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.archaeopteryx.tools.AncestralTaxonomyInferrer;\r
import org.forester.archaeopteryx.tools.InferenceManager;\r
import org.forester.archaeopteryx.tools.ProcessPool;\r
import org.forester.archaeopteryx.tools.ProcessRunning;\r
static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";\r
static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\r
static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";\r
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
JMenuBar _jmenubar;\r
JMenu _file_jmenu;\r
JMenu _tools_menu;\r
JMenuItem _phyloxml_ref_item;\r
JMenuItem _aptx_ref_item;\r
//\r
- JFileChooser _writetopdf_filechooser;\r
File _current_dir;\r
+ JFileChooser _writetopdf_filechooser;\r
JFileChooser _save_filechooser;\r
JFileChooser _writetographics_filechooser;\r
// process menu:\r
JMenu _process_menu;\r
- // Handy pointers to child components:\r
MainPanel _mainpanel;\r
Container _contentpane;\r
final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
MainFrame() {\r
_process_pool = ProcessPool.createInstance();\r
_writetopdf_filechooser = new JFileChooser();\r
+ _writetopdf_filechooser.setMultiSelectionEnabled( false );\r
+ _writetopdf_filechooser.addChoosableFileFilter( pdffilter );\r
+ _writetographics_filechooser = new JFileChooser();\r
+ _writetographics_filechooser.setMultiSelectionEnabled( false );\r
+ _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter );\r
_save_filechooser = new JFileChooser();\r
- _save_filechooser.setCurrentDirectory( new File( "." ) );\r
_save_filechooser.setMultiSelectionEnabled( false );\r
- _save_filechooser.setFileFilter( MainFrame.xmlfilter );\r
+ _save_filechooser.setFileFilter( xmlfilter );\r
_save_filechooser.addChoosableFileFilter( nhfilter );\r
_save_filechooser.addChoosableFileFilter( nexusfilter );\r
_save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );\r
- _writetographics_filechooser = new JFileChooser();\r
- _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );\r
+ try {\r
+ final String home_dir = System.getProperty( "user.home" );\r
+ _save_filechooser.setCurrentDirectory( new File( home_dir ) );\r
+ _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) );\r
+ _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) );\r
+ }\r
+ catch ( final Exception e ) {\r
+ e.printStackTrace();\r
+ // Do nothing. Not important.\r
+ }\r
}\r
\r
/**\r
if ( new_dir != null ) {\r
setCurrentDir( new_dir );\r
}\r
- \r
}\r
else if ( o == _write_to_tif_item ) {\r
final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
if ( new_dir != null ) {\r
setCurrentDir( new_dir );\r
}\r
- \r
}\r
else if ( o == _write_to_bmp_item ) {\r
final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
if ( new_dir != null ) {\r
setCurrentDir( new_dir );\r
}\r
- \r
}\r
else if ( o == _write_to_png_item ) {\r
final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
print( getCurrentTreePanel(), getOptions(), this );\r
}\r
else if ( o == _save_item ) {\r
- writeToFile( _mainpanel.getCurrentPhylogeny() );\r
+ final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(),\r
+ getMainPanel(),\r
+ _save_filechooser,\r
+ _current_dir,\r
+ getContentPane(),\r
+ this );\r
+ if ( new_dir != null ) {\r
+ setCurrentDir( new_dir );\r
+ }\r
}\r
- \r
else if ( o == _graphics_export_visible_only_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
else if ( o == _choose_pdf_width_mi ) {\r
choosePdfWidth();\r
}\r
+ else if ( o == _lineage_inference ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Subtree is shown.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ executeLineageInference();\r
+ }\r
else {\r
if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
} );\r
}\r
\r
- void activateSaveAllIfNeeded() {\r
- if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
- _save_all_item.setEnabled( true );\r
- }\r
- else {\r
- _save_all_item.setEnabled( false );\r
- }\r
- }\r
-\r
- void buildFileMenu() {\r
- _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
- _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\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( _exit_item = new JMenuItem( "Exit" ) );\r
- customizeJMenuItem( _save_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 buildFontSizeMenu() {\r
- _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
- _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
- _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
- _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
- _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
- _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
- customizeJMenuItem( _super_tiny_fonts_item );\r
- customizeJMenuItem( _tiny_fonts_item );\r
- customizeJMenuItem( _small_fonts_item );\r
- customizeJMenuItem( _medium_fonts_item );\r
- customizeJMenuItem( _large_fonts_item );\r
- _jmenubar.add( _font_size_menu );\r
- }\r
-\r
- void buildHelpMenu() {\r
- _help_jmenu = createMenu( "Help", getConfiguration() );\r
- _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
- _help_jmenu.addSeparator();\r
- _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
- _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
- _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
- _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
- _help_jmenu.addSeparator();\r
- _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
- customizeJMenuItem( _help_item );\r
- customizeJMenuItem( _website_item );\r
- customizeJMenuItem( _phyloxml_website_item );\r
- customizeJMenuItem( _aptx_ref_item );\r
- customizeJMenuItem( _phyloxml_ref_item );\r
- customizeJMenuItem( _about_item );\r
- _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
- _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
- _jmenubar.add( _help_jmenu );\r
- }\r
-\r
- void buildTypeMenu() {\r
- _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
- _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
- _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
- customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
- customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
- _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
- _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
- initializeTypeMenu( getOptions() );\r
- _jmenubar.add( _type_menu );\r
- }\r
-\r
- void buildViewMenu() {\r
- _view_jmenu = createMenu( "View", getConfiguration() );\r
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
- _view_jmenu.addSeparator();\r
- _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
- customizeJMenuItem( _display_basic_information_item );\r
- customizeJMenuItem( _view_as_NH_item );\r
- customizeJMenuItem( _view_as_XML_item );\r
- customizeJMenuItem( _view_as_nexus_item );\r
- _jmenubar.add( _view_jmenu );\r
- }\r
-\r
- void checkTextFrames() {\r
- if ( _textframes.size() > 5 ) {\r
- try {\r
- if ( _textframes.getFirst() != null ) {\r
- _textframes.getFirst().removeMe();\r
- }\r
- else {\r
- _textframes.removeFirst();\r
- }\r
+ private void annotateSequences() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ List<PhylogenyNode> nodes = null;\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
+ || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
}\r
- catch ( final NoSuchElementException e ) {\r
- // Ignore.\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+ "No nodes selected for annotation",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final JTextField ref_field = new JTextField( 10 );\r
+ final JTextField desc_filed = new JTextField( 20 );\r
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
+ : getPreviousNodeAnnotationReference() );\r
+ final JPanel my_panel = new JPanel();\r
+ my_panel.add( new JLabel( "Reference " ) );\r
+ my_panel.add( ref_field );\r
+ my_panel.add( Box.createHorizontalStrut( 15 ) );\r
+ my_panel.add( new JLabel( "Description " ) );\r
+ my_panel.add( desc_filed );\r
+ final int result = JOptionPane.showConfirmDialog( null,\r
+ my_panel,\r
+ "Enter the sequence annotation(s) for the "\r
+ + nodes.size() + " selected nodes",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ String ref = ref_field.getText();\r
+ String desc = desc_filed.getText();\r
+ if ( !ForesterUtil.isEmpty( ref ) ) {\r
+ ref = ref.trim();\r
+ ref = ref.replaceAll( "\\s+", " " );\r
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
+ || ( ref.length() < 3 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Reference needs to be in the form of \"GO:1234567\"",\r
+ "Illegal Format for Annotation Reference",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ }\r
+ if ( ref != null ) {\r
+ setPreviousNodeAnnotationReference( ref );\r
+ }\r
+ if ( desc != null ) {\r
+ desc = desc.trim();\r
+ desc = desc.replaceAll( "\\s+", " " );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
+ for( final PhylogenyNode n : nodes ) {\r
+ ForesterUtil.ensurePresenceOfSequence( n );\r
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
+ : new Annotation( ref );\r
+ if ( !ForesterUtil.isEmpty( desc ) ) {\r
+ ann.setDesc( desc );\r
+ }\r
+ n.getNodeData().getSequence().addAnnotation( ann );\r
+ }\r
+ }\r
+ getMainPanel().getControlPanel().showAnnotations();\r
+ }\r
}\r
}\r
}\r
\r
- void choosePdfWidth() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the default line width for PDF export.\n"\r
- + "[current value: "\r
- + getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
+ private void chooseFont() {\r
+ final FontChooser fc = new FontChooser();\r
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
+ fc.showDialog( this, "Select the Base Font" );\r
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
+ }\r
+\r
+ private void chooseMinimalConfidence() {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum for confidence values to be displayed.\n"\r
+ + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getMinConfidenceValue() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
- float f = 0.0f;\r
+ double m = 0.0;\r
final String m_str = s.trim();\r
if ( !ForesterUtil.isEmpty( m_str ) ) {\r
try {\r
- f = Float.parseFloat( m_str );\r
+ m = Double.parseDouble( m_str );\r
}\r
catch ( final Exception ex ) {\r
success = false;\r
else {\r
success = false;\r
}\r
- if ( success && ( f > 0.0 ) ) {\r
- getOptions().setPrintLineWidth( f );\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ getOptions().setMinConfidenceValue( m );\r
}\r
}\r
}\r
\r
- void choosePrintSize() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter values for width and height,\nseparated by a comma.\n"\r
- + "[current values: "\r
- + getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() + "]\n"\r
- + "[A4: " + Constants.A4_SIZE_X + ", "\r
- + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
- + Constants.US_LETTER_SIZE_X + ", "\r
- + Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
- if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
- boolean success = true;\r
- int x = 0;\r
- int y = 0;\r
- final String[] str_ary = s.split( "," );\r
- if ( str_ary.length == 2 ) {\r
- final String x_str = str_ary[ 0 ].trim();\r
- final String y_str = str_ary[ 1 ].trim();\r
- if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
- try {\r
- x = Integer.parseInt( x_str );\r
- y = Integer.parseInt( y_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
+ private void deleteSelectedNodes( final boolean delete ) {\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
+ return;\r
+ }\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ for( final PhylogenyNode n : all_selected_nodes ) {\r
+ if ( n.isExternal() ) {\r
+ nodes.add( n );\r
+ }\r
+ }\r
+ }\r
+ String function = "Retain";\r
+ if ( delete ) {\r
+ function = "Delete";\r
+ }\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
+ "No external nodes selected to " + function.toLowerCase(),\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final int todo = nodes.size();\r
+ final int ext = phy.getNumberOfExternalNodes();\r
+ int res = todo;\r
+ if ( delete ) {\r
+ res = ext - todo;\r
+ }\r
+ if ( res < 1 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Cannot delete all nodes",\r
+ "Attempt to delete all nodes ",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ if ( !delete ) {\r
+ final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !nodes.contains( n ) ) {\r
+ to_delete.add( n );\r
}\r
}\r
- else {\r
- success = false;\r
+ for( final PhylogenyNode n : to_delete ) {\r
+ phy.deleteSubtree( n, true );\r
}\r
}\r
else {\r
- success = false;\r
- }\r
- if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
- getOptions().setPrintSizeX( x );\r
- getOptions().setPrintSizeY( y );\r
+ for( final PhylogenyNode n : nodes ) {\r
+ phy.deleteSubtree( n, true );\r
+ }\r
}\r
+ resetSearch();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().setEdited( true );\r
+ repaint();\r
}\r
}\r
\r
- void close() {\r
- removeAllTextFrames();\r
- if ( _mainpanel != null ) {\r
- _mainpanel.terminate();\r
- }\r
- if ( _contentpane != null ) {\r
- _contentpane.removeAll();\r
+ private void doUpdateProcessMenu() {\r
+ if ( _process_pool.size() > 0 ) {\r
+ if ( _process_menu == null ) {\r
+ _process_menu = createMenu( "", getConfiguration() );\r
+ _process_menu.setForeground( Color.RED );\r
+ }\r
+ _process_menu.removeAll();\r
+ final String text = "processes running: " + _process_pool.size();\r
+ _process_menu.setText( text );\r
+ _jmenubar.add( _process_menu );\r
+ for( int i = 0; i < _process_pool.size(); ++i ) {\r
+ final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
+ _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
+ }\r
}\r
- setVisible( false );\r
- dispose();\r
- }\r
-\r
- void colorRank() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- final String[] ranks = AptxUtil.getAllPossibleRanks();\r
- final String rank = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "What rank should the colorization be based on",\r
- "Rank Selection",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- ranks,\r
- null );\r
- if ( !ForesterUtil.isEmpty( rank ) ) {\r
- _mainpanel.getCurrentTreePanel().colorRank( rank );\r
+ else {\r
+ if ( _process_menu != null ) {\r
+ _process_menu.removeAll();\r
+ _jmenubar.remove( _process_menu );\r
}\r
}\r
+ _jmenubar.validate();\r
+ _jmenubar.repaint();\r
+ repaint();\r
}\r
\r
- void confColor() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().confColor();\r
- }\r
+ private String getPreviousNodeAnnotationReference() {\r
+ return _previous_node_annotation_ref;\r
}\r
\r
- void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
- if ( item != null ) {\r
- item.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- item.setSelected( is_selected );\r
- item.addActionListener( this );\r
+ private void removeBranchColors() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
}\r
}\r
\r
- JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
- if ( jmi != null ) {\r
- jmi.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- jmi.addActionListener( this );\r
+ private void removeVisualStyles() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
}\r
- return jmi;\r
}\r
\r
- void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
- if ( item != null ) {\r
- item.setFont( MainFrame.menu_font );\r
- if ( !getConfiguration().isUseNativeUI() ) {\r
- item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
- item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
- }\r
- item.setSelected( is_selected );\r
- item.addActionListener( this );\r
- }\r
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
+ _previous_node_annotation_ref = previous_node_annotation_ref;\r
}\r
\r
- void displayBasicInformation( final File treefile ) {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "Basic Information";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
- }\r
- showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
+ private void writeAllToFile() {\r
+ if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {\r
+ return;\r
}\r
- }\r
-\r
- void exceptionOccuredDuringOpenFile( final Exception e ) {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _save_filechooser.setCurrentDirectory( my_dir );\r
}\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
+ _save_filechooser.setSelectedFile( new File( "" ) );\r
+ final int result = _save_filechooser.showSaveDialog( _contentpane );\r
+ final File file = _save_filechooser.getSelectedFile();\r
+ setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "Warning",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ final int count = getMainPanel().getTabbedPane().getTabCount();\r
+ final List<Phylogeny> trees = new ArrayList<Phylogeny>();\r
+ for( int i = 0; i < count; ++i ) {\r
+ final Phylogeny phy = getMainPanel().getPhylogeny( i );\r
+ if ( ForesterUtil.isEmpty( phy.getName() )\r
+ && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {\r
+ phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );\r
+ }\r
+ trees.add( phy );\r
+ getMainPanel().getTreePanels().get( i ).setEdited( false );\r
+ }\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ try {\r
+ writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );\r
+ }\r
+ catch ( final IOException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to write to: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
}\r
- JOptionPane.showMessageDialog( this,\r
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Error during File|Open",\r
- JOptionPane.ERROR_MESSAGE );\r
}\r
\r
- void exceptionOccuredDuringSaveAs( final Exception e ) {\r
- try {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ void activateSaveAllIfNeeded() {\r
+ if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {\r
+ _save_all_item.setEnabled( true );\r
}\r
- catch ( final Exception ex ) {\r
- // Do nothing.\r
+ else {\r
+ _save_all_item.setEnabled( false );\r
}\r
- JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
}\r
\r
- void executeGSDI() {\r
- if ( !isOKforSDI( false, true ) ) {\r
- return;\r
+ void buildFileMenu() {\r
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\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
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not rooted.",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\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
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
- gene_tree.setAllNodesToNotCollapse();\r
- gene_tree.recalculateNumberOfExternalDescendants( false );\r
- GSDI gsdi = null;\r
- final Phylogeny species_tree = getSpeciesTree().copy();\r
- try {\r
- gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
- }\r
- catch ( final SDIException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Error during GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- AptxUtil.unexpectedException( e );\r
- return;\r
- }\r
- gene_tree.setRerootable( false );\r
- gene_tree.clearHashIdToNodeMap();\r
- gene_tree.recalculateNumberOfExternalDescendants( true );\r
- _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
- getMainPanel().getControlPanel().setShowEvents( true );\r
- showWhole();\r
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
- showWhole();\r
- _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
- showWhole();\r
- _mainpanel.getCurrentTreePanel().setEdited( true );\r
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
- if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
- + "Potential duplications: "\r
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
- + "Potential duplications: "\r
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
-\r
- void executeGSDIR() {\r
- if ( !isOKforSDI( false, false ) ) {\r
- return;\r
- }\r
- final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
- if ( ( p > 0 )\r
- && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
- gene_tree.setAllNodesToNotCollapse();\r
- gene_tree.recalculateNumberOfExternalDescendants( false );\r
- GSDIR gsdir = null;\r
- final Phylogeny species_tree = getSpeciesTree().copy();\r
- try {\r
- gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
- }\r
- catch ( final SDIException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Error during GSDIR",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- AptxUtil.unexpectedException( e );\r
- return;\r
- }\r
- final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
- result_gene_tree.setRerootable( false );\r
- result_gene_tree.clearHashIdToNodeMap();\r
- result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
- PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
- _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
- getMainPanel().getControlPanel().setShowEvents( true );\r
- showWhole();\r
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
- showWhole();\r
- _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
- showWhole();\r
- _mainpanel.getCurrentTreePanel().setEdited( true );\r
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
- if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
- + "Stripped gene tree nodes: "\r
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
- + "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
-\r
- boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
- if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree and species tree have no species in common.",\r
- "Error during SDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree and species tree have only one species in common.",\r
- "Error during SDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else {\r
- return true;\r
- }\r
- }\r
-\r
- ControlPanel getControlPanel() {\r
- return getMainPanel().getControlPanel();\r
- }\r
-\r
- File getCurrentDir() {\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( ForesterUtil.isWindows() ) {\r
- try {\r
- _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
- }\r
- catch ( final Exception e ) {\r
- _current_dir = null;\r
- }\r
- }\r
- }\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( System.getProperty( "user.home" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.home" ) );\r
- }\r
- else if ( System.getProperty( "user.dir" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.dir" ) );\r
- }\r
- }\r
- return _current_dir;\r
- }\r
-\r
- TreePanel getCurrentTreePanel() {\r
- return getMainPanel().getCurrentTreePanel();\r
- }\r
-\r
- JMenu getHelpMenu() {\r
- return _help_jmenu;\r
- }\r
-\r
- JCheckBoxMenuItem getlabelDirectionCbmi() {\r
- return _label_direction_cbmi;\r
- }\r
-\r
- JMenuBar getMenuBarOfMainFrame() {\r
- return _jmenubar;\r
- }\r
-\r
- final Phylogeny getSpeciesTree() {\r
- return _species_tree;\r
- }\r
-\r
- void initializeTypeMenu( final Options options ) {\r
- setTypeMenuToAllUnselected();\r
- switch ( options.getPhylogenyGraphicsType() ) {\r
- case CONVEX:\r
- _convex_type_cbmi.setSelected( true );\r
- break;\r
- case CURVED:\r
- _curved_type_cbmi.setSelected( true );\r
- break;\r
- case EURO_STYLE:\r
- _euro_type_cbmi.setSelected( true );\r
- break;\r
- case ROUNDED:\r
- _rounded_type_cbmi.setSelected( true );\r
- break;\r
- case TRIANGULAR:\r
- _triangular_type_cbmi.setSelected( true );\r
- break;\r
- case UNROOTED:\r
- _unrooted_type_cbmi.setSelected( true );\r
- break;\r
- case CIRCULAR:\r
- _circular_type_cbmi.setSelected( true );\r
- break;\r
- default:\r
- _rectangular_type_cbmi.setSelected( true );\r
- break;\r
- }\r
- }\r
-\r
- boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- return false;\r
- }\r
- else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "No species tree loaded",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Species tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Gene tree is not completely binary",\r
- "Cannot execute GSDI",\r
- JOptionPane.ERROR_MESSAGE );\r
- return false;\r
- }\r
- else {\r
- return true;\r
- }\r
- }\r
-\r
- boolean isSubtreeDisplayed() {\r
- if ( getCurrentTreePanel() != null ) {\r
- if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
- "Operation can not be exectuted on a sub-tree",\r
- JOptionPane.WARNING_MESSAGE );\r
- return true;\r
- }\r
- }\r
- return false;\r
- }\r
-\r
- void midpointRoot() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().midpointRoot();\r
- }\r
- }\r
-\r
- static void printPhylogenyToPdf( final String file_name,\r
- final Options opts,\r
- final TreePanel tp,\r
- final Component comp ) {\r
- if ( !opts.isPrintUsingActualSize() ) {\r
- tp.calcParametersForPainting( opts.getPrintSizeX(), opts.getPrintSizeY() );\r
- tp.resetPreferredSize();\r
- tp.repaint();\r
- }\r
- String pdf_written_to = "";\r
- boolean error = false;\r
- try {\r
- if ( opts.isPrintUsingActualSize() ) {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth(), tp.getHeight() );\r
- }\r
- else {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
- tp,\r
- opts.getPrintSizeX(),\r
- opts.getPrintSizeY() );\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Wrote PDF to: " + pdf_written_to,\r
- "Information",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( comp,\r
- "There was an unknown problem when attempting to write to PDF file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- if ( !opts.isPrintUsingActualSize() ) {\r
- tp.getControlPanel().showWhole();\r
- }\r
- }\r
-\r
- void readPhylogeniesFromWebservice( final int i ) {\r
- final UrlTreeReader reader = new UrlTreeReader( this, i );\r
- new Thread( reader ).start();\r
- }\r
-\r
- void removeAllTextFrames() {\r
- for( final TextFrame tf : _textframes ) {\r
- if ( tf != null ) {\r
- tf.close();\r
- }\r
- }\r
- _textframes.clear();\r
- }\r
-\r
- void resetSearch() {\r
- getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
- getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
- }\r
-\r
- void setConfiguration( final Configuration configuration ) {\r
- _configuration = configuration;\r
- }\r
-\r
- void setCurrentDir( final File current_dir ) {\r
- _current_dir = current_dir;\r
- }\r
-\r
- void setInferenceManager( final InferenceManager i ) {\r
- _inference_manager = i;\r
- }\r
-\r
- void setOptions( final Options options ) {\r
- _options = options;\r
- }\r
-\r
- void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
- setTypeMenuToAllUnselected();\r
- switch ( type ) {\r
- case CIRCULAR:\r
- _circular_type_cbmi.setSelected( true );\r
- break;\r
- case CONVEX:\r
- _convex_type_cbmi.setSelected( true );\r
- break;\r
- case CURVED:\r
- _curved_type_cbmi.setSelected( true );\r
- break;\r
- case EURO_STYLE:\r
- _euro_type_cbmi.setSelected( true );\r
- break;\r
- case ROUNDED:\r
- _rounded_type_cbmi.setSelected( true );\r
- break;\r
- case RECTANGULAR:\r
- _rectangular_type_cbmi.setSelected( true );\r
- break;\r
- case TRIANGULAR:\r
- _triangular_type_cbmi.setSelected( true );\r
- break;\r
- case UNROOTED:\r
- _unrooted_type_cbmi.setSelected( true );\r
- break;\r
- default:\r
- throw new IllegalArgumentException( "unknown type: " + type );\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( _exit_item = new JMenuItem( "Exit" ) );\r
+ customizeJMenuItem( _save_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
- final void setSpeciesTree( final Phylogeny species_tree ) {\r
- _species_tree = species_tree;\r
+ void buildFontSizeMenu() {\r
+ _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );\r
+ _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );\r
+ _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );\r
+ _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );\r
+ _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );\r
+ _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );\r
+ customizeJMenuItem( _super_tiny_fonts_item );\r
+ customizeJMenuItem( _tiny_fonts_item );\r
+ customizeJMenuItem( _small_fonts_item );\r
+ customizeJMenuItem( _medium_fonts_item );\r
+ customizeJMenuItem( _large_fonts_item );\r
+ _jmenubar.add( _font_size_menu );\r
}\r
\r
- void setTypeMenuToAllUnselected() {\r
- _convex_type_cbmi.setSelected( false );\r
- _curved_type_cbmi.setSelected( false );\r
- _euro_type_cbmi.setSelected( false );\r
- _rounded_type_cbmi.setSelected( false );\r
- _triangular_type_cbmi.setSelected( false );\r
- _rectangular_type_cbmi.setSelected( false );\r
- _unrooted_type_cbmi.setSelected( false );\r
- _circular_type_cbmi.setSelected( false );\r
+ void buildHelpMenu() {\r
+ _help_jmenu = createMenu( "Help", getConfiguration() );\r
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );\r
+ _help_jmenu.addSeparator();\r
+ _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );\r
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...\r
+ _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );\r
+ _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );\r
+ _help_jmenu.addSeparator();\r
+ _help_jmenu.add( _about_item = new JMenuItem( "About" ) );\r
+ customizeJMenuItem( _help_item );\r
+ customizeJMenuItem( _website_item );\r
+ customizeJMenuItem( _phyloxml_website_item );\r
+ customizeJMenuItem( _aptx_ref_item );\r
+ customizeJMenuItem( _phyloxml_ref_item );\r
+ customizeJMenuItem( _about_item );\r
+ _phyloxml_ref_item.setToolTipText( PHYLOXML_REF_TOOL_TIP );\r
+ _aptx_ref_item.setToolTipText( APTX_REF_TOOL_TIP );\r
+ _jmenubar.add( _help_jmenu );\r
}\r
\r
- void switchColors() {\r
- final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
- final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
- csc.setVisible( true );\r
+ void buildTypeMenu() {\r
+ _type_menu = createMenu( TYPE_MENU_HEADER, getConfiguration() );\r
+ _type_menu.add( _rectangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.RECTANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _euro_type_cbmi = new JCheckBoxMenuItem( MainFrame.EURO_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _rounded_type_cbmi = new JCheckBoxMenuItem( MainFrame.ROUNDED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _curved_type_cbmi = new JCheckBoxMenuItem( MainFrame.CURVED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _triangular_type_cbmi = new JCheckBoxMenuItem( MainFrame.TRIANGULAR_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _convex_type_cbmi = new JCheckBoxMenuItem( MainFrame.CONVEX_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _unrooted_type_cbmi = new JCheckBoxMenuItem( MainFrame.UNROOTED_TYPE_CBMI_LABEL ) );\r
+ _type_menu.add( _circular_type_cbmi = new JCheckBoxMenuItem( MainFrame.CIRCULAR_TYPE_CBMI_LABEL ) );\r
+ customizeCheckBoxMenuItem( _rectangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _triangular_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _euro_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _rounded_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _curved_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _convex_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );\r
+ customizeCheckBoxMenuItem( _circular_type_cbmi, false );\r
+ _unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ _circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );\r
+ initializeTypeMenu( getOptions() );\r
+ _jmenubar.add( _type_menu );\r
}\r
\r
- void taxColor() {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().taxColor();\r
- }\r
+ void buildViewMenu() {\r
+ _view_jmenu = createMenu( "View", getConfiguration() );\r
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );\r
+ _view_jmenu.addSeparator();\r
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );\r
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );\r
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );\r
+ customizeJMenuItem( _display_basic_information_item );\r
+ customizeJMenuItem( _view_as_NH_item );\r
+ customizeJMenuItem( _view_as_XML_item );\r
+ customizeJMenuItem( _view_as_nexus_item );\r
+ _jmenubar.add( _view_jmenu );\r
}\r
\r
- void typeChanged( final Object o ) {\r
- updateTypeCheckboxes( getOptions(), o );\r
- updateOptions( getOptions() );\r
- if ( getCurrentTreePanel() != null ) {\r
- final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
- final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
- if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
- || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
- || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
- getCurrentTreePanel().getControlPanel().showWhole();\r
- }\r
- if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
- }\r
- else {\r
- getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
- }\r
- getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
- updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
- if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
- if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
+ void checkTextFrames() {\r
+ if ( _textframes.size() > 5 ) {\r
+ try {\r
+ if ( _textframes.getFirst() != null ) {\r
+ _textframes.getFirst().removeMe();\r
}\r
else {\r
- getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
+ _textframes.removeFirst();\r
}\r
}\r
+ catch ( final NoSuchElementException e ) {\r
+ // Ignore.\r
+ }\r
}\r
}\r
\r
- void updateOptions( final Options options ) {\r
- options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
- options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
- && _background_gradient_cbmi.isSelected() );\r
- options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
- options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
- && _show_annotation_ref_source.isSelected() );\r
- options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
- && _abbreviate_scientific_names.isSelected() );\r
- options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
- && _color_labels_same_as_parent_branch.isSelected() );\r
- options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
- && _show_default_node_shapes_internal_cbmi.isSelected() );\r
- options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
- && _show_default_node_shapes_external_cbmi.isSelected() );\r
- options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
- && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
- if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
- }\r
- else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
- }\r
- else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
- options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
- }\r
- options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
- && _search_case_senstive_cbmi.isSelected() );\r
- if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
- options.setShowScale( _show_scale_cbmi.isSelected() );\r
- }\r
- if ( _label_direction_cbmi != null ) {\r
- if ( _label_direction_cbmi.isSelected() ) {\r
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
+ void choosePdfWidth() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the default line width for PDF export.\n"\r
+ + "[current value: "\r
+ + getOptions().getPrintLineWidth() + "]\n",\r
+ "Line Width for PDF Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintLineWidth() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ float f = 0.0f;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ f = Float.parseFloat( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
}\r
else {\r
- options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
+ success = false;\r
+ }\r
+ if ( success && ( f > 0.0 ) ) {\r
+ getOptions().setPrintLineWidth( f );\r
}\r
}\r
- options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
- options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
- && _show_confidence_stddev_cbmi.isSelected() );\r
- if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
- options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
- }\r
- options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
- && ( _print_using_actual_size_cbmi.isSelected() ) );\r
- options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
- options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
- if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
- && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
- }\r
- else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
- && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
- }\r
- else {\r
- options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
- }\r
- options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
- && _print_black_and_white_cbmi.isSelected() );\r
- options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
- && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
- if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
- }\r
- else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
- }\r
- else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
- }\r
- else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
- options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
- }\r
- options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
- && _replace_underscores_cbmi.isSelected() );\r
- options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
- && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
- options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
- && _search_whole_words_only_cbmi.isSelected() );\r
- options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
- options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
- && _inverse_search_result_cbmi.isSelected() );\r
- if ( _graphics_export_visible_only_cbmi != null ) {\r
- options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
- if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
- _graphics_export_using_actual_size_cbmi.setSelected( true );\r
- _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
+ }\r
+\r
+ void choosePrintSize() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter values for width and height,\nseparated by a comma.\n"\r
+ + "[current values: "\r
+ + getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() + "]\n"\r
+ + "[A4: " + Constants.A4_SIZE_X + ", "\r
+ + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
+ + Constants.US_LETTER_SIZE_X + ", "\r
+ + Constants.US_LETTER_SIZE_Y + "]",\r
+ "Default Size for Graphics Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() );\r
+ if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
+ boolean success = true;\r
+ int x = 0;\r
+ int y = 0;\r
+ final String[] str_ary = s.split( "," );\r
+ if ( str_ary.length == 2 ) {\r
+ final String x_str = str_ary[ 0 ].trim();\r
+ final String y_str = str_ary[ 1 ].trim();\r
+ if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
+ try {\r
+ x = Integer.parseInt( x_str );\r
+ y = Integer.parseInt( y_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
}\r
else {\r
- _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
+ success = false;\r
+ }\r
+ if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
+ getOptions().setPrintSizeX( x );\r
+ getOptions().setPrintSizeY( y );\r
}\r
}\r
- if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
- }\r
- else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
- }\r
- else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
- }\r
- else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
- }\r
- else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
- }\r
- else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
- }\r
- else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
+ }\r
+\r
+ void close() {\r
+ removeAllTextFrames();\r
+ if ( _mainpanel != null ) {\r
+ _mainpanel.terminate();\r
}\r
- else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
- options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
+ if ( _contentpane != null ) {\r
+ _contentpane.removeAll();\r
}\r
- if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
- options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ void colorRank() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ final String[] ranks = AptxUtil.getAllPossibleRanks();\r
+ final String rank = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "What rank should the colorization be based on",\r
+ "Rank Selection",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ ranks,\r
+ null );\r
+ if ( !ForesterUtil.isEmpty( rank ) ) {\r
+ _mainpanel.getCurrentTreePanel().colorRank( rank );\r
+ }\r
}\r
- if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
- options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
+ }\r
+\r
+ void confColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().confColor();\r
}\r
}\r
\r
- void updateTypeCheckboxes( final Options options, final Object o ) {\r
- setTypeMenuToAllUnselected();\r
- ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
+ void customizeCheckBoxMenuItem( final JCheckBoxMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
+ }\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
+ }\r
}\r
\r
- void viewAsNexus() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "Nexus";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ JMenuItem customizeJMenuItem( final JMenuItem jmi ) {\r
+ if ( jmi != null ) {\r
+ jmi.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ jmi.setForeground( getConfiguration().getGuiMenuTextColor() );\r
}\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
- title );\r
+ jmi.addActionListener( this );\r
}\r
+ return jmi;\r
}\r
\r
- void viewAsNH() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "New Hampshire";\r
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) {\r
+ if ( item != null ) {\r
+ item.setFont( MainFrame.menu_font );\r
+ if ( !getConfiguration().isUseNativeUI() ) {\r
+ item.setBackground( getConfiguration().getGuiMenuBackgroundColor() );\r
+ item.setForeground( getConfiguration().getGuiMenuTextColor() );\r
}\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
- .getNhConversionSupportValueStyle() ),\r
- title );\r
+ item.setSelected( is_selected );\r
+ item.addActionListener( this );\r
}\r
}\r
\r
- void viewAsXML() {\r
+ void displayBasicInformation( final File treefile ) {\r
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
- String title = "phyloXML";\r
+ String title = "Basic Information";\r
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
- title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";\r
}\r
- showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );\r
}\r
}\r
\r
- boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {\r
+ void exceptionOccuredDuringOpenFile( final Exception e ) {\r
try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
}\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
}\r
- return exception;\r
+ JOptionPane.showMessageDialog( this,\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Error during File|Open",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
\r
- boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );\r
+ void executeGSDI() {\r
+ if ( !isOKforSDI( false, true ) ) {\r
+ return;\r
}\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not rooted.",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- return exception;\r
- }\r
-\r
- boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {\r
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+ gene_tree.setAllNodesToNotCollapse();\r
+ gene_tree.recalculateNumberOfExternalDescendants( false );\r
+ GSDI gsdi = null;\r
+ final Phylogeny species_tree = getSpeciesTree().copy();\r
try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toPhyloXML( file, t, 0 );\r
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );\r
+ }\r
+ catch ( final SDIException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Error during GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
+ AptxUtil.unexpectedException( e );\r
+ return;\r
+ }\r
+ gene_tree.setRerootable( false );\r
+ gene_tree.clearHashIdToNodeMap();\r
+ gene_tree.recalculateNumberOfExternalDescendants( true );\r
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );\r
+ getMainPanel().getControlPanel().setShowEvents( true );\r
+ showWhole();\r
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+ showWhole();\r
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+ showWhole();\r
+ _mainpanel.getCurrentTreePanel().setEdited( true );\r
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+ + "Potential duplications: "\r
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDI successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"\r
+ + "Potential duplications: "\r
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"\r
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDI successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
- return exception;\r
}\r
\r
- static void writePhylogenyToGraphicsFile( final String file_name,\r
- final GraphicsExportType type,\r
- final MainPanel mp,\r
- final Component comp,\r
- final Container contentpane ) {\r
- mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),\r
- mp.getCurrentTreePanel().getHeight() );\r
- String file_written_to = "";\r
- boolean error = false;\r
+ void executeGSDIR() {\r
+ if ( !isOKforSDI( false, false ) ) {\r
+ return;\r
+ }\r
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );\r
+ if ( ( p > 0 )\r
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();\r
+ gene_tree.setAllNodesToNotCollapse();\r
+ gene_tree.recalculateNumberOfExternalDescendants( false );\r
+ GSDIR gsdir = null;\r
+ final Phylogeny species_tree = getSpeciesTree().copy();\r
try {\r
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
- mp.getCurrentTreePanel().getWidth(),\r
- mp.getCurrentTreePanel().getHeight(),\r
- mp.getCurrentTreePanel(),\r
- mp.getControlPanel(),\r
- type,\r
- mp.getOptions() );\r
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );\r
}\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ catch ( final SDIException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Error during GSDIR",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- if ( !error ) {\r
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
- JOptionPane.showMessageDialog( comp,\r
- "Wrote image to: " + file_written_to,\r
- "Graphics Export",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( comp,\r
- "There was an unknown problem when attempting to write to an image file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
+ catch ( final Exception e ) {\r
+ AptxUtil.unexpectedException( e );\r
+ return;\r
+ }\r
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();\r
+ result_gene_tree.setRerootable( false );\r
+ result_gene_tree.clearHashIdToNodeMap();\r
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );\r
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );\r
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );\r
+ getMainPanel().getControlPanel().setShowEvents( true );\r
+ showWhole();\r
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();\r
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );\r
+ showWhole();\r
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );\r
+ showWhole();\r
+ _mainpanel.getCurrentTreePanel().setEdited( true );\r
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );\r
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDIR successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"\r
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"\r
+ + "Stripped gene tree nodes: "\r
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ + "Number of polytomies in species tree used: " + poly + "\n",\r
+ "GSDIR successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
- contentpane.repaint();\r
}\r
\r
- void writeToFile( final Phylogeny t ) {\r
- if ( t == null ) {\r
+ void executeLineageInference() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
return;\r
}\r
- String initial_filename = null;\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- try {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
- }\r
- catch ( final IOException e ) {\r
- initial_filename = null;\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
- if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
- _save_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getCurrentPhylogeny()\r
+ .copy() );\r
+ new Thread( inferrer ).start();\r
+ }\r
+\r
+ boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {\r
+ if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree and species tree have no species in common.",\r
+ "Error during SDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
}\r
- else {\r
- _save_filechooser.setSelectedFile( new File( "" ) );\r
+ else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree and species tree have only one species in common.",\r
+ "Error during SDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
}\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _save_filechooser.setCurrentDirectory( my_dir );\r
+ else {\r
+ return true;\r
}\r
- final int result = _save_filechooser.showSaveDialog( _contentpane );\r
- final File file = _save_filechooser.getSelectedFile();\r
- setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
- boolean exception = false;\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists.\nOverwrite?",\r
- "Overwrite?",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.QUESTION_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
+ }\r
+\r
+ ControlPanel getControlPanel() {\r
+ return getMainPanel().getControlPanel();\r
+ }\r
+\r
+ File getCurrentDir() {\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( ForesterUtil.isWindows() ) {\r
+ try {\r
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
}\r
- else {\r
- final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
- try {\r
- ForesterUtil.copyFile( file, to );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to create backup copy " + to,\r
- "Failed to Create Backup Copy",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Failed to Delete",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
+ catch ( final Exception e ) {\r
+ _current_dir = null;\r
}\r
}\r
- if ( _save_filechooser.getFileFilter() == MainFrame.nhfilter ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // "*.*":\r
- else {\r
- final String file_name = file.getName().trim().toLowerCase();\r
- if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tree" ) ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // XML is default:\r
- else {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
+ }\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( System.getProperty( "user.home" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.home" ) );\r
}\r
- if ( !exception ) {\r
- getMainPanel().setTitleOfSelectedTab( file.getName() );\r
- getMainPanel().getCurrentTreePanel().setTreeFile( file );\r
- getMainPanel().getCurrentTreePanel().setEdited( false );\r
+ else if ( System.getProperty( "user.dir" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.dir" ) );\r
}\r
}\r
+ return _current_dir;\r
}\r
\r
- static File writeToGraphicsFile( final Phylogeny t,\r
- final GraphicsExportType type,\r
- final MainPanel mp,\r
- final JFileChooser writetographics_filechooser,\r
- final Component component,\r
- final Container contentpane,\r
- final File current_dir ) {\r
- File new_dir = null;\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return null;\r
+ TreePanel getCurrentTreePanel() {\r
+ return getMainPanel().getCurrentTreePanel();\r
+ }\r
+\r
+ JMenu getHelpMenu() {\r
+ return _help_jmenu;\r
+ }\r
+\r
+ JCheckBoxMenuItem getlabelDirectionCbmi() {\r
+ return _label_direction_cbmi;\r
+ }\r
+\r
+ JMenuBar getMenuBarOfMainFrame() {\r
+ return _jmenubar;\r
+ }\r
+\r
+ final Phylogeny getSpeciesTree() {\r
+ return _species_tree;\r
+ }\r
+\r
+ void initializeTypeMenu( final Options options ) {\r
+ setTypeMenuToAllUnselected();\r
+ switch ( options.getPhylogenyGraphicsType() ) {\r
+ case CONVEX:\r
+ _convex_type_cbmi.setSelected( true );\r
+ break;\r
+ case CURVED:\r
+ _curved_type_cbmi.setSelected( true );\r
+ break;\r
+ case EURO_STYLE:\r
+ _euro_type_cbmi.setSelected( true );\r
+ break;\r
+ case ROUNDED:\r
+ _rounded_type_cbmi.setSelected( true );\r
+ break;\r
+ case TRIANGULAR:\r
+ _triangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case UNROOTED:\r
+ _unrooted_type_cbmi.setSelected( true );\r
+ break;\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
+ default:\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
}\r
- String initial_filename = "";\r
- if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
+ }\r
+\r
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ return false;\r
}\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No species tree loaded",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
}\r
- initial_filename = initial_filename + "." + type;\r
- writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = current_dir;\r
- if ( my_dir != null ) {\r
- writetographics_filechooser.setCurrentDirectory( my_dir );\r
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Species tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
}\r
- final int result = writetographics_filechooser.showSaveDialog( contentpane );\r
- File file = writetographics_filechooser.getSelectedFile();\r
- //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );\r
- new_dir = writetographics_filechooser.getCurrentDirectory();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
- file = new File( file.toString() + "." + type );\r
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Gene tree is not completely binary",\r
+ "Cannot execute GSDI",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return false;\r
+ }\r
+ else {\r
+ return true;\r
+ }\r
+ }\r
+\r
+ boolean isSubtreeDisplayed() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
+ "Operation can not be exectuted on a sub-tree",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return true;\r
}\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( component,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return null;\r
- }\r
- else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( component,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ void midpointRoot() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().midpointRoot();\r
+ }\r
+ }\r
+\r
+ void readPhylogeniesFromWebservice( final int i ) {\r
+ final UrlTreeReader reader = new UrlTreeReader( this, i );\r
+ new Thread( reader ).start();\r
+ }\r
+\r
+ void removeAllTextFrames() {\r
+ for( final TextFrame tf : _textframes ) {\r
+ if ( tf != null ) {\r
+ tf.close();\r
}\r
- writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );\r
}\r
- return new_dir;\r
+ _textframes.clear();\r
}\r
\r
- static File writeToPdf( final Phylogeny t,\r
- final MainPanel mp,\r
- final JFileChooser writetopdf_filechooser,\r
- final File curr_dir,\r
- final Container contentpane,\r
- final Component component ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return null;\r
- }\r
- String initial_filename = "";\r
- if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + ".pdf";\r
- writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = curr_dir;\r
- if ( my_dir != null ) {\r
- writetopdf_filechooser.setCurrentDirectory( my_dir );\r
+ void resetSearch() {\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
+ }\r
+\r
+ void setConfiguration( final Configuration configuration ) {\r
+ _configuration = configuration;\r
+ }\r
+\r
+ void setCurrentDir( final File current_dir ) {\r
+ _current_dir = current_dir;\r
+ }\r
+\r
+ void setInferenceManager( final InferenceManager i ) {\r
+ _inference_manager = i;\r
+ }\r
+\r
+ void setOptions( final Options options ) {\r
+ _options = options;\r
+ }\r
+\r
+ void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
+ setTypeMenuToAllUnselected();\r
+ switch ( type ) {\r
+ case CIRCULAR:\r
+ _circular_type_cbmi.setSelected( true );\r
+ break;\r
+ case CONVEX:\r
+ _convex_type_cbmi.setSelected( true );\r
+ break;\r
+ case CURVED:\r
+ _curved_type_cbmi.setSelected( true );\r
+ break;\r
+ case EURO_STYLE:\r
+ _euro_type_cbmi.setSelected( true );\r
+ break;\r
+ case ROUNDED:\r
+ _rounded_type_cbmi.setSelected( true );\r
+ break;\r
+ case RECTANGULAR:\r
+ _rectangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case TRIANGULAR:\r
+ _triangular_type_cbmi.setSelected( true );\r
+ break;\r
+ case UNROOTED:\r
+ _unrooted_type_cbmi.setSelected( true );\r
+ break;\r
+ default:\r
+ throw new IllegalArgumentException( "unknown type: " + type );\r
}\r
- final int result = writetopdf_filechooser.showSaveDialog( contentpane );\r
- File file = writetopdf_filechooser.getSelectedFile();\r
- // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() );\r
- final File new_current_dir = writetopdf_filechooser.getCurrentDirectory();\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
- file = new File( file.toString() + ".pdf" );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( component,\r
- file + " already exists. Overwrite?",\r
- "WARNING",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return null;\r
- }\r
- }\r
- printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component );\r
+ }\r
+\r
+ final void setSpeciesTree( final Phylogeny species_tree ) {\r
+ _species_tree = species_tree;\r
+ }\r
+\r
+ void setTypeMenuToAllUnselected() {\r
+ _convex_type_cbmi.setSelected( false );\r
+ _curved_type_cbmi.setSelected( false );\r
+ _euro_type_cbmi.setSelected( false );\r
+ _rounded_type_cbmi.setSelected( false );\r
+ _triangular_type_cbmi.setSelected( false );\r
+ _rectangular_type_cbmi.setSelected( false );\r
+ _unrooted_type_cbmi.setSelected( false );\r
+ _circular_type_cbmi.setSelected( false );\r
+ }\r
+\r
+ void switchColors() {\r
+ final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
+ final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
+ csc.setVisible( true );\r
+ }\r
+\r
+ void taxColor() {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().taxColor();\r
}\r
- return new_current_dir;\r
}\r
\r
- private void annotateSequences() {\r
+ void typeChanged( final Object o ) {\r
+ updateTypeCheckboxes( getOptions(), o );\r
+ updateOptions( getOptions() );\r
if ( getCurrentTreePanel() != null ) {\r
- List<PhylogenyNode> nodes = null;\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
- || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ final PHYLOGENY_GRAPHICS_TYPE previous_type = getCurrentTreePanel().getPhylogenyGraphicsType();\r
+ final PHYLOGENY_GRAPHICS_TYPE new_type = getOptions().getPhylogenyGraphicsType();\r
+ if ( ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) )\r
+ || ( ( previous_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) && ( new_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) ) {\r
+ getCurrentTreePanel().getControlPanel().showWhole();\r
}\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select nodes, either via direct selection or via the \"Search\" function",\r
- "No nodes selected for annotation",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ if ( getCurrentTreePanel().isPhyHasBranchLengths() && ( new_type != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( true );\r
}\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final JTextField ref_field = new JTextField( 10 );\r
- final JTextField desc_filed = new JTextField( 20 );\r
- ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
- : getPreviousNodeAnnotationReference() );\r
- final JPanel my_panel = new JPanel();\r
- my_panel.add( new JLabel( "Reference " ) );\r
- my_panel.add( ref_field );\r
- my_panel.add( Box.createHorizontalStrut( 15 ) );\r
- my_panel.add( new JLabel( "Description " ) );\r
- my_panel.add( desc_filed );\r
- final int result = JOptionPane.showConfirmDialog( null,\r
- my_panel,\r
- "Enter the sequence annotation(s) for the "\r
- + nodes.size() + " selected nodes",\r
- JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- String ref = ref_field.getText();\r
- String desc = desc_filed.getText();\r
- if ( !ForesterUtil.isEmpty( ref ) ) {\r
- ref = ref.trim();\r
- ref = ref.replaceAll( "\\s+", " " );\r
- if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
- || ( ref.length() < 3 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Reference needs to be in the form of \"GO:1234567\"",\r
- "Illegal Format for Annotation Reference",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- }\r
- if ( ref != null ) {\r
- setPreviousNodeAnnotationReference( ref );\r
- }\r
- if ( desc != null ) {\r
- desc = desc.trim();\r
- desc = desc.replaceAll( "\\s+", " " );\r
- }\r
- if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
- for( final PhylogenyNode n : nodes ) {\r
- ForesterUtil.ensurePresenceOfSequence( n );\r
- final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
- : new Annotation( ref );\r
- if ( !ForesterUtil.isEmpty( desc ) ) {\r
- ann.setDesc( desc );\r
- }\r
- n.getNodeData().getSequence().addAnnotation( ann );\r
- }\r
- }\r
- getMainPanel().getControlPanel().showAnnotations();\r
+ else {\r
+ getCurrentTreePanel().getControlPanel().setDrawPhylogramEnabled( false );\r
+ }\r
+ getCurrentTreePanel().setPhylogenyGraphicsType( getOptions().getPhylogenyGraphicsType() );\r
+ updateScreenTextAntialias( getMainPanel().getTreePanels() );\r
+ if ( getCurrentTreePanel().getControlPanel().getDynamicallyHideData() != null ) {\r
+ if ( new_type == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( false );\r
+ }\r
+ else {\r
+ getCurrentTreePanel().getControlPanel().getDynamicallyHideData().setEnabled( true );\r
}\r
}\r
}\r
}\r
\r
- private void chooseFont() {\r
- final FontChooser fc = new FontChooser();\r
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
- fc.showDialog( this, "Select the Base Font" );\r
- getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
- }\r
-\r
- private void chooseMinimalConfidence() {\r
- final String s = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "Please enter the minimum for confidence values to be displayed.\n"\r
- + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getMinConfidenceValue() );\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
+ void updateOptions( final Options options ) {\r
+ options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
+ options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
+ && _background_gradient_cbmi.isSelected() );\r
+ options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
+ && _show_annotation_ref_source.isSelected() );\r
+ options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
+ && _abbreviate_scientific_names.isSelected() );\r
+ options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
+ && _color_labels_same_as_parent_branch.isSelected() );\r
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
+ && _show_default_node_shapes_internal_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
+ && _show_default_node_shapes_external_cbmi.isSelected() );\r
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
+ if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
+ }\r
+ else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
+ }\r
+ else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {\r
+ options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
+ }\r
+ options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
+ && _search_case_senstive_cbmi.isSelected() );\r
+ if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
+ options.setShowScale( _show_scale_cbmi.isSelected() );\r
+ }\r
+ if ( _label_direction_cbmi != null ) {\r
+ if ( _label_direction_cbmi.isSelected() ) {\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );\r
}\r
else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- getOptions().setMinConfidenceValue( m );\r
+ options.setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );\r
}\r
}\r
- }\r
-\r
- private void deleteSelectedNodes( final boolean delete ) {\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
- return;\r
+ options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
+ options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
+ && _show_confidence_stddev_cbmi.isSelected() );\r
+ if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
+ options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
}\r
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
- for( final PhylogenyNode n : all_selected_nodes ) {\r
- if ( n.isExternal() ) {\r
- nodes.add( n );\r
- }\r
- }\r
+ options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
+ && ( _print_using_actual_size_cbmi.isSelected() ) );\r
+ options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
+ options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
+ if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
+ && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
}\r
- String function = "Retain";\r
- if ( delete ) {\r
- function = "Delete";\r
+ else if ( ( _use_internal_names_for_conf_in_nh_export_cbmi != null )\r
+ && _use_internal_names_for_conf_in_nh_export_cbmi.isSelected() ) {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
}\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
- "No external nodes selected to " + function.toLowerCase(),\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ else {\r
+ options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
}\r
- final int todo = nodes.size();\r
- final int ext = phy.getNumberOfExternalNodes();\r
- int res = todo;\r
- if ( delete ) {\r
- res = ext - todo;\r
+ options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
+ && _print_black_and_white_cbmi.isSelected() );\r
+ options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
}\r
- if ( res < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Cannot delete all nodes",\r
- "Attempt to delete all nodes ",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );\r
}\r
- final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
- + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
- + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- if ( !delete ) {\r
- final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !nodes.contains( n ) ) {\r
- to_delete.add( n );\r
- }\r
- }\r
- for( final PhylogenyNode n : to_delete ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );\r
+ }\r
+ else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {\r
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
+ }\r
+ options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
+ && _replace_underscores_cbmi.isSelected() );\r
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
+ options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
+ && _search_whole_words_only_cbmi.isSelected() );\r
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
+ options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
+ && _inverse_search_result_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi != null ) {\r
+ options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
+ if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
+ _graphics_export_using_actual_size_cbmi.setSelected( true );\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( false );\r
}\r
else {\r
- for( final PhylogenyNode n : nodes ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
+ _graphics_export_using_actual_size_cbmi.setEnabled( true );\r
}\r
- resetSearch();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().setEdited( true );\r
- repaint();\r
}\r
- }\r
-\r
- private void doUpdateProcessMenu() {\r
- if ( _process_pool.size() > 0 ) {\r
- if ( _process_menu == null ) {\r
- _process_menu = createMenu( "", getConfiguration() );\r
- _process_menu.setForeground( Color.RED );\r
- }\r
- _process_menu.removeAll();\r
- final String text = "processes running: " + _process_pool.size();\r
- _process_menu.setText( text );\r
- _jmenubar.add( _process_menu );\r
- for( int i = 0; i < _process_pool.size(); ++i ) {\r
- final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
- _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
- }\r
+ if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );\r
}\r
- else {\r
- if ( _process_menu != null ) {\r
- _process_menu.removeAll();\r
- _jmenubar.remove( _process_menu );\r
- }\r
+ else if ( ( _triangular_type_cbmi != null ) && _triangular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );\r
}\r
- _jmenubar.validate();\r
- _jmenubar.repaint();\r
- repaint();\r
- }\r
-\r
- private String getPreviousNodeAnnotationReference() {\r
- return _previous_node_annotation_ref;\r
- }\r
-\r
- static void print( final TreePanel tp, final Options op, final Component c ) {\r
- if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {\r
- return;\r
+ else if ( ( _curved_type_cbmi != null ) && _curved_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );\r
}\r
- if ( !op.isPrintUsingActualSize() ) {\r
- tp.calcParametersForPainting( op.getPrintSizeX() - 80, op.getPrintSizeY() - 140 );\r
- tp.resetPreferredSize();\r
- tp.repaint();\r
+ else if ( ( _convex_type_cbmi != null ) && _convex_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );\r
}\r
- final String job_name = Constants.PRG_NAME;\r
- boolean error = false;\r
- String printer_name = null;\r
- try {\r
- printer_name = Printer.print( tp, job_name );\r
+ else if ( ( _euro_type_cbmi != null ) && _euro_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );\r
}\r
- catch ( final Exception e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );\r
+ else if ( ( _rounded_type_cbmi != null ) && _rounded_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );\r
}\r
- if ( !error && ( printer_name != null ) ) {\r
- String msg = "Printing data sent to printer";\r
- if ( printer_name.length() > 1 ) {\r
- msg += " [" + printer_name + "]";\r
- }\r
- JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );\r
+ else if ( ( _unrooted_type_cbmi != null ) && _unrooted_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );\r
}\r
- if ( !op.isPrintUsingActualSize() ) {\r
- tp.getControlPanel().showWhole();\r
+ else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {\r
+ options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );\r
+ }\r
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {\r
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );\r
+ }\r
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {\r
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );\r
}\r
}\r
\r
- private void removeBranchColors() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
- }\r
+ void updateTypeCheckboxes( final Options options, final Object o ) {\r
+ setTypeMenuToAllUnselected();\r
+ ( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
}\r
\r
- private void removeVisualStyles() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
+ void viewAsNexus() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "Nexus";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),\r
+ title );\r
}\r
}\r
\r
- private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
- _previous_node_annotation_ref = previous_node_annotation_ref;\r
+ void viewAsNH() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "New Hampshire";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
+ .getNhConversionSupportValueStyle() ),\r
+ title );\r
+ }\r
}\r
\r
- private void writeAllToFile() {\r
- if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) {\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _save_filechooser.setCurrentDirectory( my_dir );\r
+ void viewAsXML() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
+ String title = "phyloXML";\r
+ if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {\r
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
+ }\r
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );\r
}\r
- _save_filechooser.setSelectedFile( new File( "" ) );\r
- final int result = _save_filechooser.showSaveDialog( _contentpane );\r
- final File file = _save_filechooser.getSelectedFile();\r
- setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
+ }\r
+\r
+ private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {\r
+ switch ( op.getExtDescNodeDataToReturn() ) {\r
+ case UNKNOWN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
+ break;\r
+ case DOMAINS_ALL:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
+ break;\r
+ case DOMAINS_COLLAPSED_PER_PROTEIN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
+ break;\r
+ case SEQ_ANNOTATIONS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
+ break;\r
+ case GO_TERM_IDS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
+ break;\r
+ case SEQUENCE_MOL_SEQ_FASTA:\r
+ if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {\r
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
}\r
else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- final int count = getMainPanel().getTabbedPane().getTabCount();\r
- final List<Phylogeny> trees = new ArrayList<Phylogeny>();\r
- for( int i = 0; i < count; ++i ) {\r
- final Phylogeny phy = getMainPanel().getPhylogeny( i );\r
- if ( ForesterUtil.isEmpty( phy.getName() )\r
- && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) {\r
- phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) );\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
}\r
- trees.add( phy );\r
- getMainPanel().getTreePanels().get( i ).setEdited( false );\r
- }\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- try {\r
- writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR );\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to write to: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
+ break;\r
+ default:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
}\r
}\r
\r
"Please enter the default size for node shapes.\n"\r
+ "[current value: "\r
+ options.getDefaultNodeShapeSize() + "]\n",\r
- "Node Shape Size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- options.getDefaultNodeShapeSize() );\r
+ "Node Shape Size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ options.getDefaultNodeShapeSize() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
double m = 0.0;\r
}\r
}\r
\r
- static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
- mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );\r
+ static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) {\r
+ try {\r
+ tp.setArrowCursor();\r
+ }\r
+ catch ( final Exception ex ) {\r
+ // Do nothing.\r
+ }\r
+ JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+\r
+ static void print( final TreePanel tp, final Options op, final Component c ) {\r
+ if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) {\r
+ return;\r
+ }\r
+ if ( !op.isPrintUsingActualSize() ) {\r
+ tp.calcParametersForPainting( op.getPrintSizeX() - 80, op.getPrintSizeY() - 140 );\r
+ tp.resetPreferredSize();\r
+ tp.repaint();\r
+ }\r
+ final String job_name = Constants.PRG_NAME;\r
+ boolean error = false;\r
+ String printer_name = null;\r
+ try {\r
+ printer_name = Printer.print( tp, job_name );\r
+ }\r
+ catch ( final Exception e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error && ( printer_name != null ) ) {\r
+ String msg = "Printing data sent to printer";\r
+ if ( printer_name.length() > 1 ) {\r
+ msg += " [" + printer_name + "]";\r
+ }\r
+ JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ if ( !op.isPrintUsingActualSize() ) {\r
+ tp.getControlPanel().showWhole();\r
+ }\r
+ }\r
+\r
+ static void printPhylogenyToPdf( final String file_name,\r
+ final Options opts,\r
+ final TreePanel tp,\r
+ final Component comp ) {\r
+ if ( !opts.isPrintUsingActualSize() ) {\r
+ tp.calcParametersForPainting( opts.getPrintSizeX(), opts.getPrintSizeY() );\r
+ tp.resetPreferredSize();\r
+ tp.repaint();\r
+ }\r
+ String pdf_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ if ( opts.isPrintUsingActualSize() ) {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth(), tp.getHeight() );\r
+ }\r
+ else {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
+ tp,\r
+ opts.getPrintSizeX(),\r
+ opts.getPrintSizeY() );\r
+ }\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "Wrote PDF to: " + pdf_written_to,\r
+ "Information",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "There was an unknown problem when attempting to write to PDF file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ if ( !opts.isPrintUsingActualSize() ) {\r
+ tp.getControlPanel().showWhole();\r
+ }\r
+ }\r
+\r
+ static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
+ mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Return Data..." );\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Overview Placement..." );\r
+ }\r
+ }\r
+\r
+ static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
+ if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
+ + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Select Color Scheme..." );\r
+ }\r
+ }\r
+\r
+ static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
+ }\r
+\r
+ static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
+ + o.getPrintSizeY() + ")" );\r
+ }\r
+\r
+ static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
+ }\r
+\r
+ static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
+ if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else {\r
+ mi.setEnabled( false );\r
+ }\r
+ mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
+ }\r
+\r
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
+ }\r
+\r
+ static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
+ for( final TreePanel tree_panel : treepanels ) {\r
+ tree_panel.setTextAntialias();\r
+ }\r
+ }\r
+\r
+ static boolean writeAsNewHampshire( final TreePanel tp, final Options op, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e, tp, tp );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ static boolean writeAsNexus( final TreePanel tp, final Options op, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNexus( file, tp.getPhylogeny(), op.getNhConversionSupportValueStyle() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e, tp, tp );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ static boolean writeAsPhyloXml( final TreePanel tp, final Options op, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toPhyloXML( file, tp.getPhylogeny(), 0 );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e, tp, tp );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ static void writePhylogenyToGraphicsFile( final String file_name,\r
+ final GraphicsExportType type,\r
+ final MainPanel mp,\r
+ final Component comp,\r
+ final Container contentpane ) {\r
+ mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),\r
+ mp.getCurrentTreePanel().getHeight() );\r
+ String file_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
+ mp.getCurrentTreePanel().getWidth(),\r
+ mp.getCurrentTreePanel().getHeight(),\r
+ mp.getCurrentTreePanel(),\r
+ mp.getControlPanel(),\r
+ type,\r
+ mp.getOptions() );\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "Wrote image to: " + file_written_to,\r
+ "Graphics Export",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "There was an unknown problem when attempting to write to an image file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ contentpane.repaint();\r
+ }\r
+\r
+ static File writeToFile( final Phylogeny t,\r
+ final MainPanel mp,\r
+ final JFileChooser save_filechooser,\r
+ final File current_dir,\r
+ final Container contentpane,\r
+ final Component comp ) {\r
+ File new_file = null;\r
+ if ( t == null ) {\r
+ return null;\r
}\r
- else {\r
- mi.setText( "Cycle Node Return Data..." );\r
+ String initial_filename = null;\r
+ if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
+ try {\r
+ initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
+ }\r
+ catch ( final IOException e ) {\r
+ initial_filename = null;\r
+ }\r
}\r
- }\r
-\r
- static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
+ if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
+ save_filechooser.setSelectedFile( new File( initial_filename ) );\r
}\r
else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
+ save_filechooser.setSelectedFile( new File( "" ) );\r
}\r
- }\r
-\r
- static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
+ final File my_dir = current_dir;\r
+ if ( my_dir != null ) {\r
+ save_filechooser.setCurrentDirectory( my_dir );\r
}\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
+ final int result = save_filechooser.showSaveDialog( contentpane );\r
+ final File file = save_filechooser.getSelectedFile();\r
+ new_file = save_filechooser.getCurrentDirectory();\r
+ boolean exception = false;\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( comp,\r
+ file + " already exists.\nOverwrite?",\r
+ "Overwrite?",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return null;\r
+ }\r
+ else {\r
+ final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
+ try {\r
+ ForesterUtil.copyFile( file, to );\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "Failed to create backup copy " + to,\r
+ "Failed to Create Backup Copy",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( comp,\r
+ "Failed to delete: " + file,\r
+ "Failed to Delete",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) {\r
+ exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
+ exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
+ exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ // "*.*":\r
+ else {\r
+ final String file_name = file.getName().trim().toLowerCase();\r
+ if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".tree" ) ) {\r
+ exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
+ exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ // XML is default:\r
+ else {\r
+ exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file );\r
+ }\r
+ }\r
+ if ( !exception ) {\r
+ mp.setTitleOfSelectedTab( file.getName() );\r
+ mp.getCurrentTreePanel().setTreeFile( file );\r
+ mp.getCurrentTreePanel().setEdited( false );\r
+ }\r
}\r
+ return new_file;\r
}\r
\r
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
- mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
+ static File writeToGraphicsFile( final Phylogeny t,\r
+ final GraphicsExportType type,\r
+ final MainPanel mp,\r
+ final JFileChooser writetographics_filechooser,\r
+ final Component component,\r
+ final Container contentpane,\r
+ final File current_dir ) {\r
+ File new_dir = null;\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return null;\r
}\r
- else {\r
- mi.setText( "Cycle Overview Placement..." );\r
+ String initial_filename = "";\r
+ if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
}\r
- }\r
-\r
- static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
- if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
- mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
- + ")" );\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
}\r
- else {\r
- mi.setText( "Select Color Scheme..." );\r
+ initial_filename = initial_filename + "." + type;\r
+ writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = current_dir;\r
+ if ( my_dir != null ) {\r
+ writetographics_filechooser.setCurrentDirectory( my_dir );\r
}\r
+ final int result = writetographics_filechooser.showSaveDialog( contentpane );\r
+ File file = writetographics_filechooser.getSelectedFile();\r
+ //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );\r
+ new_dir = writetographics_filechooser.getCurrentDirectory();\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
+ file = new File( file.toString() + "." + type );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( component,\r
+ file + " already exists. Overwrite?",\r
+ "Warning",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return null;\r
+ }\r
+ else {\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( component,\r
+ "Failed to delete: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ }\r
+ writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );\r
+ }\r
+ return new_dir;\r
}\r
\r
- static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
- mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
- }\r
-\r
- static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
- + o.getPrintSizeY() + ")" );\r
- }\r
-\r
- static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
- }\r
-\r
- static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
- if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
- mi.setEnabled( true );\r
+ static File writeToPdf( final Phylogeny t,\r
+ final MainPanel mp,\r
+ final JFileChooser writetopdf_filechooser,\r
+ final File curr_dir,\r
+ final Container contentpane,\r
+ final Component component ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return null;\r
}\r
- else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
- mi.setEnabled( true );\r
+ String initial_filename = "";\r
+ if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
}\r
- else {\r
- mi.setEnabled( false );\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
}\r
- mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
- }\r
-\r
- static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
- mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
- }\r
-\r
- static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
- for( final TreePanel tree_panel : treepanels ) {\r
- tree_panel.setTextAntialias();\r
+ initial_filename = initial_filename + ".pdf";\r
+ writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = curr_dir;\r
+ if ( my_dir != null ) {\r
+ writetopdf_filechooser.setCurrentDirectory( my_dir );\r
}\r
- }\r
-\r
- private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {\r
- switch ( op.getExtDescNodeDataToReturn() ) {\r
- case UNKNOWN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
- break;\r
- case DOMAINS_ALL:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
- break;\r
- case DOMAINS_COLLAPSED_PER_PROTEIN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
- break;\r
- case SEQ_ANNOTATIONS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
- break;\r
- case GO_TERM_IDS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
- break;\r
- case SEQUENCE_MOL_SEQ_FASTA:\r
- if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )\r
- && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {\r
- op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
- }\r
- else {\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ final int result = writetopdf_filechooser.showSaveDialog( contentpane );\r
+ File file = writetopdf_filechooser.getSelectedFile();\r
+ // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() );\r
+ final File new_current_dir = writetopdf_filechooser.getCurrentDirectory();\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
+ file = new File( file.toString() + ".pdf" );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( component,\r
+ file + " already exists. Overwrite?",\r
+ "WARNING",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return null;\r
}\r
- break;\r
- default:\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component );\r
}\r
+ return new_current_dir;\r
}\r
}\r
\r