From 154955274422ff0b34ff51fb40c2d621269368ca Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 12 Mar 2015 02:07:20 +0000 Subject: [PATCH] in progress --- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 306 ++++++++++++++------ .../src/org/forester/archaeopteryx/MainFrame.java | 21 +- .../forester/archaeopteryx/MainFrameApplet.java | 44 +-- .../archaeopteryx/MainFrameApplication.java | 34 +-- 4 files changed, 272 insertions(+), 133 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 229b787..38f0516 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -151,6 +151,13 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private File _current_dir; private JFileChooser _save_filechooser; private JFileChooser _writetographics_filechooser; + private JCheckBoxMenuItem _graphics_export_visible_only_cbmi; + private JCheckBoxMenuItem _antialias_print_cbmi; + private JCheckBoxMenuItem _print_black_and_white_cbmi; + private JCheckBoxMenuItem _print_using_actual_size_cbmi; + private JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi; + private JMenuItem _print_size_mi; + private JMenuItem _choose_pdf_width_mi; @Override public void actionPerformed( final ActionEvent e ) { @@ -391,9 +398,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } updateOptions( getOptions() ); } - // else if ( o == _write_to_pdf_item ) { - // writeToPdf( _mainpanel.getCurrentPhylogeny() ); final File curr_dir = MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(), getMainPanel(), _writetopdf_filechooser, @@ -477,32 +482,28 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( new_dir != null ) { setCurrentDir( new_dir ); } - } // TODO - // TODO - // TODO - // TODO - // TODO - // else if ( o == _graphics_export_visible_only_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _antialias_print_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _print_black_and_white_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _print_using_actual_size_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _graphics_export_using_actual_size_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _print_size_mi ) { - // choosePrintSize(); - // } - // else if ( o == _choose_pdf_width_mi ) { - // choosePdfWidth(); - // } + } + else if ( o == _graphics_export_visible_only_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _antialias_print_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _print_black_and_white_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _print_using_actual_size_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _graphics_export_using_actual_size_cbmi ) { + updateOptions( getOptions() ); + } + else if ( o == _print_size_mi ) { + choosePrintSize(); + } + else if ( o == _choose_pdf_width_mi ) { + choosePdfWidth(); + } repaint(); } @@ -603,16 +604,18 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { @Override public void init() { - _writetographics_filechooser = new JFileChooser(); _writetopdf_filechooser = new JFileChooser(); + _writetopdf_filechooser.setMultiSelectionEnabled( false ); + _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter ); + _writetographics_filechooser = new JFileChooser(); + _writetographics_filechooser.setMultiSelectionEnabled( false ); + _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter ); _save_filechooser = new JFileChooser(); _save_filechooser.setMultiSelectionEnabled( false ); _save_filechooser.setFileFilter( MainFrame.xmlfilter ); _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter ); _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter ); _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); - _writetographics_filechooser = new JFileChooser(); - _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter ); try { final String home_dir = System.getProperty( "user.home" ); _save_filechooser.setCurrentDirectory( new File( home_dir ) ); @@ -620,6 +623,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) ); } catch ( final Exception e ) { + e.printStackTrace(); // Do nothing. Not important. } final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL ); @@ -646,7 +650,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { ForesterUtil.printErrorMessage( NAME, "error: " + e ); e.printStackTrace(); JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str - + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE ); + + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE ); } if ( phys_url == null ) { ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from " @@ -710,7 +714,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } catch ( final IOException e ) { ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str - + "]" ); + + "]" ); JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from [" + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE ); } @@ -758,11 +762,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { public void componentResized( final ComponentEvent e ) { if ( getMainPanel().getCurrentTreePanel() != null ) { getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel() - .getCurrentTreePanel() - .getWidth(), + .getCurrentTreePanel() + .getWidth(), getMainPanel() - .getCurrentTreePanel() - .getHeight() ); + .getCurrentTreePanel() + .getHeight() ); } } } ); @@ -784,7 +788,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { AptxUtil.printAppletMessage( NAME, "not using tabbed display" ); if ( getSpeciesTree() != null ) { AptxUtil.printAppletMessage( NAME, - "Warning: gsdi (gene duplication inference) only available tabbed display" ); + "Warning: gsdi (gene duplication inference) only available tabbed display" ); } AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() ); } @@ -845,11 +849,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .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() ); + "Minimal Confidence Value", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getMinConfidenceValue() ); if ( !ForesterUtil.isEmpty( s ) ) { boolean success = true; double m = 0.0; @@ -871,6 +875,84 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } + 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 ); @@ -1024,9 +1106,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); MainFrame - .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); + .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame - .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); + .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); + 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() ); @@ -1042,10 +1126,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), getConfiguration() ) ); _options_jmenu - .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); + .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu - .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) ); + .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) ); _radio_group_1 = new ButtonGroup(); _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); _radio_group_1.add( _uniform_cladograms_rbmi ); @@ -1053,11 +1137,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); + .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 ) ); + .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 ) ); + .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 ) ); @@ -1066,9 +1150,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu - .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); _options_jmenu - .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); + .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); @@ -1086,12 +1170,36 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _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 ) ); + .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 ) ); + .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 ); @@ -1105,11 +1213,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() - .isShowDefaultNodeShapesExternal() ); + .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() - .isShowDefaultNodeShapesInternal() ); + .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() - .isShowDefaultNodeShapesForMarkedNodes() ); + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -1141,7 +1249,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _tools_menu.addSeparator(); _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); _remove_visual_styles_item - .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); customizeJMenuItem( _remove_visual_styles_item ); _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); @@ -1182,7 +1290,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { void buildViewMenu() { _view_jmenu = MainFrame.createMenu( "View", getConfiguration() ); _view_jmenu - .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) ); + .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) ); _view_jmenu.addSeparator(); _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) ); _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) ); @@ -1301,8 +1409,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.WARNING_MESSAGE ); + "GSDI successfully completed", + JOptionPane.WARNING_MESSAGE ); } else { JOptionPane.showMessageDialog( this, @@ -1314,8 +1422,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.INFORMATION_MESSAGE ); + "GSDI successfully completed", + JOptionPane.INFORMATION_MESSAGE ); } } @@ -1374,8 +1482,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.WARNING_MESSAGE ); + "GSDIR successfully completed", + JOptionPane.WARNING_MESSAGE ); } else { JOptionPane.showMessageDialog( this, @@ -1385,8 +1493,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.INFORMATION_MESSAGE ); + "GSDIR successfully completed", + JOptionPane.INFORMATION_MESSAGE ); } } @@ -1501,10 +1609,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( getCurrentTreePanel() != null ) { if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { JOptionPane - .showMessageDialog( this, - "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", - "Operation can not be exectuted on a sub-tree", - JOptionPane.WARNING_MESSAGE ); + .showMessageDialog( this, + "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", + "Operation can not be exectuted on a sub-tree", + JOptionPane.WARNING_MESSAGE ); return true; } } @@ -1633,20 +1741,20 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { void updateOptions( final Options options ) { options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() ); options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) - && _background_gradient_cbmi.isSelected() ); + && _background_gradient_cbmi.isSelected() ); options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) - && _show_annotation_ref_source.isSelected() ); + && _show_annotation_ref_source.isSelected() ); options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) - && _abbreviate_scientific_names.isSelected() ); + && _abbreviate_scientific_names.isSelected() ); options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) - && _color_labels_same_as_parent_branch.isSelected() ); + && _color_labels_same_as_parent_branch.isSelected() ); options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) - && _show_default_node_shapes_internal_cbmi.isSelected() ); + && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) - && _show_default_node_shapes_external_cbmi.isSelected() ); + && _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() ); + && _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 ); } @@ -1657,7 +1765,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); } options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null ) - && _search_case_senstive_cbmi.isSelected() ); + && _search_case_senstive_cbmi.isSelected() ); if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) { options.setShowScale( _show_scale_cbmi.isSelected() ); } @@ -1671,12 +1779,19 @@ 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() ); + && _show_confidence_stddev_cbmi.isSelected() ); options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) - && _search_whole_words_only_cbmi.isSelected() ); + && _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() ); + && _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 ); } @@ -1710,6 +1825,16 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { 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 ) { @@ -1724,8 +1849,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions() - .getNhConversionSupportValueStyle() ), - title ); + .getNhConversionSupportValueStyle() ), + title ); } } @@ -1736,8 +1861,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions() - .getNhConversionSupportValueStyle() ), - title ); + .getNhConversionSupportValueStyle() ), + title ); } } @@ -1751,6 +1876,15 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } } + static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) { + mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", " + + o.getPrintSizeY() + ")" ); + } + + 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 ) { for( final TreePanel tree_panel : treepanels ) { tree_panel.setTextAntialias(); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index d91758d..28398f7 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -273,13 +273,12 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _phyloxml_ref_item; JMenuItem _aptx_ref_item; // - JFileChooser _writetopdf_filechooser; File _current_dir; + JFileChooser _writetopdf_filechooser; JFileChooser _save_filechooser; JFileChooser _writetographics_filechooser; // process menu: JMenu _process_menu; - // Handy pointers to child components: MainPanel _mainpanel; Container _contentpane; final LinkedList _textframes = new LinkedList(); ; @@ -293,15 +292,27 @@ public abstract class MainFrame extends JFrame implements ActionListener { MainFrame() { _process_pool = ProcessPool.createInstance(); _writetopdf_filechooser = new JFileChooser(); + _writetopdf_filechooser.setMultiSelectionEnabled( false ); + _writetopdf_filechooser.addChoosableFileFilter( pdffilter ); + _writetographics_filechooser = new JFileChooser(); + _writetographics_filechooser.setMultiSelectionEnabled( false ); + _writetographics_filechooser.addChoosableFileFilter( graphicsfilefilter ); _save_filechooser = new JFileChooser(); - _save_filechooser.setCurrentDirectory( new File( "." ) ); _save_filechooser.setMultiSelectionEnabled( false ); _save_filechooser.setFileFilter( xmlfilter ); _save_filechooser.addChoosableFileFilter( nhfilter ); _save_filechooser.addChoosableFileFilter( nexusfilter ); _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); - _writetographics_filechooser = new JFileChooser(); - _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter ); + try { + final String home_dir = System.getProperty( "user.home" ); + _save_filechooser.setCurrentDirectory( new File( home_dir ) ); + _writetopdf_filechooser.setCurrentDirectory( new File( home_dir ) ); + _writetographics_filechooser.setCurrentDirectory( new File( home_dir ) ); + } + catch ( final Exception e ) { + e.printStackTrace(); + // Do nothing. Not important. + } } /** diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index 2547acf..6374275 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -99,7 +99,7 @@ public final class MainFrameApplet extends MainFrame { _contentpane.setLayout( new BorderLayout() ); _contentpane.add( _mainpanel, BorderLayout.CENTER ); setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE, - getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE ); + getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE ); addWindowListener( new WindowAdapter() { @Override @@ -113,9 +113,9 @@ public final class MainFrameApplet extends MainFrame { public void componentResized( final ComponentEvent e ) { if ( _mainpanel.getCurrentTreePanel() != null ) { _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() - .getWidth(), + .getWidth(), _mainpanel.getCurrentTreePanel() - .getHeight() ); + .getHeight() ); } } } ); @@ -136,9 +136,9 @@ public final class MainFrameApplet extends MainFrame { final URL species_tree_url = new URL( species_tree_url_str ); final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url, configuration - .isValidatePhyloXmlAgainstSchema(), + .isValidatePhyloXmlAgainstSchema(), configuration - .isReplaceUnderscoresInNhParsing(), + .isReplaceUnderscoresInNhParsing(), false, TAXONOMY_EXTRACTION.NO, false ); @@ -183,9 +183,9 @@ public final class MainFrameApplet extends MainFrame { MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); MainFrame - .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); + .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel() - .getTreeFontSet() ) ); + .getTreeFontSet() ) ); setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); @@ -203,7 +203,7 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), getConfiguration() ) ); _options_jmenu - .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); + .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) ); _radio_group_1 = new ButtonGroup(); @@ -213,11 +213,11 @@ public final class MainFrameApplet extends MainFrame { _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_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); + .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 ) ); + .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 ) ); + .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 ) ); @@ -226,9 +226,9 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu - .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); _options_jmenu - .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); + .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); @@ -246,7 +246,7 @@ public final class MainFrameApplet extends MainFrame { _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 ) ); + .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 ); @@ -258,11 +258,11 @@ public final class MainFrameApplet extends MainFrame { _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" ) ); + .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" ) ); + .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" ) ); + .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( "" ) ); // @@ -271,7 +271,7 @@ public final class MainFrameApplet extends MainFrame { 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() ); + .isGraphicsExportUsingActualSize() ); customizeJMenuItem( _print_size_mi ); customizeJMenuItem( _choose_pdf_width_mi ); // @@ -280,11 +280,11 @@ public final class MainFrameApplet extends MainFrame { customizeJMenuItem( _choose_minimal_confidence_mi ); customizeJMenuItem( _overview_placment_mi ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() - .isShowDefaultNodeShapesInternal() ); + .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() - .isShowDefaultNodeShapesExternal() ); + .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() - .isShowDefaultNodeShapesForMarkedNodes() ); + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -324,7 +324,7 @@ public final class MainFrameApplet extends MainFrame { _tools_menu.addSeparator(); _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); _remove_visual_styles_item - .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); customizeJMenuItem( _remove_visual_styles_item ); _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 853b1d5..3b5138b 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -244,14 +244,12 @@ public final class MainFrameApplication extends MainFrame { setOptions( Options.createInstance( _configuration ) ); setInferenceManager( InferenceManager.createInstance( _configuration ) ); setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) ); - // _textframe = null; #~~~~ // set title setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" ); _mainpanel = new MainPanel( _configuration, this ); // The file dialogs _open_filechooser = new JFileChooser(); - _open_filechooser.setCurrentDirectory( new File( "." ) ); - _open_filechooser.setMultiSelectionEnabled( false ); + _open_filechooser.setMultiSelectionEnabled( true ); _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter ); _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter ); _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter ); @@ -260,44 +258,41 @@ public final class MainFrameApplication extends MainFrame { _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() ); _open_filechooser.setFileFilter( MainFrame.defaultfilter ); _open_filechooser_for_species_tree = new JFileChooser(); - _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) ); _open_filechooser_for_species_tree.setMultiSelectionEnabled( false ); _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter ); _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter ); _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter ); - _save_filechooser = new JFileChooser(); - _save_filechooser.setCurrentDirectory( new File( "." ) ); - _save_filechooser.setMultiSelectionEnabled( false ); - _save_filechooser.setFileFilter( MainFrame.xmlfilter ); - _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter ); - _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter ); - _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); - _writetopdf_filechooser = new JFileChooser(); - _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter ); - _writetographics_filechooser = new JFileChooser(); - _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter ); // Msa: _msa_filechooser = new JFileChooser(); _msa_filechooser.setName( "Read Multiple Sequence Alignment File" ); - _msa_filechooser.setCurrentDirectory( new File( "." ) ); _msa_filechooser.setMultiSelectionEnabled( false ); _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() ); _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter ); // Seqs: _seqs_pi_filechooser = new JFileChooser(); _seqs_pi_filechooser.setName( "Read Sequences File" ); - _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) ); _seqs_pi_filechooser.setMultiSelectionEnabled( false ); _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() ); _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter ); // Expression _values_filechooser = new JFileChooser(); - _values_filechooser.setCurrentDirectory( new File( "." ) ); _values_filechooser.setMultiSelectionEnabled( false ); // Sequences _sequences_filechooser = new JFileChooser(); - _sequences_filechooser.setCurrentDirectory( new File( "." ) ); _sequences_filechooser.setMultiSelectionEnabled( false ); + try { + final String home_dir = System.getProperty( "user.home" ); + _open_filechooser.setCurrentDirectory( new File( home_dir ) ); + _open_filechooser_for_species_tree.setCurrentDirectory( new File( home_dir ) ); + _msa_filechooser.setCurrentDirectory( new File( home_dir ) ); + _seqs_pi_filechooser.setCurrentDirectory( new File( home_dir ) ); + _values_filechooser.setCurrentDirectory( new File( home_dir ) ); + _sequences_filechooser.setCurrentDirectory( new File( home_dir ) ); + } + catch ( final Exception e ) { + e.printStackTrace(); + // Do nothing. Not important. + } // build the menu bar _jmenubar = new JMenuBar(); if ( !_configuration.isUseNativeUI() ) { @@ -1440,7 +1435,6 @@ public final class MainFrameApplication extends MainFrame { Phylogeny[] phys = null; // Set an initial directory if none set yet final File my_dir = getCurrentDir(); - _open_filechooser.setMultiSelectionEnabled( true ); // Open file-open dialog and set current directory if ( my_dir != null ) { _open_filechooser.setCurrentDirectory( my_dir ); -- 1.7.10.2