidatePhyloXmlAgainstSchema(),
+                                                        configuration.isReplaceUnderscoresInNhParsing(),
+                                                        configuration.isInternalNumberAreConfidenceForNhParsing(),
+                                                        configuration.getTaxonomyExtraction() );
             }
             catch ( final Exception e ) {
                 ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, e.toString() );
@@ -108,6 +113,8 @@ public final class MainFrameApplet extends MainFrame {
         if ( !_configuration.isUseNativeUI() ) {
             _jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
         }
+        //TODO if species tree...
+        buildAnalysisMenu();
         buildToolsMenu();
         buildViewMenu();
         buildFontSizeMenu();
@@ -118,7 +125,8 @@ public final class MainFrameApplet extends MainFrame {
         _contentpane = getContentPane();
         _contentpane.setLayout( new BorderLayout() );
         _contentpane.add( _mainpanel, BorderLayout.CENTER );
-        setSize( FRAME_X_SIZE, FRAME_Y_SIZE );
+        setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE,
+                 getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE );
         addWindowListener( new WindowAdapter() {
 
             @Override
@@ -131,11 +139,11 @@ public final class MainFrameApplet extends MainFrame {
             @Override
             public void componentResized( final ComponentEvent e ) {
                 if ( _mainpanel.getCurrentTreePanel() != null ) {
-                    _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel()
-                                                                                       .getWidth(),
-                                                                               _mainpanel.getCurrentTreePanel()
-                                                                                       .getHeight(),
-                                                                               false );
+                    _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
+                                                                                        .getWidth(),
+                                                                                _mainpanel.getCurrentTreePanel()
+                                                                                        .getHeight(),
+                                                                                getOptions().isAllowFontSizeChange() );
                 }
             }
         } );
@@ -146,6 +154,19 @@ public final class MainFrameApplet extends MainFrame {
         System.gc();
     }
 
+    void buildAnalysisMenu() {
+        _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
+        _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
+        _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
+        customizeJMenuItem( _gsdi_item );
+        customizeJMenuItem( _gsdir_item );
+        //  _analysis_menu.addSeparator();
+        //  _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
+        //  customizeJMenuItem( _lineage_inference );
+        //  _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
+        _jmenubar.add( _analysis_menu );
+    }
+
     void buildOptionsMenu() {
         _options_jmenu = MainFrame.createMenu( MainFrame.OPTIONS_HEADER, getConfiguration() );
         _options_jmenu.addChangeListener( new ChangeListener() {
@@ -185,7 +206,10 @@ public final class MainFrameApplet extends MainFrame {
         _options_jmenu
                 .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
         _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );
-        _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
+        _options_jmenu
+                .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+        _options_jmenu
+                .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
         _options_jmenu
                 .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
         _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
@@ -216,7 +240,10 @@ public final class MainFrameApplet extends MainFrame {
         customizeJMenuItem( _switch_colors_mi );
         customizeJMenuItem( _choose_minimal_confidence_mi );
         customizeJMenuItem( _overview_placment_mi );
-        customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
+                .isShowDefaultNodeShapesInternal() );
+        customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
+                .isShowDefaultNodeShapesExternal() );
         customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
         customizeJMenuItem( _cycle_node_shape_mi );
         customizeJMenuItem( _cycle_node_fill_mi );
@@ -275,4 +302,8 @@ public final class MainFrameApplet extends MainFrame {
     void readPhylogeniesFromURL() {
         throw new NoSuchMethodError( "not implemented" );
     }
+
+    void setSpeciesTree( final Phylogeny species_tree ) {
+        _species_tree = species_tree;
+    }
 }