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 5053d83..f717323 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;
@@ -784,16 +785,17 @@ public final class MainFrameApplication extends MainFrame {
         _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
         _radio_group_1.add( _uniform_cladograms_rbmi );
         _radio_group_1.add( _non_lined_up_cladograms_rbmi );
+        _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
+        _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
+        _options_jmenu
+                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( 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( _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 ) );
         _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
         _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
-        _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
-        _options_jmenu
-                .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
-        _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
         _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
         _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
         _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
@@ -827,13 +829,19 @@ 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:" ), getConfiguration() ) );
         _options_jmenu
-                .add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Parsing:" ), 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 );
@@ -875,6 +883,11 @@ public final class MainFrameApplication extends MainFrame {
         customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
         customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
                 .isGraphicsExportUsingActualSize() );
+        customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+        customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
+                .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 );
     }
 
@@ -897,10 +910,10 @@ 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" ) );
@@ -1090,8 +1103,14 @@ 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()
@@ -2312,7 +2331,7 @@ 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, file );
+            writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
         }
         catch ( final Exception e ) {
             exception = true;
@@ -2324,7 +2343,7 @@ 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;