import javax.swing.plaf.synth.SynthLookAndFeel;\r
\r
import org.forester.analysis.TaxonomyDataManager;\r
-import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;\r
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;\r
import org.forester.io.parsers.tol.TolParser;\r
import org.forester.io.parsers.util.ParserUtils;\r
-import org.forester.io.writers.PhylogenyWriter;\r
import org.forester.io.writers.SequenceWriter;\r
import org.forester.msa.Msa;\r
import org.forester.msa.MsaFormatException;\r
\r
public final class MainFrameApplication extends MainFrame {\r
\r
- public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
- return new MainFrameApplication( phys, config );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
- return new MainFrameApplication( phys, config, title );\r
- }\r
-\r
- public static MainFrame createInstance( final Phylogeny[] phys,\r
- final Configuration config,\r
- final String title,\r
- final File current_dir ) {\r
- return new MainFrameApplication( phys, config, title, current_dir );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
- return new MainFrameApplication( phys, config_file_name, title );\r
- }\r
-\r
- static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
- if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
- JOptionPane\r
- .showMessageDialog( null,\r
- ForesterUtil\r
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
- 80 ),\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
private final static int FRAME_X_SIZE = 800;\r
public void componentResized( final ComponentEvent e ) {\r
if ( _mainpanel.getCurrentTreePanel() != null ) {\r
_mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()\r
- .getWidth(),\r
+ .getWidth(),\r
_mainpanel.getCurrentTreePanel()\r
- .getHeight() );\r
+ .getHeight() );\r
}\r
}\r
} );\r
else if ( o == _new_item ) {\r
newTree();\r
}\r
- \r
else if ( o == _close_item ) {\r
closeCurrentPane();\r
}\r
- \r
else if ( o == _load_species_tree_item ) {\r
readSpeciesTreeFromFile();\r
}\r
}\r
}\r
\r
+ public void end() {\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ @Override\r
+ public MainPanel getMainPanel() {\r
+ return _mainpanel;\r
+ }\r
+\r
+ public Msa getMsa() {\r
+ return _msa;\r
+ }\r
+\r
+ public File getMsaFile() {\r
+ return _msa_file;\r
+ }\r
+\r
+ public List<MolecularSequence> getSeqs() {\r
+ return _seqs;\r
+ }\r
+\r
+ public File getSeqsFile() {\r
+ return _seqs_file;\r
+ }\r
+\r
+ public void readMsaFromFile() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _msa_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _msa_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the msa\r
+ final File file = _msa_filechooser.getSelectedFile();\r
+ setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setMsaFile( null );\r
+ setMsa( null );\r
+ Msa msa = null;\r
+ try {\r
+ final InputStream is = new FileInputStream( file );\r
+ if ( FastaParser.isLikelyFasta( file ) ) {\r
+ msa = FastaParser.parseMsa( is );\r
+ }\r
+ else {\r
+ msa = GeneralMsaParser.parse( is );\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence alignment format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment is empty",\r
+ "Illegal Multiple Sequence Alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getNumberOfSequences() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getLength() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 2 residues",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ System.gc();\r
+ setMsaFile( _msa_filechooser.getSelectedFile() );\r
+ setMsa( msa );\r
+ }\r
+ }\r
+\r
+ public void readSeqsFromFileforPI() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the seqs\r
+ final File file = _seqs_pi_filechooser.getSelectedFile();\r
+ setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setSeqsFile( null );\r
+ setSeqs( null );\r
+ List<MolecularSequence> seqs = null;\r
+ try {\r
+ if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
+ seqs = FastaParser.parse( new FileInputStream( file ) );\r
+ for( final MolecularSequence seq : seqs ) {\r
+ System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
+ }\r
+ }\r
+ else {\r
+ //TODO error\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence file format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file is empty",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( seqs.size() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ // if ( msa.getLength() < 2 ) {\r
+ // JOptionPane.showMessageDialog( this,\r
+ // "Multiple sequence alignment needs to contain at least 2 residues",\r
+ // "Illegal multiple sequence file",\r
+ // JOptionPane.ERROR_MESSAGE );\r
+ // return;\r
+ // }\r
+ System.gc();\r
+ setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
+ setSeqs( seqs );\r
+ }\r
+ }\r
+\r
private void addExpressionValuesFromFile() {\r
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
JOptionPane.showMessageDialog( this,\r
JOptionPane.showMessageDialog( this,\r
"Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
+ phy.getNumberOfExternalNodes() + " external nodes",\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
int not_found = 0;\r
}\r
catch ( final IllegalArgumentException e ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- e.getMessage(),\r
- "Error Mapping Node Identifiers to Expression Value Identifiers",\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ e.getMessage(),\r
+ "Error Mapping Node Identifiers to Expression Value Identifiers",\r
+ JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
if ( row < 0 ) {\r
catch ( final NumberFormatException e ) {\r
JOptionPane.showMessageDialog( this,\r
"Could not parse \"" + t.getValueAsString( col, row )\r
- + "\" into a decimal value",\r
+ + "\" into a decimal value",\r
"Issue with Expression Value Table",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
if ( !l.isEmpty() ) {\r
if ( node.getNodeData().getProperties() != null ) {\r
node.getNodeData().getProperties()\r
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
+ .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
}\r
node.getNodeData().setVector( l );\r
}\r
}\r
if ( not_found > 0 ) {\r
JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
+ + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
}\r
getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
}\r
}\r
if ( nodes.size() > 1 ) {\r
JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
+ + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
setArrowCursor();\r
return;\r
}\r
}\r
else {\r
JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
- + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
+ + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
+ + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
}\r
}\r
else {\r
JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
+ + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
}\r
\r
- void buildAnalysisMenu() {\r
- _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );\r
- _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );\r
- _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );\r
- _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );\r
- customizeJMenuItem( _gsdi_item );\r
- customizeJMenuItem( _gsdir_item );\r
- customizeJMenuItem( _load_species_tree_item );\r
- _analysis_menu.addSeparator();\r
- _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );\r
- customizeJMenuItem( _lineage_inference );\r
- _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );\r
- _jmenubar.add( _analysis_menu );\r
+ private void closeCurrentPane() {\r
+ if ( getMainPanel().getCurrentTreePanel() != null ) {\r
+ if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
+ final int r = JOptionPane.showConfirmDialog( this,\r
+ "Close tab despite potentially unsaved changes?",\r
+ "Close Tab?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ getMainPanel().closeCurrentPane();\r
+ activateSaveAllIfNeeded();\r
+ }\r
}\r
\r
- @Override\r
- void buildFileMenu() {\r
- _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
- _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );\r
- _file_jmenu.addSeparator();\r
- final WebservicesManager webservices_manager = WebservicesManager.getInstance();\r
- _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager\r
- .getAvailablePhylogeniesWebserviceClients().size() ];\r
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
- final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );\r
- _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );\r
- _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );\r
- }\r
- if ( getConfiguration().isEditable() ) {\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _new_item = new JMenuItem( "New" ) );\r
- _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );\r
- }\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
- _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
- _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
- _save_all_item.setEnabled( false );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
- if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
- _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
- }\r
- _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
- _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
- if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
- _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
- }\r
- if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
- _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+ private void collapse( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
+ double min_support = Double.MAX_VALUE;\r
+ boolean conf_present = false;\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ final List<Confidence> c = n.getBranchData().getConfidences();\r
+ if ( ( c != null ) && ( c.size() > 0 ) ) {\r
+ conf_present = true;\r
+ double max = 0;\r
+ for( final Confidence confidence : c ) {\r
+ if ( confidence.getValue() > max ) {\r
+ max = confidence.getValue();\r
+ }\r
+ }\r
+ if ( max < getMinNotCollapseConfidenceValue() ) {\r
+ to_be_removed.add( n );\r
+ }\r
+ if ( max < min_support ) {\r
+ min_support = max;\r
+ }\r
+ }\r
+ }\r
}\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );\r
- _close_item.setToolTipText( "To close the current pane." );\r
- _close_item.setEnabled( true );\r
- _file_jmenu.addSeparator();\r
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- customizeJMenuItem( _open_item );\r
- _open_item\r
- .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
- customizeJMenuItem( _open_url_item );\r
- for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
- customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ if ( conf_present ) {\r
+ for( final PhylogenyNode node : to_be_removed ) {\r
+ PhylogenyMethods.removeNode( node, phy );\r
+ }\r
+ if ( to_be_removed.size() > 0 ) {\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
+ getCurrentTreePanel().calculateLongestExtNodeInfo();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().setEdited( true );\r
+ getCurrentTreePanel().repaint();\r
+ repaint();\r
+ }\r
+ if ( to_be_removed.size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
+ + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
+ + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
}\r
- customizeJMenuItem( _save_item );\r
- if ( getConfiguration().isEditable() ) {\r
- customizeJMenuItem( _new_item );\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No branch collapsed because no confidence values present",\r
+ "No confidence values present",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
- customizeJMenuItem( _close_item );\r
- customizeJMenuItem( _save_all_item );\r
- customizeJMenuItem( _write_to_pdf_item );\r
- customizeJMenuItem( _write_to_png_item );\r
- customizeJMenuItem( _write_to_jpg_item );\r
- customizeJMenuItem( _write_to_gif_item );\r
- customizeJMenuItem( _write_to_tif_item );\r
- customizeJMenuItem( _write_to_bmp_item );\r
- customizeJMenuItem( _print_item );\r
- customizeJMenuItem( _exit_item );\r
- _jmenubar.add( _file_jmenu );\r
}\r
\r
- void buildOptionsMenu() {\r
- _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );\r
- _options_jmenu.addChangeListener( new ChangeListener() {\r
+ private void collapseBelowBranchLengthThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum branch length value\n",\r
+ "Minimal Branch Length Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseBlValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseBlValue( m );\r
+ collapseBl( phy );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
- @Override\r
- public void stateChanged( final ChangeEvent e ) {\r
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );\r
- MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );\r
- MainFrame\r
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
- MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
- MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
- MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
- MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
- MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
- MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );\r
- MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
- try {\r
- getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();\r
- getMainPanel().getControlPanel().setVisibilityOfX();\r
+ private void collapseBelowThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the minimum confidence value\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseConfidenceValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseConfidenceValue( m );\r
+ collapse( phy );\r
+ }\r
}\r
- catch ( final Exception ignore ) {\r
- // do nothing, not important.\r
+ }\r
+ }\r
+ }\r
+\r
+ private void collapseBl( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
+ double min_bl = Double.MAX_VALUE;\r
+ boolean bl_present = false;\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ final double bl = n.getDistanceToParent();\r
+ if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {\r
+ bl_present = true;\r
+ if ( bl < getMinNotCollapseBlValue() ) {\r
+ to_be_removed.add( n );\r
+ }\r
+ if ( bl < min_bl ) {\r
+ min_bl = bl;\r
+ }\r
}\r
}\r
- } );\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );\r
- _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );\r
- _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );\r
- _radio_group_1 = new ButtonGroup();\r
- _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
- _radio_group_1.add( _uniform_cladograms_rbmi );\r
- _radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
- _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
- _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
- _options_jmenu\r
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
- _options_jmenu\r
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
- _options_jmenu\r
- .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
- _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
- _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );\r
}\r
- _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );\r
- _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );\r
- _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );\r
- _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );\r
- _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );\r
- _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );\r
- _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );\r
- _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );\r
- _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );\r
- _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );\r
- _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );\r
- _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );\r
- _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );\r
- _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
- _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
- _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );\r
- _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
- _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
- _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
- getConfiguration() ) );\r
- _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );\r
- _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );\r
- _options_jmenu\r
- .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
- _options_jmenu\r
- .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
- _options_jmenu\r
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
- _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
- _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
- _options_jmenu.addSeparator();\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
- _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
- _options_jmenu\r
- .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
- _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
- _options_jmenu\r
- .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
- _options_jmenu\r
- .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );\r
- _options_jmenu\r
- .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );\r
- _extract_taxonomy_pfam_strict_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );\r
- _extract_taxonomy_pfam_relaxed_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );\r
- _extract_taxonomy_agressive_rbmi\r
- .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );\r
- _radio_group_2 = new ButtonGroup();\r
- _radio_group_2.add( _extract_taxonomy_no_rbmi );\r
- _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
- _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
- _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
- _options_jmenu\r
- .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
- _use_brackets_for_conf_in_nh_export_cbmi\r
- .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
- _options_jmenu\r
- .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
- customizeJMenuItem( _choose_font_mi );\r
- customizeJMenuItem( _choose_minimal_confidence_mi );\r
- customizeJMenuItem( _switch_colors_mi );\r
- customizeJMenuItem( _print_size_mi );\r
- customizeJMenuItem( _choose_pdf_width_mi );\r
- customizeJMenuItem( _overview_placment_mi );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()\r
- .isShowDefaultNodeShapesExternal() );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
- .isShowDefaultNodeShapesInternal() );\r
- customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
- .isShowDefaultNodeShapesForMarkedNodes() );\r
- customizeJMenuItem( _cycle_node_shape_mi );\r
- customizeJMenuItem( _cycle_node_fill_mi );\r
- customizeJMenuItem( _choose_node_size_mi );\r
- customizeJMenuItem( _cycle_data_return );\r
- customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
- customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
- customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
- customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );\r
- customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );\r
- customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );\r
- customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );\r
- customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );\r
- customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );\r
- customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,\r
- getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );\r
- customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,\r
- getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
- customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
- getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
- customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
- customizeCheckBoxMenuItem( _label_direction_cbmi,\r
- getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r
- customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );\r
- customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );\r
- customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()\r
- .isInternalNumberAreConfidenceForNhParsing() );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
- customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,\r
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );\r
- customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
- customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
- .isReplaceUnderscoresInNhParsing() );\r
- customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
- customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
- customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
- customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
- customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
- customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r
- .isGraphicsExportUsingActualSize() );\r
- customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );\r
- customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
- customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
- customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );\r
- customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );\r
- _jmenubar.add( _options_jmenu );\r
- }\r
-\r
- void buildPhylogeneticInferenceMenu() {\r
- final InferenceManager im = getInferenceManager();\r
- _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );\r
- _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );\r
- customizeJMenuItem( _inference_from_msa_item );\r
- _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );\r
- if ( im.canDoMsa() ) {\r
- _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );\r
- customizeJMenuItem( _inference_from_seqs_item );\r
- _inference_from_seqs_item\r
- .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );\r
- }\r
- else {\r
- _inference_menu\r
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );\r
- customizeJMenuItem( _inference_from_seqs_item );\r
- _inference_from_seqs_item.setEnabled( false );\r
- }\r
- _jmenubar.add( _inference_menu );\r
- }\r
-\r
- void buildToolsMenu() {\r
- _tools_menu = createMenu( "Tools", getConfiguration() );\r
- _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );\r
- customizeJMenuItem( _confcolor_item );\r
- _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );\r
- customizeJMenuItem( _color_rank_jmi );\r
- _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );\r
- _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );\r
- customizeJMenuItem( _taxcolor_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );\r
- _remove_visual_styles_item\r
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );\r
- customizeJMenuItem( _remove_visual_styles_item );\r
- _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );\r
- _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );\r
- customizeJMenuItem( _remove_branch_color_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );\r
- customizeJMenuItem( _annotate_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );\r
- customizeJMenuItem( _midpoint_root_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );\r
- _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );\r
- customizeJMenuItem( _delete_selected_nodes_item );\r
- _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );\r
- _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );\r
- customizeJMenuItem( _delete_not_selected_nodes_item );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );\r
- customizeJMenuItem( _collapse_species_specific_subtrees );\r
- _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );\r
- _tools_menu\r
- .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
- customizeJMenuItem( _collapse_below_threshold );\r
- _collapse_below_threshold\r
- .setToolTipText( "To (permanently) 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)" );\r
- //\r
- _tools_menu\r
- .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
- customizeJMenuItem( _collapse_below_branch_length );\r
- _collapse_below_branch_length\r
- .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
- //\r
- _tools_menu.addSeparator();\r
- _tools_menu\r
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
- customizeJMenuItem( _extract_tax_code_from_node_names_jmi );\r
- _extract_tax_code_from_node_names_jmi\r
- .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );\r
- _tools_menu\r
- .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );\r
- customizeJMenuItem( _move_node_names_to_tax_sn_jmi );\r
- _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );\r
- _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );\r
- customizeJMenuItem( _move_node_names_to_seq_names_jmi );\r
- _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );\r
- customizeJMenuItem( _obtain_seq_information_jmi );\r
- _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );\r
- _tools_menu\r
- .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );\r
- customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );\r
- _obtain_detailed_taxonomic_information_jmi\r
- .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );\r
- _tools_menu\r
- .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );\r
- customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );\r
- _obtain_detailed_taxonomic_information_deleting_jmi\r
- .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );\r
- _tools_menu.addSeparator();\r
- _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );\r
- customizeJMenuItem( _read_values_jmi );\r
- _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );\r
- _jmenubar.add( _tools_menu );\r
- _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );\r
- customizeJMenuItem( _read_seqs_jmi );\r
- _read_seqs_jmi\r
- .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );\r
- _jmenubar.add( _tools_menu );\r
- }\r
-\r
- @Override\r
- void close() {\r
- if ( isUnsavedDataPresent() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Exit despite potentially unsaved changes?",\r
- "Exit?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- exit();\r
- }\r
-\r
- private void closeCurrentPane() {\r
- if ( getMainPanel().getCurrentTreePanel() != null ) {\r
- if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Close tab despite potentially unsaved changes?",\r
- "Close Tab?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- getMainPanel().closeCurrentPane();\r
- activateSaveAllIfNeeded();\r
- }\r
- }\r
-\r
- private void collapse( final Phylogeny phy ) {\r
- final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
- final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
- double min_support = Double.MAX_VALUE;\r
- boolean conf_present = false;\r
- while ( it.hasNext() ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !n.isExternal() && !n.isRoot() ) {\r
- final List<Confidence> c = n.getBranchData().getConfidences();\r
- if ( ( c != null ) && ( c.size() > 0 ) ) {\r
- conf_present = true;\r
- double max = 0;\r
- for( final Confidence confidence : c ) {\r
- if ( confidence.getValue() > max ) {\r
- max = confidence.getValue();\r
- }\r
- }\r
- if ( max < getMinNotCollapseConfidenceValue() ) {\r
- to_be_removed.add( n );\r
- }\r
- if ( max < min_support ) {\r
- min_support = max;\r
- }\r
- }\r
- }\r
- }\r
- if ( conf_present ) {\r
+ if ( bl_present ) {\r
for( final PhylogenyNode node : to_be_removed ) {\r
PhylogenyMethods.removeNode( node, phy );\r
}\r
}\r
if ( to_be_removed.size() > 0 ) {\r
JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
+ + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
- JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
- + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
+ JOptionPane.showMessageDialog( this,\r
+ "No branch collapsed,\nminimum branch length is " + min_bl,\r
+ "No branch collapsed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
- "No branch collapsed because no confidence values present",\r
- "No confidence values present",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
-\r
- private void collapseBelowBranchLengthThreshold() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final String s = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "Please enter the minimum branch length value\n",\r
- "Minimal Branch Length Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getMinNotCollapseBlValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- setMinNotCollapseBlValue( m );\r
- collapseBl( phy );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void collapseBelowThreshold() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the minimum confidence value\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getMinNotCollapseConfidenceValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- setMinNotCollapseConfidenceValue( m );\r
- collapse( phy );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void collapseBl( final Phylogeny phy ) {\r
- final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
- final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
- double min_bl = Double.MAX_VALUE;\r
- boolean bl_present = false;\r
- while ( it.hasNext() ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !n.isExternal() && !n.isRoot() ) {\r
- final double bl = n.getDistanceToParent();\r
- if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {\r
- bl_present = true;\r
- if ( bl < getMinNotCollapseBlValue() ) {\r
- to_be_removed.add( n );\r
- }\r
- if ( bl < min_bl ) {\r
- min_bl = bl;\r
- }\r
- }\r
- }\r
- }\r
- if ( bl_present ) {\r
- for( final PhylogenyNode node : to_be_removed ) {\r
- PhylogenyMethods.removeNode( node, phy );\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
- getCurrentTreePanel().calculateLongestExtNodeInfo();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().setEdited( true );\r
- getCurrentTreePanel().repaint();\r
- repaint();\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "\r
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No branch collapsed,\nminimum branch length is " + min_bl,\r
- "No branch collapsed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No branch collapsed because no branch length values present",\r
- "No branch length values present",\r
+ "No branch collapsed because no branch length values present",\r
+ "No branch length values present",\r
JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
return xml_parser;\r
}\r
\r
- public void end() {\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- }\r
-\r
- void executeLineageInference() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Phylogeny is not rooted.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getCurrentPhylogeny()\r
- .copy() );\r
- new Thread( inferrer ).start();\r
- }\r
-\r
private void executePhyleneticInference( final boolean from_unaligned_seqs ) {\r
final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,\r
getPhylogeneticInferenceOptions(),\r
if ( getMsa() != null ) {\r
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),\r
getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
+ .copy(), this );\r
new Thread( inferrer ).start();\r
}\r
else {\r
if ( getSeqs() != null ) {\r
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),\r
getPhylogeneticInferenceOptions()\r
- .copy(), this );\r
+ .copy(), this );\r
new Thread( inferrer ).start();\r
}\r
else {\r
}\r
}\r
\r
- void exit() {\r
- removeAllTextFrames();\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.\r
- }\r
-\r
private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {\r
final StringBuilder sb = new StringBuilder();\r
final StringBuilder sb_failed = new StringBuilder();\r
}\r
JOptionPane.showMessageDialog( this,\r
"Extracted taxonomic data from " + all + counter\r
- + " named external nodes:\n" + sb.toString() + failed,\r
+ + " named external nodes:\n" + sb.toString() + failed,\r
"Taxonomic Data Extraction Completed",\r
counter_failed > 0 ? JOptionPane.WARNING_MESSAGE\r
: JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Could not extract any taxonomic data.\nMaybe node names are empty\n"\r
- + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"\r
- + "or nodes already have taxonomic data?\n",\r
+ .showMessageDialog( this,\r
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"\r
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"\r
+ + "or nodes already have taxonomic data?\n",\r
"No Taxonomic Data Extracted",\r
JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
}\r
\r
- @Override\r
- public MainPanel getMainPanel() {\r
- return _mainpanel;\r
- }\r
-\r
private double getMinNotCollapseBlValue() {\r
return _min_not_collapse_bl;\r
}\r
return _min_not_collapse;\r
}\r
\r
- public Msa getMsa() {\r
- return _msa;\r
- }\r
-\r
- public File getMsaFile() {\r
- return _msa_file;\r
- }\r
-\r
private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {\r
if ( _phylogenetic_inference_options == null ) {\r
_phylogenetic_inference_options = new PhylogeneticInferenceOptions();\r
return _phylogenetic_inference_options;\r
}\r
\r
- public List<MolecularSequence> getSeqs() {\r
- return _seqs;\r
- }\r
-\r
- public File getSeqsFile() {\r
- return _seqs_file;\r
- }\r
-\r
private boolean isUnsavedDataPresent() {\r
final List<TreePanel> tps = getMainPanel().getTreePanels();\r
for( final TreePanel tp : tps ) {\r
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
if ( ( phy != null ) && !phy.isEmpty() ) {\r
PhylogenyMethods\r
- .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );\r
+ .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );\r
}\r
}\r
}\r
if ( getMainPanel().getMainFrame() == null ) {\r
// Must be "E" applet version.\r
( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )\r
- .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
+ .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
}\r
else {\r
getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
}\r
}\r
\r
- \r
-\r
- public void readMsaFromFile() {\r
+ private void readPhylogeniesFromFile() {\r
+ boolean exception = false;\r
+ Phylogeny[] phys = null;\r
// Set an initial directory if none set yet\r
final File my_dir = getCurrentDir();\r
- _msa_filechooser.setMultiSelectionEnabled( false );\r
+ _open_filechooser.setMultiSelectionEnabled( true );\r
// Open file-open dialog and set current directory\r
if ( my_dir != null ) {\r
- _msa_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the msa\r
- final File file = _msa_filechooser.getSelectedFile();\r
- setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setMsaFile( null );\r
- setMsa( null );\r
- Msa msa = null;\r
- try {\r
- final InputStream is = new FileInputStream( file );\r
- if ( FastaParser.isLikelyFasta( file ) ) {\r
- msa = FastaParser.parseMsa( is );\r
- }\r
- else {\r
- msa = GeneralMsaParser.parse( is );\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence alignment format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment is empty",\r
- "Illegal Multiple Sequence Alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( msa.getNumberOfSequences() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 3 sequences",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( msa.getLength() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 2 residues",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- System.gc();\r
- setMsaFile( _msa_filechooser.getSelectedFile() );\r
- setMsa( msa );\r
- }\r
- }\r
-\r
- private void readPhylogeniesFromFile() {\r
- boolean exception = false;\r
- Phylogeny[] phys = null;\r
- // Set an initial directory if none set yet\r
- final File my_dir = getCurrentDir();\r
- _open_filechooser.setMultiSelectionEnabled( true );\r
- // Open file-open dialog and set current directory\r
- if ( my_dir != null ) {\r
- _open_filechooser.setCurrentDirectory( my_dir );\r
+ _open_filechooser.setCurrentDirectory( my_dir );\r
}\r
final int result = _open_filechooser.showOpenDialog( _contentpane );\r
// All done: get the file\r
try {\r
final PhylogenyParser parser = ParserUtils\r
.createParserDependingOnFileType( file, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
+ .isValidatePhyloXmlAgainstSchema() );\r
if ( parser instanceof NexusPhylogeniesParser ) {\r
final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;\r
setSpecialOptionsForNexParser( nex );\r
_mainpanel.getControlPanel().showWhole();\r
if ( nhx_or_nexus && one_desc ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "One or more trees contain (a) node(s) with one descendant, "\r
- + ForesterUtil.LINE_SEPARATOR\r
- + "possibly indicating illegal parentheses within node names.",\r
+ .showMessageDialog( this,\r
+ "One or more trees contain (a) node(s) with one descendant, "\r
+ + ForesterUtil.LINE_SEPARATOR\r
+ + "possibly indicating illegal parentheses within node names.",\r
"Warning: Possible Error in New Hampshire Formatted Data",\r
JOptionPane.WARNING_MESSAGE );\r
}\r
}\r
}\r
}\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
+ activateSaveAllIfNeeded();\r
+ System.gc();\r
+ }\r
+\r
+ private void readSpeciesTreeFromFile() {\r
+ Phylogeny t = null;\r
+ boolean exception = false;\r
+ final File my_dir = getCurrentDir();\r
+ _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );\r
+ if ( my_dir != null ) {\r
+ _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
+ final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
+ .createPhyloXmlParserXsdValidating(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ // "*.*":\r
+ else {\r
+ try {\r
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
+ .createPhyloXmlParserXsdValidating(), file );\r
+ t = trees[ 0 ];\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringOpenFile( e );\r
+ }\r
+ }\r
+ if ( !exception && ( t != null ) && !t.isRooted() ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree is not rooted",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !exception && ( t != null ) ) {\r
+ final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();\r
+ for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode node = it.next();\r
+ if ( !node.getNodeData().isHasTaxonomy() ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Species tree contains external node(s) without taxonomy information",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ break;\r
+ }\r
+ else {\r
+ if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {\r
+ exception = true;\r
+ t = null;\r
+ JOptionPane.showMessageDialog( this,\r
+ "Taxonomy ["\r
+ + node.getNodeData().getTaxonomy().asSimpleText()\r
+ + "] is not unique in species tree",\r
+ "Species tree not loaded",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ break;\r
+ }\r
+ else {\r
+ tax_set.add( node.getNodeData().getTaxonomy() );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if ( !exception && ( t != null ) ) {\r
+ setSpeciesTree( t );\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree successfully loaded",\r
+ "Species tree loaded",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ _contentpane.repaint();\r
+ System.gc();\r
+ }\r
+ }\r
+\r
+ private void setArrowCursor() {\r
+ try {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ }\r
+\r
+ private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
+ _min_not_collapse_bl = min_not_collapse_bl;\r
+ }\r
+\r
+ private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
+ _min_not_collapse = min_not_collapse;\r
+ }\r
+\r
+ private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
+ _phylogenetic_inference_options = phylogenetic_inference_options;\r
+ }\r
+\r
+ private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
+ nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
+ nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ }\r
+\r
+ private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {\r
+ nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
+ nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );\r
+ }\r
+\r
+ void buildAnalysisMenu() {\r
+ _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );\r
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );\r
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );\r
+ _analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );\r
+ customizeJMenuItem( _gsdi_item );\r
+ customizeJMenuItem( _gsdir_item );\r
+ customizeJMenuItem( _load_species_tree_item );\r
+ _analysis_menu.addSeparator();\r
+ _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );\r
+ customizeJMenuItem( _lineage_inference );\r
+ _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );\r
+ _jmenubar.add( _analysis_menu );\r
+ }\r
+\r
+ @Override\r
+ void buildFileMenu() {\r
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+ _file_jmenu.add( _open_item = new JMenuItem( "Read Tree from File..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _open_url_item = new JMenuItem( "Read Tree from URL/Webservice..." ) );\r
+ _file_jmenu.addSeparator();\r
+ final WebservicesManager webservices_manager = WebservicesManager.getInstance();\r
+ _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager\r
+ .getAvailablePhylogeniesWebserviceClients().size() ];\r
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
+ final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );\r
+ _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );\r
+ _file_jmenu.add( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ }\r
+ if ( getConfiguration().isEditable() ) {\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _new_item = new JMenuItem( "New" ) );\r
+ _new_item.setToolTipText( "to create a new tree with one node, as source for manual tree construction" );\r
+ }\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+ _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
+ _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
+ _save_all_item.setEnabled( false );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
+ }\r
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
+ }\r
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+ }\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _close_item = new JMenuItem( "Close Tab" ) );\r
+ _close_item.setToolTipText( "To close the current pane." );\r
+ _close_item.setEnabled( true );\r
+ _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ customizeJMenuItem( _open_item );\r
+ _open_item\r
+ .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );\r
+ customizeJMenuItem( _open_url_item );\r
+ for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {\r
+ customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );\r
+ }\r
+ customizeJMenuItem( _save_item );\r
+ if ( getConfiguration().isEditable() ) {\r
+ customizeJMenuItem( _new_item );\r
+ }\r
+ customizeJMenuItem( _close_item );\r
+ customizeJMenuItem( _save_all_item );\r
+ customizeJMenuItem( _write_to_pdf_item );\r
+ customizeJMenuItem( _write_to_png_item );\r
+ customizeJMenuItem( _write_to_jpg_item );\r
+ customizeJMenuItem( _write_to_gif_item );\r
+ customizeJMenuItem( _write_to_tif_item );\r
+ customizeJMenuItem( _write_to_bmp_item );\r
+ customizeJMenuItem( _print_item );\r
+ customizeJMenuItem( _exit_item );\r
+ _jmenubar.add( _file_jmenu );\r
+ }\r
+\r
+ void buildOptionsMenu() {\r
+ _options_jmenu = MainFrame.createMenu( OPTIONS_HEADER, getConfiguration() );\r
+ _options_jmenu.addChangeListener( new ChangeListener() {\r
+\r
+ @Override\r
+ public void stateChanged( final ChangeEvent e ) {\r
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );\r
+ MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );\r
+ MainFrame\r
+ .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
+ MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
+ .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
+ MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
+ MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
+ MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );\r
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
+ try {\r
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();\r
+ getMainPanel().getControlPanel().setVisibilityOfX();\r
+ }\r
+ catch ( final Exception ignore ) {\r
+ // do nothing, not important.\r
+ }\r
+ }\r
+ } );\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );\r
+ _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );\r
+ _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );\r
+ _radio_group_1 = new ButtonGroup();\r
+ _radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
+ _radio_group_1.add( _uniform_cladograms_rbmi );\r
+ _radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
+ _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
+ _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
+ _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );\r
+ }\r
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );\r
+ _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );\r
+ _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );\r
+ _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );\r
+ _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );\r
+ _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );\r
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );\r
+ _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );\r
+ _options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );\r
+ _options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );\r
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );\r
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );\r
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );\r
+ _options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
+ _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
+ _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );\r
+ _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
+ _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
+ _options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
+ getConfiguration() ) );\r
+ _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );\r
+ _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );\r
+ _options_jmenu\r
+ .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );\r
+ _options_jmenu\r
+ .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );\r
+ _options_jmenu\r
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );\r
+ _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );\r
+ _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
+ _options_jmenu\r
+ .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
+ _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );\r
+ _options_jmenu\r
+ .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );\r
+ _extract_taxonomy_pfam_strict_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );\r
+ _extract_taxonomy_pfam_relaxed_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );\r
+ _extract_taxonomy_agressive_rbmi\r
+ .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );\r
+ _radio_group_2 = new ButtonGroup();\r
+ _radio_group_2.add( _extract_taxonomy_no_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
+ _radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
+ _options_jmenu\r
+ .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
+ _use_brackets_for_conf_in_nh_export_cbmi\r
+ .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );\r
+ _options_jmenu\r
+ .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );\r
+ customizeJMenuItem( _choose_font_mi );\r
+ customizeJMenuItem( _choose_minimal_confidence_mi );\r
+ customizeJMenuItem( _switch_colors_mi );\r
+ customizeJMenuItem( _print_size_mi );\r
+ customizeJMenuItem( _choose_pdf_width_mi );\r
+ customizeJMenuItem( _overview_placment_mi );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesExternal() );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesInternal() );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesForMarkedNodes() );\r
+ customizeJMenuItem( _cycle_node_shape_mi );\r
+ customizeJMenuItem( _cycle_node_fill_mi );\r
+ customizeJMenuItem( _choose_node_size_mi );\r
+ customizeJMenuItem( _cycle_data_return );\r
+ customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
+ customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
+ customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
+ customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );\r
+ customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );\r
+ customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );\r
+ customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );\r
+ customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );\r
+ customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );\r
+ customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );\r
+ customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
+ customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
+ customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
+ customizeCheckBoxMenuItem( _label_direction_cbmi,\r
+ getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r
+ customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );\r
+ customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );\r
+ customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()\r
+ .isInternalNumberAreConfidenceForNhParsing() );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
+ customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,\r
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+ customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
+ .isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
+ customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
+ customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
+ customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
+ customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );\r
+ customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()\r
+ .isGraphicsExportUsingActualSize() );\r
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );\r
+ customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
+ customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );\r
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );\r
+ _jmenubar.add( _options_jmenu );\r
+ }\r
+\r
+ void buildPhylogeneticInferenceMenu() {\r
+ final InferenceManager im = getInferenceManager();\r
+ _inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );\r
+ _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );\r
+ customizeJMenuItem( _inference_from_msa_item );\r
+ _inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );\r
+ if ( im.canDoMsa() ) {\r
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );\r
+ customizeJMenuItem( _inference_from_seqs_item );\r
+ _inference_from_seqs_item\r
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );\r
+ }\r
+ else {\r
+ _inference_menu\r
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );\r
+ customizeJMenuItem( _inference_from_seqs_item );\r
+ _inference_from_seqs_item.setEnabled( false );\r
+ }\r
+ _jmenubar.add( _inference_menu );\r
+ }\r
+\r
+ void buildToolsMenu() {\r
+ _tools_menu = createMenu( "Tools", getConfiguration() );\r
+ _tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );\r
+ customizeJMenuItem( _confcolor_item );\r
+ _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );\r
+ customizeJMenuItem( _color_rank_jmi );\r
+ _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );\r
+ _tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );\r
+ customizeJMenuItem( _taxcolor_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );\r
+ _remove_visual_styles_item\r
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );\r
+ customizeJMenuItem( _remove_visual_styles_item );\r
+ _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );\r
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );\r
+ customizeJMenuItem( _remove_branch_color_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );\r
+ customizeJMenuItem( _annotate_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );\r
+ customizeJMenuItem( _midpoint_root_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );\r
+ _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );\r
+ customizeJMenuItem( _delete_selected_nodes_item );\r
+ _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );\r
+ _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );\r
+ customizeJMenuItem( _delete_not_selected_nodes_item );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );\r
+ customizeJMenuItem( _collapse_species_specific_subtrees );\r
+ _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );\r
+ _tools_menu\r
+ .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
+ customizeJMenuItem( _collapse_below_threshold );\r
+ _collapse_below_threshold\r
+ .setToolTipText( "To (permanently) 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)" );\r
+ //\r
+ _tools_menu\r
+ .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
+ customizeJMenuItem( _collapse_below_branch_length );\r
+ _collapse_below_branch_length\r
+ .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
+ //\r
+ _tools_menu.addSeparator();\r
+ _tools_menu\r
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
+ customizeJMenuItem( _extract_tax_code_from_node_names_jmi );\r
+ _extract_tax_code_from_node_names_jmi\r
+ .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );\r
+ _tools_menu\r
+ .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );\r
+ customizeJMenuItem( _move_node_names_to_tax_sn_jmi );\r
+ _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );\r
+ _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );\r
+ customizeJMenuItem( _move_node_names_to_seq_names_jmi );\r
+ _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );\r
+ customizeJMenuItem( _obtain_seq_information_jmi );\r
+ _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );\r
+ _tools_menu\r
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );\r
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );\r
+ _obtain_detailed_taxonomic_information_jmi\r
+ .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );\r
+ _tools_menu\r
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );\r
+ customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );\r
+ _obtain_detailed_taxonomic_information_deleting_jmi\r
+ .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );\r
+ _tools_menu.addSeparator();\r
+ _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );\r
+ customizeJMenuItem( _read_values_jmi );\r
+ _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" );\r
+ _jmenubar.add( _tools_menu );\r
+ _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );\r
+ customizeJMenuItem( _read_seqs_jmi );\r
+ _read_seqs_jmi\r
+ .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );\r
+ _jmenubar.add( _tools_menu );\r
+ }\r
+\r
+ @Override\r
+ void close() {\r
+ if ( isUnsavedDataPresent() ) {\r
+ final int r = JOptionPane.showConfirmDialog( this,\r
+ "Exit despite potentially unsaved changes?",\r
+ "Exit?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ exit();\r
+ }\r
+\r
+ void executeLineageInference() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Phylogeny is not rooted.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getCurrentPhylogeny()\r
+ .copy() );\r
+ new Thread( inferrer ).start();\r
+ }\r
+\r
+ void exit() {\r
+ removeAllTextFrames();\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.\r
}\r
\r
void readPhylogeniesFromURL() {\r
}\r
else {\r
parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
+ .isValidatePhyloXmlAgainstSchema() );\r
}\r
if ( parser instanceof NexusPhylogeniesParser ) {\r
nhx_or_nexus = true;\r
JOptionPane.showMessageDialog( this,\r
"Could not read from " + url + "\n"\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Failed to read URL",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Failed to read URL",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
catch ( final Exception e ) {\r
JOptionPane.showMessageDialog( this,\r
System.gc();\r
}\r
\r
- public void readSeqsFromFileforPI() {\r
- // Set an initial directory if none set yet\r
- final File my_dir = getCurrentDir();\r
- _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
- // Open file-open dialog and set current directory\r
- if ( my_dir != null ) {\r
- _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the seqs\r
- final File file = _seqs_pi_filechooser.getSelectedFile();\r
- setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setSeqsFile( null );\r
- setSeqs( null );\r
- List<MolecularSequence> seqs = null;\r
- try {\r
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
- seqs = FastaParser.parse( new FileInputStream( file ) );\r
- for( final MolecularSequence seq : seqs ) {\r
- System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
- }\r
- }\r
- else {\r
- //TODO error\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file is empty",\r
- "Illegal multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( seqs.size() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file needs to contain at least 3 sequences",\r
- "Illegal multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- // if ( msa.getLength() < 2 ) {\r
- // JOptionPane.showMessageDialog( this,\r
- // "Multiple sequence alignment needs to contain at least 2 residues",\r
- // "Illegal multiple sequence file",\r
- // JOptionPane.ERROR_MESSAGE );\r
- // return;\r
- // }\r
- System.gc();\r
- setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
- setSeqs( seqs );\r
- }\r
- }\r
-\r
- private void readSpeciesTreeFromFile() {\r
- Phylogeny t = null;\r
- boolean exception = false;\r
- final File my_dir = getCurrentDir();\r
- _open_filechooser_for_species_tree.setSelectedFile( new File( "" ) );\r
- if ( my_dir != null ) {\r
- _open_filechooser_for_species_tree.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
- final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- // "*.*":\r
- else {\r
- try {\r
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
- .createPhyloXmlParserXsdValidating(), file );\r
- t = trees[ 0 ];\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringOpenFile( e );\r
- }\r
- }\r
- if ( !exception && ( t != null ) && !t.isRooted() ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree is not rooted",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !exception && ( t != null ) ) {\r
- final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();\r
- for( final PhylogenyNodeIterator it = t.iteratorExternalForward(); it.hasNext(); ) {\r
- final PhylogenyNode node = it.next();\r
- if ( !node.getNodeData().isHasTaxonomy() ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Species tree contains external node(s) without taxonomy information",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- break;\r
- }\r
- else {\r
- if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {\r
- exception = true;\r
- t = null;\r
- JOptionPane.showMessageDialog( this,\r
- "Taxonomy ["\r
- + node.getNodeData().getTaxonomy().asSimpleText()\r
- + "] is not unique in species tree",\r
- "Species tree not loaded",\r
- JOptionPane.ERROR_MESSAGE );\r
- break;\r
- }\r
- else {\r
- tax_set.add( node.getNodeData().getTaxonomy() );\r
- }\r
- }\r
- }\r
- }\r
- if ( !exception && ( t != null ) ) {\r
- setSpeciesTree( t );\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree successfully loaded",\r
- "Species tree loaded",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- _contentpane.repaint();\r
- System.gc();\r
- }\r
- }\r
-\r
- private void setArrowCursor() {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
- }\r
- }\r
-\r
- private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
- _min_not_collapse_bl = min_not_collapse_bl;\r
- }\r
-\r
- private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
- _min_not_collapse = min_not_collapse;\r
- }\r
-\r
void setMsa( final Msa msa ) {\r
_msa = msa;\r
}\r
_msa_file = msa_file;\r
}\r
\r
- private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
- _phylogenetic_inference_options = phylogenetic_inference_options;\r
- }\r
-\r
void setSeqs( final List<MolecularSequence> seqs ) {\r
_seqs = seqs;\r
}\r
_seqs_file = seqs_file;\r
}\r
\r
- private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
- nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
- nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
+ public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
+ return new MainFrameApplication( phys, config );\r
}\r
\r
- private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {\r
- nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
- nhx.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
- nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() );\r
+ public static MainFrame createInstance( final Phylogeny[] phys,\r
+ final Configuration config,\r
+ final String title,\r
+ final File current_dir ) {\r
+ return new MainFrameApplication( phys, config, title, current_dir );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
+ return new MainFrameApplication( phys, config, title );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
+ return new MainFrameApplication( phys, config_file_name, title );\r
}\r
\r
- \r
+ static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
+ if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
+ JOptionPane\r
+ .showMessageDialog( null,\r
+ ForesterUtil\r
+ .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
+ 80 ),\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
} // MainFrameApplication.\r
git://source.jalview.org / jalview.git / blobdiff