import javax.swing.filechooser.FileFilter;
import javax.swing.plaf.synth.SynthLookAndFeel;
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
-import org.forester.archaeopteryx.Util.GraphicsExportType;
import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
import org.forester.archaeopteryx.tools.GoAnnotation;
import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
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;
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" );
//UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
}
catch ( final UnsupportedLookAndFeelException e ) {
- Util.dieWithSystemError( "unsupported look and feel: " + e.toString() );
+ AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
}
catch ( final ClassNotFoundException e ) {
- Util.dieWithSystemError( "class not found exception: " + e.toString() );
+ AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
}
catch ( final InstantiationException e ) {
- Util.dieWithSystemError( "instantiation exception: " + e.toString() );
+ AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
}
catch ( final IllegalAccessException e ) {
- Util.dieWithSystemError( "illegal access exception: " + e.toString() );
+ AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
}
catch ( final Exception e ) {
- Util.dieWithSystemError( e.toString() );
+ AptxUtil.dieWithSystemError( e.toString() );
+ }
+ if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
+ setCurrentDir( current_dir );
}
// hide until everything is ready
setVisible( false );
// addKeyListener( this );
setVisible( true );
if ( ( phys != null ) && ( phys.length > 0 ) ) {
- Util.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
+ AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
validate();
getMainPanel().getControlPanel().showWholeAll();
getMainPanel().getControlPanel().showWhole();
System.gc();
}
+ private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
+ _configuration = config;
+ if ( _configuration == null ) {
+ throw new IllegalArgumentException( "configuration is null" );
+ }
+ setVisible( false );
+ setOptions( Options.createInstance( _configuration ) );
+ _mainpanel = new MainPanel( _configuration, this );
+ _open_filechooser = null;
+ _open_filechooser_for_species_tree = null;
+ _save_filechooser = null;
+ _writetopdf_filechooser = null;
+ _writetographics_filechooser = null;
+ _msa_filechooser = null;
+ _seqs_filechooser = null;
+ _values_filechooser = null;
+ _jmenubar = new JMenuBar();
+ buildFileMenu();
+ buildTypeMenu();
+ _contentpane = getContentPane();
+ _contentpane.setLayout( new BorderLayout() );
+ _contentpane.add( _mainpanel, BorderLayout.CENTER );
+ // App is this big
+ setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
+ // The window listener
+ setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
+ addWindowListener( new WindowAdapter() {
+
+ @Override
+ public void windowClosing( final WindowEvent e ) {
+ exit();
+ }
+ } );
+ // setVisible( true );
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {
+ AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
+ validate();
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ }
+ //activateSaveAllIfNeeded();
+ // ...and its children
+ _contentpane.repaint();
+ }
+
private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
// Reads the config file (false, false => not url, not applet):
- this( phys, new Configuration( config_file, false, false ), title );
+ this( phys, new Configuration( config_file, false, false, true ), title );
}
@Override
_contentpane.repaint();
}
catch ( final Exception ex ) {
- Util.unexpectedException( ex );
+ AptxUtil.unexpectedException( ex );
}
catch ( final Error err ) {
- Util.unexpectedError( err );
+ AptxUtil.unexpectedError( err );
}
}
_save_all_item.setEnabled( false );
_file_jmenu.addSeparator();
_file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
- if ( Util.canWriteFormat( "tif" ) || Util.canWriteFormat( "tiff" ) || Util.canWriteFormat( "TIF" ) ) {
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
_file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
}
_file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
_file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
- if ( Util.canWriteFormat( "gif" ) ) {
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {
_file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
}
- if ( Util.canWriteFormat( "bmp" ) ) {
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {
_file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
}
_file_jmenu.addSeparator();
_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 ) );
_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 );
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 );
}
_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" ) );
phy.hashIDs();
phy.recalculateNumberOfExternalDescendants( true );
getCurrentTreePanel().resetNodeIdToDistToLeafMap();
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();
+ 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()
System.exit( 0 );
}
+ public void end() {
+ _mainpanel.terminate();
+ _contentpane.removeAll();
+ setVisible( false );
+ dispose();
+ }
+
private void extractTaxCodeFromNodeNames() {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
phy.setRoot( node );
phy.setRooted( true );
phys[ 0 ] = phy;
- Util.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
+ AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
_mainpanel.getControlPanel().showWhole();
_mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
_mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
}
}
}
- Util.addPhylogeniesToTabs( phys,
- file.getName(),
- file.getAbsolutePath(),
- getConfiguration(),
- getMainPanel() );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ file.getName(),
+ file.getAbsolutePath(),
+ getConfiguration(),
+ getMainPanel() );
_mainpanel.getControlPanel().showWhole();
if ( nhx_or_nexus && one_desc ) {
JOptionPane
PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
}
- Util.addPhylogeniesToTabs( phys,
- new File( url.getFile() ).getName(),
- new File( url.getFile() ).toString(),
- getConfiguration(),
- getMainPanel() );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( url.getFile() ).getName(),
+ new File( url.getFile() ).toString(),
+ getConfiguration(),
+ getMainPanel() );
_mainpanel.getControlPanel().showWhole();
}
}
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;
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;
return exception;
}
- private void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
+ void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
_mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
_mainpanel.getCurrentTreePanel().getHeight(),
true );
String file_written_to = "";
boolean error = false;
try {
- file_written_to = Util.writePhylogenyToGraphicsFile( file_name,
- _mainpanel.getCurrentTreePanel().getWidth(),
- _mainpanel.getCurrentTreePanel().getHeight(),
- _mainpanel.getCurrentTreePanel(),
- _mainpanel.getControlPanel(),
- type,
- getOptions() );
+ file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
+ _mainpanel.getCurrentTreePanel().getWidth(),
+ _mainpanel.getCurrentTreePanel().getHeight(),
+ _mainpanel.getCurrentTreePanel(),
+ _mainpanel.getControlPanel(),
+ type,
+ getOptions() );
}
catch ( final IOException e ) {
error = true;
return new MainFrameApplication( phys, config, title );
}
+ public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
+ return new MainFrameApplication( phys, config );
+ }
+
static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
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() + ")" );
git://source.jalview.org / jalview.git / blobdiff