import javax.swing.filechooser.FileFilter;
import javax.swing.plaf.synth.SynthLookAndFeel;
+import org.forester.analysis.TaxonomyDataManager;
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.tools.AncestralTaxonomyInferrer;
import org.forester.archaeopteryx.tools.GoAnnotation;
+import org.forester.archaeopteryx.tools.InferenceManager;
import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
import org.forester.archaeopteryx.tools.PhylogeneticInferrer;
import org.forester.archaeopteryx.tools.SequenceDataRetriver;
-import org.forester.archaeopteryx.tools.TaxonomyDataObtainer;
import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
import org.forester.archaeopteryx.webservices.WebservicesManager;
import org.forester.io.parsers.FastaParser;
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 ) {
+ super();
_configuration = config;
if ( _configuration == null ) {
throw new IllegalArgumentException( "configuration is null" );
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 ) );
}
void buildPhylogeneticInferenceMenu() {
+ final InferenceManager inference_manager = InferenceManager.getInstance();
_inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
- _inference_menu
- .add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment...(EXPERIMENTAL - DO NOT USE!!) " ) );
+ _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
customizeJMenuItem( _inference_from_msa_item );
_inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
- _inference_menu
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences...(EXPERIMENTAL - DO NOT USE!!) " ) );
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
customizeJMenuItem( _inference_from_seqs_item );
_inference_from_seqs_item.setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
_jmenubar.add( _inference_menu );
_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" ) );
_obtain_detailed_taxonomic_information_deleting_jmi
.setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
_tools_menu
- .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
+ .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
- _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
+ _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu.addSeparator();
if ( !Constants.__RELEASE ) {
_tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
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()
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,
_mainpanel.getCurrentTreePanel(),
- phy.copy() );
+ phy.copy(), false,true );
new Thread( t ).start();
}
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,
_mainpanel.getCurrentTreePanel(),
phy.copy(),
- true );
+ true,true );
new Thread( t ).start();
}
}
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 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() + ")" );