X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FArchaeopteryxE.java;h=288cc142f9ae082b1d4fc6376dceed7c4ec6fd10;hb=97358f7a982d67831aedc14d5ab193727f6bdc83;hp=3954da02587b4b9c5b90f64c03178729b1ac243e;hpb=c956545c704f53df5c8711ede20e786641bfc7be;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 3954da0..288cc14 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -18,6 +18,7 @@ import java.util.NoSuchElementException; import javax.swing.ButtonGroup; import javax.swing.JApplet; import javax.swing.JCheckBoxMenuItem; +import javax.swing.JFileChooser; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JMenuItem; @@ -43,6 +44,7 @@ import org.forester.sdi.GSDIR; import org.forester.sdi.SDIException; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; +import org.forester.util.WindowsUtils; // Use like this: // = 0.0 ) ) { + getOptions().setMinConfidenceValue( m ); + } + } + } + + private void choosePdfWidth() { + final String s = ( String ) JOptionPane.showInputDialog( this, + "Please enter the default line width for PDF export.\n" + + "[current value: " + + getOptions().getPrintLineWidth() + "]\n", + "Line Width for PDF Export", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getPrintLineWidth() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + float f = 0.0f; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + f = Float.parseFloat( m_str ); + } + catch ( final Exception ex ) { + success = false; + } + } + else { + success = false; + } + if ( success && ( f > 0.0 ) ) { + getOptions().setPrintLineWidth( f ); + } + } + } + + private void choosePrintSize() { + final String s = ( String ) JOptionPane.showInputDialog( this, + "Please enter values for width and height,\nseparated by a comma.\n" + + "[current values: " + + getOptions().getPrintSizeX() + ", " + + getOptions().getPrintSizeY() + "]\n" + + "[A4: " + Constants.A4_SIZE_X + ", " + + Constants.A4_SIZE_Y + "]\n" + "[US Letter: " + + Constants.US_LETTER_SIZE_X + ", " + + Constants.US_LETTER_SIZE_Y + "]", + "Default Size for Graphics Export", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getPrintSizeX() + ", " + + getOptions().getPrintSizeY() ); + if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) { + boolean success = true; + int x = 0; + int y = 0; + final String[] str_ary = s.split( "," ); + if ( str_ary.length == 2 ) { + final String x_str = str_ary[ 0 ].trim(); + final String y_str = str_ary[ 1 ].trim(); + if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) { + try { + x = Integer.parseInt( x_str ); + y = Integer.parseInt( y_str ); + } + catch ( final Exception ex ) { + success = false; + } + } + else { + success = false; + } + } + else { + success = false; + } + if ( success && ( x > 1 ) && ( y > 1 ) ) { + getOptions().setPrintSizeX( x ); + getOptions().setPrintSizeY( y ); + } + } + } + + private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) { + if ( item != null ) { + item.setFont( MainFrame.menu_font ); + if ( !getConfiguration().isUseNativeUI() ) { + item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); + item.setForeground( getConfiguration().getGuiMenuTextColor() ); + } + item.setSelected( is_selected ); + item.addActionListener( this ); + } + } + + private Phylogeny getSpeciesTree() { + return _species_tree; + } + + private boolean isScreenAntialias() { + return true; + } + + private void removeBranchColors() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); + } + } + + private void removeVisualStyles() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); + } + } + + private void setMainPanel( final MainPanelApplets main_panel ) { + _mainpanel = main_panel; + } + + private void setSpeciesTree( final Phylogeny species_tree ) { + _species_tree = species_tree; + } + + private void setupUI() { + try { + if ( getConfiguration().isUseNativeUI() ) { + UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); + } + else { + UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() ); + } + } + catch ( final UnsupportedLookAndFeelException e ) { + AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() ); + } + catch ( final ClassNotFoundException e ) { + AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() ); + } + catch ( final InstantiationException e ) { + AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() ); + } + catch ( final IllegalAccessException e ) { + AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() ); + } + catch ( final Exception e ) { + AptxUtil.dieWithSystemError( e.toString() ); + } + } + void buildAnalysisMenu() { _analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() ); _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) ); _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) ); customizeJMenuItem( _gsdi_item ); customizeJMenuItem( _gsdir_item ); - // _analysis_menu.addSeparator(); - // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) ); - // customizeJMenuItem( _lineage_inference ); - // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" ); + _analysis_menu.addSeparator(); _jmenubar.add( _analysis_menu ); } + void buildFileMenu() { + _file_jmenu = MainFrame.createMenu( "File", getConfiguration() ); + _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) ); + _file_jmenu.addSeparator(); + _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) ); + if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) { + _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) ); + } + _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) ); + _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) ); + if ( AptxUtil.canWriteFormat( "gif" ) ) { + _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) ); + } + if ( AptxUtil.canWriteFormat( "bmp" ) ) { + _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) ); + } + _file_jmenu.addSeparator(); + _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) ); + customizeJMenuItem( _save_item ); + customizeJMenuItem( _write_to_pdf_item ); + customizeJMenuItem( _write_to_png_item ); + customizeJMenuItem( _write_to_jpg_item ); + customizeJMenuItem( _write_to_gif_item ); + customizeJMenuItem( _write_to_tif_item ); + customizeJMenuItem( _write_to_bmp_item ); + customizeJMenuItem( _print_item ); + _jmenubar.add( _file_jmenu ); + } + void buildFontSizeMenu() { _font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() ); _font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) ); @@ -674,7 +1074,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { void buildHelpMenu() { _help_jmenu = MainFrame.createMenu( "Help", getConfiguration() ); - _help_jmenu.add( _help_item = new JMenuItem( "Help" ) ); + _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) ); + _help_jmenu.addSeparator(); _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) ); _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) ); @@ -704,16 +1105,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); - MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(), - _show_scale_cbmi, - _show_branch_length_values_cbmi, - _non_lined_up_cladograms_rbmi, - _uniform_cladograms_rbmi, - _ext_node_dependent_cladogram_rbmi, - _label_direction_cbmi ); + setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); + setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); + try { + getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB(); + getMainPanel().getControlPanel().setVisibilityOfX(); + } + catch ( final Exception ignore ) { + // do nothing, not important. + } } } ); _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), @@ -727,16 +1130,17 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); _radio_group_1.add( _uniform_cladograms_rbmi ); _radio_group_1.add( _non_lined_up_cladograms_rbmi ); - ///// _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); _options_jmenu - .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); - _options_jmenu .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + _options_jmenu + .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); + _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { + _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) ); } _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); @@ -758,15 +1162,40 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) ); _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); - ///// _options_jmenu.addSeparator(); _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), getConfiguration() ) ); _options_jmenu .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) ); + _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); + _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); _options_jmenu .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) ); + // + _options_jmenu.addSeparator(); + _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), + getConfiguration() ) ); + _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); + _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); + _options_jmenu + .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) ); + _options_jmenu + .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) ); + _options_jmenu + .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); + _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) ); + _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); + // + customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() ); + customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() ); + customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() ); + customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() ); + customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions() + .isGraphicsExportUsingActualSize() ); + customizeJMenuItem( _print_size_mi ); + customizeJMenuItem( _choose_pdf_width_mi ); + // customizeJMenuItem( _choose_font_mi ); customizeJMenuItem( _choose_minimal_confidence_mi ); customizeJMenuItem( _switch_colors_mi ); @@ -783,6 +1212,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() .isShowDefaultNodeShapesInternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -795,11 +1226,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi, getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() ); customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() ); + customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() ); customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); + customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); + customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); _jmenubar.add( _options_jmenu ); } @@ -898,16 +1331,19 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } void customizeJMenuItem( final JMenuItem jmi ) { - jmi.setFont( MainFrame.menu_font ); - if ( !getConfiguration().isUseNativeUI() ) { - jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - jmi.setForeground( getConfiguration().getGuiMenuTextColor() ); + if ( jmi != null ) { + jmi.setFont( MainFrame.menu_font ); + if ( !getConfiguration().isUseNativeUI() ) { + jmi.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); + jmi.setForeground( getConfiguration().getGuiMenuTextColor() ); + } + jmi.addActionListener( this ); } - jmi.addActionListener( this ); } void displayBasicInformation() { - if ( ( getMainPanel().getCurrentPhylogeny() != null ) && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { + if ( ( getMainPanel() != null ) && ( getMainPanel().getCurrentPhylogeny() != null ) + && !getMainPanel().getCurrentPhylogeny().isEmpty() ) { String title = "Basic Information"; if ( !ForesterUtil.isEmpty( getMainPanel().getCurrentPhylogeny().getName() ) ) { title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\""; @@ -1062,6 +1498,28 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { return _configuration; } + File getCurrentDir() { + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( ForesterUtil.isWindows() ) { + try { + _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); + } + catch ( final Exception e ) { + _current_dir = null; + } + } + } + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( System.getProperty( "user.home" ) != null ) { + _current_dir = new File( System.getProperty( "user.home" ) ); + } + else if ( System.getProperty( "user.dir" ) != null ) { + _current_dir = new File( System.getProperty( "user.dir" ) ); + } + } + return _current_dir; + } + TreePanel getCurrentTreePanel() { return getMainPanel().getCurrentTreePanel(); } @@ -1070,52 +1528,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { return _label_direction_cbmi; } - Options getOtions() { - return _options; + MainPanel getMainPanel() { + return _mainpanel; } - void help() { - final StringBuilder sb = new StringBuilder(); - sb.append( "Display options\n" ); - sb.append( "-------------------\n" ); - sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" ); - sb.append( "Clickable tree nodes\n" ); - sb.append( "--------------------\n" ); - sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" ); - sb.append( "or by right clicking:\n" ); - sb.append( "o Display Node Data -- display information for a node\n" ); - sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" ); - sb.append( "o Root/Reroot -- change tree root to clicked node\n" ); - sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" ); - sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" ); - sb.append( "o Colorize Subtree -- color a subtree\n" ); - sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" ); - sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" ); - sb.append( "- there may be additional choices depending on this particular setup\n\n" ); - sb.append( "Right clicking on a node always displays the information of a node.\n\n" ); - sb.append( "Zooming\n" ); - sb.append( "---------\n" ); - sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" ); - sb.append( "Mouse wheel+Ctrl changes the text size.\n" ); - sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" ); - sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" ); - sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" ); - sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" ); - sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" ); - sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" ); - sb.append( "Quick tree manipulation:\n" ); - sb.append( "------------------------\n" ); - sb.append( "Order Subtrees -- order the tree by branch length\n" ); - sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" ); - sb.append( "phyloXML\n" ); - sb.append( "-------------------\n" ); - sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" ); - sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" ); - sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); - sb.append( "\n" ); - sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" ); - sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" ); - TextFrame.instantiate( sb.toString(), "Help", _textframes ); + Options getOtions() { + return _options; } void initializeTypeMenu( final Options options ) { @@ -1210,6 +1628,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _configuration = configuration; } + void setCurrentDir( final File current_dir ) { + _current_dir = current_dir; + } + void setOptions( final Options options ) { _options = options; } @@ -1327,6 +1749,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) && _show_default_node_shapes_external_cbmi.isSelected() ); + options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) + && _show_default_node_shapes_for_marked_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } @@ -1352,13 +1776,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() ); options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null ) && _show_confidence_stddev_cbmi.isSelected() ); - if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) { - options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() ); - } options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ); + options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() ); options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) && _inverse_search_result_cbmi.isSelected() ); + options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null ) + && ( _print_using_actual_size_cbmi.isSelected() ) ); + options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null ) + && ( _graphics_export_using_actual_size_cbmi.isSelected() ) ); + options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); + options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) + && _print_black_and_white_cbmi.isSelected() ); if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) { options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); } @@ -1386,6 +1815,22 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); } + if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) { + options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() ); + } + if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) { + options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() ); + } + if ( _graphics_export_visible_only_cbmi != null ) { + options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() ); + if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) { + _graphics_export_using_actual_size_cbmi.setSelected( true ); + _graphics_export_using_actual_size_cbmi.setEnabled( false ); + } + else { + _graphics_export_using_actual_size_cbmi.setEnabled( true ); + } + } } void updateTypeCheckboxes( final Options options, final Object o ) { @@ -1427,112 +1872,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } - private void chooseFont() { - final FontChooser fc = new FontChooser(); - fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); - fc.showDialog( this, "Select the Base Font" ); - getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() ); - } - - private void chooseMinimalConfidence() { - final String s = ( String ) JOptionPane - .showInputDialog( this, - "Please the minimum for confidence values to be displayed.\n" + "[current value: " - + getOptions().getMinConfidenceValue() + "]\n", - "Minimal Confidence Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getMinConfidenceValue() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - getOptions().setMinConfidenceValue( m ); - } - } - } - - private void customizeRadioButtonMenuItem( final JRadioButtonMenuItem item, final boolean is_selected ) { - if ( item != null ) { - item.setFont( MainFrame.menu_font ); - if ( !getConfiguration().isUseNativeUI() ) { - item.setBackground( getConfiguration().getGuiMenuBackgroundColor() ); - item.setForeground( getConfiguration().getGuiMenuTextColor() ); - } - item.setSelected( is_selected ); - item.addActionListener( this ); - } - } - - private MainPanel getMainPanel() { - return _mainpanel; - } - - private Phylogeny getSpeciesTree() { - return _species_tree; - } - - private boolean isScreenAntialias() { - return true; - } - - private void removeBranchColors() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); - } - } - - private void removeVisualStyles() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); - } - } - - private void setMainPanel( final MainPanelApplets main_panel ) { - _mainpanel = main_panel; + static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) { + mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", " + + o.getPrintSizeY() + ")" ); } - private void setSpeciesTree( final Phylogeny species_tree ) { - _species_tree = species_tree; - } - - private void setupUI() { - try { - if ( getConfiguration().isUseNativeUI() ) { - UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); - } - else { - UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() ); - } - } - catch ( final UnsupportedLookAndFeelException e ) { - AptxUtil.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() ); - } - catch ( final ClassNotFoundException e ) { - AptxUtil.dieWithSystemError( "ClassNotFoundException: " + e.toString() ); - } - catch ( final InstantiationException e ) { - AptxUtil.dieWithSystemError( "InstantiationException: " + e.toString() ); - } - catch ( final IllegalAccessException e ) { - AptxUtil.dieWithSystemError( "IllegalAccessException: " + e.toString() ); - } - catch ( final Exception e ) { - AptxUtil.dieWithSystemError( e.toString() ); - } + static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) { + mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" ); } static void setupScreenTextAntialias( final List treepanels, final boolean antialias ) {