in progress

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

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index efbd7ae..b1688a3 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -88,6 +88,7 @@ import org.forester.msa.MsaFormatException;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
@@ -233,6 +234,13 @@ public final class MainFrameApplication extends MainFrame {
     JMenuItem                                _read_values_jmi;
 
     private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
+        this( phys, config, title, null );
+    }
+
+    private MainFrameApplication( final Phylogeny[] phys,
+                                  final Configuration config,
+                                  final String title,
+                                  final File current_dir ) {
         _configuration = config;
         if ( _configuration == null ) {
             throw new IllegalArgumentException( "configuration is null" );
@@ -278,6 +286,9 @@ public final class MainFrameApplication extends MainFrame {
         catch ( final Exception e ) {
             AptxUtil.dieWithSystemError( e.toString() );
         }
+        if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
+            setCurrentDir( current_dir );
+        }
         // hide until everything is ready
         setVisible( false );
         setOptions( Options.createInstance( _configuration ) );
@@ -828,15 +839,19 @@ public final class MainFrameApplication extends MainFrame {
         _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
         _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
         _options_jmenu.addSeparator();
-        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input/Output:" ),
-                                                      getConfiguration() ) );
+        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
         _options_jmenu
-                .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Numbers Are Confidence Values" ) );
+                .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
         _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
         _options_jmenu
                 .add( _extract_pfam_style_tax_codes_cbmi = new JCheckBoxMenuItem( "Extract Taxonomy Codes from Pfam-style Labels" ) );
+        _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
         _options_jmenu
                 .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
+        _use_brackets_for_conf_in_nh_export_cbmi
+                .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
+        _options_jmenu
+                .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
         customizeJMenuItem( _choose_font_mi );
         customizeJMenuItem( _choose_minimal_confidence_mi );
         customizeJMenuItem( _switch_colors_mi );
@@ -880,7 +895,9 @@ public final class MainFrameApplication extends MainFrame {
                 .isGraphicsExportUsingActualSize() );
         customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
         customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
-                .isUseBracketsForConfInNhExport() );
+                .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+        customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
+                .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
         _jmenubar.add( _options_jmenu );
     }
 
@@ -903,10 +920,10 @@ public final class MainFrameApplication extends MainFrame {
         _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
         customizeJMenuItem( _collapse_species_specific_subtrees );
         _tools_menu
-                .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold" ) );
+                .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
         customizeJMenuItem( _collapse_below_threshold );
         _collapse_below_threshold
-                .setToolTipText( "To permanently collapse branches without at least one support value above a given threshold" );
+                .setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
         _tools_menu.addSeparator();
         _tools_menu
                 .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
@@ -1096,8 +1113,14 @@ public final class MainFrameApplication extends MainFrame {
                 phy.hashIDs();
                 phy.recalculateNumberOfExternalDescendants( true );
                 getCurrentTreePanel().resetNodeIdToDistToLeafMap();
+                getCurrentTreePanel().updateSetOfCollapsedExternalNodes( phy );
+                getCurrentTreePanel().calculateLongestExtNodeInfo();
+                getCurrentTreePanel().setNodeInPreorderToNull();
+                getCurrentTreePanel().recalculateMaxDistanceToRoot();
+                getCurrentTreePanel().resetPreferredSize();
                 getCurrentTreePanel().setEdited( true );
                 getCurrentTreePanel().repaint();
+                repaint();
             }
             if ( to_be_removed.size() > 0 ) {
                 JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
@@ -2318,7 +2341,7 @@ public final class MainFrameApplication extends MainFrame {
     private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();
-            writer.toNewHampshire( t, false, true, getOptions().isUseBracketsForConfInNhExport(), file );
+            writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
         }
         catch ( final Exception e ) {
             exception = true;
@@ -2330,7 +2353,7 @@ public final class MainFrameApplication extends MainFrame {
     private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();
-            writer.toNexus( file, t );
+            writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
         }
         catch ( final Exception e ) {
             exception = true;
@@ -2596,6 +2619,13 @@ public final class MainFrameApplication extends MainFrame {
         return new MainFrameApplication( phys, config_file_name, title );
     }
 
+    public static MainFrame createInstance( final Phylogeny[] phys,
+                                            final Configuration config,
+                                            final String title,
+                                            final File current_dir ) {
+        return new MainFrameApplication( phys, config, title, current_dir );
+    }
+
     static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
         mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
                 + o.getPrintSizeY() + ")" );