X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=4c85a4a28975b5e1e106b0040afba37afdca0825;hb=a9e626aa67ff9cb1649c371f9d705eb04498cc33;hp=505918e7e984a5cd15d14464cf26f48a17cc771c;hpb=09028c5abedb9492d6fc76b4274f6dd46bcf6cd6;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 505918e..4c85a4a 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -41,6 +41,7 @@ import java.util.NoSuchElementException; import javax.swing.Box; import javax.swing.JApplet; import javax.swing.JCheckBoxMenuItem; +import javax.swing.JFileChooser; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JMenu; @@ -51,14 +52,18 @@ import javax.swing.JPanel; import javax.swing.JRadioButtonMenuItem; import javax.swing.JTextField; import javax.swing.SwingUtilities; +import javax.swing.filechooser.FileFilter; +import org.forester.archaeopteryx.AptxUtil.GraphicsExportType; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; +import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer; import org.forester.archaeopteryx.tools.InferenceManager; import org.forester.archaeopteryx.tools.ProcessPool; import org.forester.archaeopteryx.tools.ProcessRunning; import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.io.writers.PhylogenyWriter; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; @@ -74,197 +79,244 @@ 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; public abstract class MainFrame extends JFrame implements ActionListener { - static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; - static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME - static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE; - private static final long serialVersionUID = 3655000897845508358L; - final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), - Font.PLAIN, - 10 ); - static final String TYPE_MENU_HEADER = "Type"; - static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; - static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; - static final String CURVED_TYPE_CBMI_LABEL = "Curved"; - static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; - static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; - static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; - static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO - static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO - static final String OPTIONS_HEADER = "Options"; - static final String SEARCH_SUBHEADER = "Search:"; - static final String DISPLAY_SUBHEADER = "Display:"; - static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; - static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions"; - static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; - static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; - static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group"; - static final String DISPLAY_SCALE_LABEL = "Scale"; - static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms"; - static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms"; - static final String LABEL_DIRECTION_LABEL = "Radial Labels"; - static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types"; - static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits."; - static final String SCREEN_ANTIALIAS_LABEL = "Antialias"; - static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; - static final String BG_GRAD_LABEL = "Background Color Gradient"; - static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes"; - static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes"; - static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data"; - static final String SHOW_OVERVIEW_LABEL = "Overview"; - static final String FONT_SIZE_MENU_LABEL = "Font Size"; - static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; - static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels"; - static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources"; - static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent"; - static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names"; - static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy"; - static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes"; - static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type"; - static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size"; - static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations"; - static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values"; - static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values"; - static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information"; - static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures"; - static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)"; - JMenuBar _jmenubar; - JMenu _file_jmenu; - JMenu _tools_menu; - JMenu _view_jmenu; - JMenu _options_jmenu; - JMenu _font_size_menu; - JMenu _help_jmenu; - JMenuItem[] _load_phylogeny_from_webservice_menu_items; + final static NHFilter nhfilter = new NHFilter(); + final static NHXFilter nhxfilter = new NHXFilter(); + final static XMLFilter xmlfilter = new XMLFilter(); + final static TolFilter tolfilter = new TolFilter(); + final static NexusFilter nexusfilter = new NexusFilter(); + final static PdfFilter pdffilter = new PdfFilter(); + final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter(); + final static MsaFileFilter msafilter = new MsaFileFilter(); + final static SequencesFileFilter seqsfilter = new SequencesFileFilter(); + final static DefaultFilter defaultfilter = new DefaultFilter(); + static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]"; + static final String PHYLOXML_REF_TOOL_TIP = AptxConstants.PHYLOXML_REFERENCE; //TODO //FIXME + static final String APTX_REF_TOOL_TIP = AptxConstants.APTX_REFERENCE; + private static final long serialVersionUID = 3655000897845508358L; + final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(), + Font.PLAIN, + 10 ); + static final String TYPE_MENU_HEADER = "Type"; + static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular"; + static final String EURO_TYPE_CBMI_LABEL = "Euro Type"; + static final String CURVED_TYPE_CBMI_LABEL = "Curved"; + static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular"; + static final String CONVEX_TYPE_CBMI_LABEL = "Convex"; + static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded"; + static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO + static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO + static final String OPTIONS_HEADER = "Options"; + static final String SEARCH_SUBHEADER = "Search:"; + static final String DISPLAY_SUBHEADER = "Display:"; + static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only"; + static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions"; + static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive"; + static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result"; + static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group"; + static final String DISPLAY_SCALE_LABEL = "Scale"; + static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms"; + static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms"; + static final String LABEL_DIRECTION_LABEL = "Radial Labels"; + static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types"; + static final String SEARCH_WITH_REGEX_TIP = "To search using regular expressions (~Java/Perl syntax). For example, use \"^B.+\\d{2,}$\" to search for everything starting with a B and ending with at least two digits."; + static final String SCREEN_ANTIALIAS_LABEL = "Antialias"; + static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch"; + static final String BG_GRAD_LABEL = "Background Color Gradient"; + static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes"; + static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes"; + static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data"; + static final String SHOW_OVERVIEW_LABEL = "Overview"; + static final String FONT_SIZE_MENU_LABEL = "Font Size"; + static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms"; + static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels"; + static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources"; + static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent"; + static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names"; + static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy"; + static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes"; + static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type"; + static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size"; + static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations"; + static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values"; + static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values"; + static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information"; + static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures"; + static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)"; + static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies"; + static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information"; + JMenuBar _jmenubar; + JMenu _file_jmenu; + JMenu _tools_menu; + JMenu _view_jmenu; + JMenu _options_jmenu; + JMenu _font_size_menu; + JMenu _help_jmenu; + JMenuItem[] _load_phylogeny_from_webservice_menu_items; // Analysis menu - JMenu _analysis_menu; - JMenuItem _load_species_tree_item; - JMenuItem _gsdi_item; - JMenuItem _gsdir_item; - JMenuItem _lineage_inference; + JMenu _analysis_menu; + JMenuItem _load_species_tree_item; + JMenuItem _gsdi_item; + JMenuItem _gsdir_item; + JMenuItem _lineage_inference; // file menu: - JMenuItem _open_item; - JMenuItem _open_url_item; - JMenuItem _save_item; - JMenuItem _save_all_item; - JMenuItem _close_item; - JMenuItem _exit_item; - JMenuItem _new_item; + JMenuItem _open_item; + JMenuItem _open_url_item; + JMenuItem _save_item; + JMenuItem _save_all_item; + JMenuItem _close_item; + JMenuItem _exit_item; + JMenuItem _new_item; + JMenuItem _print_item; + JMenuItem _write_to_pdf_item; + JMenuItem _write_to_jpg_item; + JMenuItem _write_to_gif_item; + JMenuItem _write_to_tif_item; + JMenuItem _write_to_png_item; + JMenuItem _write_to_bmp_item; // tools menu: - JMenuItem _midpoint_root_item; - JMenuItem _taxcolor_item; - JMenuItem _confcolor_item; - JMenuItem _color_rank_jmi; - JMenuItem _collapse_species_specific_subtrees; - JMenuItem _obtain_detailed_taxonomic_information_jmi; - JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi; - JMenuItem _obtain_seq_information_jmi; - JMenuItem _move_node_names_to_tax_sn_jmi; - JMenuItem _move_node_names_to_seq_names_jmi; - JMenuItem _extract_tax_code_from_node_names_jmi; - JMenuItem _annotate_item; - JMenuItem _remove_branch_color_item; - JMenuItem _remove_visual_styles_item; - JMenuItem _delete_selected_nodes_item; - JMenuItem _delete_not_selected_nodes_item; + JMenuItem _midpoint_root_item; + JMenuItem _taxcolor_item; + JMenuItem _confcolor_item; + JMenuItem _color_rank_jmi; + JMenuItem _collapse_species_specific_subtrees; + JMenuItem _obtain_detailed_taxonomic_information_jmi; + JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi; + JMenuItem _obtain_seq_information_jmi; + JMenuItem _move_node_names_to_tax_sn_jmi; + JMenuItem _move_node_names_to_seq_names_jmi; + JMenuItem _extract_tax_code_from_node_names_jmi; + JMenuItem _annotate_item; + JMenuItem _remove_branch_color_item; + JMenuItem _remove_visual_styles_item; + JMenuItem _delete_selected_nodes_item; + JMenuItem _delete_not_selected_nodes_item; // font size menu: - JMenuItem _super_tiny_fonts_item; - JMenuItem _tiny_fonts_item; - JMenuItem _small_fonts_item; - JMenuItem _medium_fonts_item; - JMenuItem _large_fonts_item; + JMenuItem _super_tiny_fonts_item; + JMenuItem _tiny_fonts_item; + JMenuItem _small_fonts_item; + JMenuItem _medium_fonts_item; + JMenuItem _large_fonts_item; // options menu: // _ screen and print - JMenuItem _choose_font_mi; - JMenuItem _switch_colors_mi; - JCheckBoxMenuItem _label_direction_cbmi; + JMenuItem _choose_font_mi; + JMenuItem _switch_colors_mi; + JCheckBoxMenuItem _label_direction_cbmi; // _ screen display - JCheckBoxMenuItem _screen_antialias_cbmi; - JCheckBoxMenuItem _background_gradient_cbmi; - JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; - JRadioButtonMenuItem _uniform_cladograms_rbmi; - JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; - JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; - JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me - JCheckBoxMenuItem _show_overview_cbmi; - JCheckBoxMenuItem _show_domain_labels; - JCheckBoxMenuItem _show_annotation_ref_source; - JCheckBoxMenuItem _abbreviate_scientific_names; - JCheckBoxMenuItem _color_labels_same_as_parent_branch; - JMenuItem _overview_placment_mi; - JMenuItem _choose_minimal_confidence_mi; - JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; - JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; - JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi; - JMenuItem _cycle_node_shape_mi; - JMenuItem _cycle_node_fill_mi; - JMenuItem _choose_node_size_mi; - JMenuItem _cycle_data_return; - JCheckBoxMenuItem _show_confidence_stddev_cbmi; - JCheckBoxMenuItem _right_line_up_domains_cbmi; - JCheckBoxMenuItem _line_up_renderable_data_cbmi; + JCheckBoxMenuItem _screen_antialias_cbmi; + JCheckBoxMenuItem _background_gradient_cbmi; + JRadioButtonMenuItem _non_lined_up_cladograms_rbmi; + JRadioButtonMenuItem _uniform_cladograms_rbmi; + JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi; + JCheckBoxMenuItem _color_by_taxonomic_group_cbmi; + JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me + JCheckBoxMenuItem _show_overview_cbmi; + JCheckBoxMenuItem _show_domain_labels; + JCheckBoxMenuItem _show_annotation_ref_source; + JCheckBoxMenuItem _abbreviate_scientific_names; + JCheckBoxMenuItem _color_labels_same_as_parent_branch; + JMenuItem _overview_placment_mi; + JMenuItem _choose_minimal_confidence_mi; + JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi; + JCheckBoxMenuItem _show_default_node_shapes_external_cbmi; + JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi; + JMenuItem _cycle_node_shape_mi; + JMenuItem _cycle_node_fill_mi; + JMenuItem _choose_node_size_mi; + JMenuItem _cycle_data_return; + JCheckBoxMenuItem _show_confidence_stddev_cbmi; + JCheckBoxMenuItem _right_line_up_domains_cbmi; + JCheckBoxMenuItem _line_up_renderable_data_cbmi; // _ print - JCheckBoxMenuItem _graphics_export_visible_only_cbmi; - JCheckBoxMenuItem _antialias_print_cbmi; - JCheckBoxMenuItem _print_black_and_white_cbmi; - JCheckBoxMenuItem _print_using_actual_size_cbmi; - JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi; - JMenuItem _print_size_mi; - JMenuItem _choose_pdf_width_mi; + JCheckBoxMenuItem _graphics_export_visible_only_cbmi; + JCheckBoxMenuItem _antialias_print_cbmi; + JCheckBoxMenuItem _print_black_and_white_cbmi; + JCheckBoxMenuItem _print_using_actual_size_cbmi; + JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi; + JMenuItem _print_size_mi; + JMenuItem _choose_pdf_width_mi; // _ parsing - JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; - JRadioButtonMenuItem _extract_taxonomy_no_rbmi; - JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi; - JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi; - JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi; - JCheckBoxMenuItem _replace_underscores_cbmi; - JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi; - JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi; - JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi; + JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi; + JRadioButtonMenuItem _extract_taxonomy_no_rbmi; + JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi; + JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi; + JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi; + JCheckBoxMenuItem _replace_underscores_cbmi; + JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi; + JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi; + JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi; // _ search - JCheckBoxMenuItem _search_case_senstive_cbmi; - JCheckBoxMenuItem _search_whole_words_only_cbmi; - JCheckBoxMenuItem _inverse_search_result_cbmi; - JCheckBoxMenuItem _search_with_regex_cbmi; + JCheckBoxMenuItem _search_case_senstive_cbmi; + JCheckBoxMenuItem _search_whole_words_only_cbmi; + JCheckBoxMenuItem _inverse_search_result_cbmi; + JCheckBoxMenuItem _search_with_regex_cbmi; + JCheckBoxMenuItem _color_all_found_nodes_when_coloring_subtree_cbmi; // type menu: - JMenu _type_menu; - JCheckBoxMenuItem _rectangular_type_cbmi; - JCheckBoxMenuItem _triangular_type_cbmi; - JCheckBoxMenuItem _curved_type_cbmi; - JCheckBoxMenuItem _convex_type_cbmi; - JCheckBoxMenuItem _euro_type_cbmi; - JCheckBoxMenuItem _rounded_type_cbmi; - JCheckBoxMenuItem _unrooted_type_cbmi; - JCheckBoxMenuItem _circular_type_cbmi; + JMenu _type_menu; + JCheckBoxMenuItem _rectangular_type_cbmi; + JCheckBoxMenuItem _triangular_type_cbmi; + JCheckBoxMenuItem _curved_type_cbmi; + JCheckBoxMenuItem _convex_type_cbmi; + JCheckBoxMenuItem _euro_type_cbmi; + JCheckBoxMenuItem _rounded_type_cbmi; + JCheckBoxMenuItem _unrooted_type_cbmi; + JCheckBoxMenuItem _circular_type_cbmi; // view as text menu: - JMenuItem _view_as_NH_item; - JMenuItem _view_as_XML_item; - JMenuItem _view_as_nexus_item; - JMenuItem _display_basic_information_item; + JMenuItem _view_as_NH_item; + JMenuItem _view_as_XML_item; + JMenuItem _view_as_nexus_item; + JMenuItem _display_basic_information_item; // help menu: - JMenuItem _about_item; - JMenuItem _help_item; - JMenuItem _website_item; - JMenuItem _phyloxml_website_item; - JMenuItem _phyloxml_ref_item; - JMenuItem _aptx_ref_item; + JMenuItem _about_item; + JMenuItem _help_item; + JMenuItem _website_item; + JMenuItem _phyloxml_website_item; + JMenuItem _phyloxml_ref_item; + JMenuItem _aptx_ref_item; + // + 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(); ; - Configuration _configuration; - Options _options; - private Phylogeny _species_tree; - InferenceManager _inference_manager; - final ProcessPool _process_pool; - private String _previous_node_annotation_ref; + JMenu _process_menu; + MainPanel _mainpanel; + Container _contentpane; + final LinkedList _textframes = new LinkedList(); ; + Configuration _configuration; + Options _options; + private Phylogeny _species_tree; + InferenceManager _inference_manager; + final ProcessPool _process_pool; + private String _previous_node_annotation_ref; 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.setMultiSelectionEnabled( false ); + _save_filechooser.setFileFilter( xmlfilter ); + _save_filechooser.addChoosableFileFilter( nhfilter ); + _save_filechooser.addChoosableFileFilter( nexusfilter ); + _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); + 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. + } } /** @@ -483,6 +535,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { getMainPanel().getControlPanel().search0(); getMainPanel().getControlPanel().search1(); } + else if ( o == _color_all_found_nodes_when_coloring_subtree_cbmi ) { + updateOptions( getOptions() ); + } else if ( o == _show_scale_cbmi ) { updateOptions( getOptions() ); } @@ -535,43 +590,162 @@ public abstract class MainFrame extends JFrame implements ActionListener { } else if ( o == _help_item ) { try { - AptxUtil.openWebsite( Constants.APTX_DOC_SITE, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE, is_applet, applet ); } catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _website_item ) { try { - AptxUtil.openWebsite( Constants.APTX_WEB_SITE, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.APTX_WEB_SITE, is_applet, applet ); } catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _phyloxml_website_item ) { try { - AptxUtil.openWebsite( Constants.PHYLOXML_WEB_SITE, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, is_applet, applet ); } catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _aptx_ref_item ) { try { - AptxUtil.openWebsite( Constants.APTX_REFERENCE_URL, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.APTX_REFERENCE_URL, is_applet, applet ); } catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); } } else if ( o == _phyloxml_ref_item ) { try { - AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet ); + AptxUtil.openWebsite( AptxConstants.PHYLOXML_REFERENCE_URL, is_applet, applet ); } catch ( final IOException e1 ) { - ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); + ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() ); + } + } + else if ( o == _write_to_pdf_item ) { + final File curr_dir = writeToPdf( _mainpanel.getCurrentPhylogeny(), + getMainPanel(), + _writetopdf_filechooser, + _current_dir, + getContentPane(), + this ); + if ( curr_dir != null ) { + setCurrentDir( curr_dir ); + } + } + else if ( o == _save_all_item ) { + writeAllToFile(); + } + else if ( o == _write_to_jpg_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.JPG, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _write_to_gif_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.GIF, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _write_to_tif_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.TIFF, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _write_to_bmp_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.BMP, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _write_to_png_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.PNG, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + else if ( o == _print_item ) { + print( getCurrentTreePanel(), getOptions(), this ); + } + else if ( o == _save_item ) { + final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(), + getMainPanel(), + _save_filechooser, + _current_dir, + getContentPane(), + this ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } + 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 == _lineage_inference ) { + if ( isSubtreeDisplayed() ) { + JOptionPane.showMessageDialog( this, + "Subtree is shown.", + "Cannot infer ancestral taxonomies", + JOptionPane.ERROR_MESSAGE ); + return; } + executeLineageInference(); } else { if ( _load_phylogeny_from_webservice_menu_items != null ) { @@ -585,6 +759,176 @@ public abstract class MainFrame extends JFrame implements ActionListener { _contentpane.repaint(); } + public Configuration getConfiguration() { + return _configuration; + } + + /** + * This method returns the current external node data which + * has been selected by the user by clicking the "Return ..." + * menu item. This method is expected to be called from Javascript or + * something like it. + * + * @return current external node data as String + */ + public String getCurrentExternalNodesDataBuffer() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); + } + + public int getCurrentExternalNodesDataBufferChangeCounter() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); + } + + public int getCurrentExternalNodesDataBufferLength() { + return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); + } + + public InferenceManager getInferenceManager() { + return _inference_manager; + } + + public MainPanel getMainPanel() { + return _mainpanel; + } + + public Options getOptions() { + return _options; + } + + public ProcessPool getProcessPool() { + return _process_pool; + } + + public void showTextFrame( final String s, final String title ) { + checkTextFrames(); + _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); + } + + public void showWhole() { + _mainpanel.getControlPanel().showWhole(); + } + + public void updateProcessMenu() { + // In general Swing is not thread safe. + // See "Swing's Threading Policy". + SwingUtilities.invokeLater( new Runnable() { + + @Override + public void run() { + doUpdateProcessMenu(); + } + } ); + } + + private void annotateSequences() { + if ( getCurrentTreePanel() != null ) { + List nodes = null; + if ( ( getCurrentTreePanel().getFoundNodes0() != null ) + || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { + nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); + } + if ( ( nodes == null ) || nodes.isEmpty() ) { + JOptionPane + .showMessageDialog( this, + "Need to select nodes, either via direct selection or via the \"Search\" function", + "No nodes selected for annotation", + JOptionPane.ERROR_MESSAGE ); + return; + } + final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final JTextField ref_field = new JTextField( 10 ); + final JTextField desc_filed = new JTextField( 20 ); + ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? "" + : getPreviousNodeAnnotationReference() ); + final JPanel my_panel = new JPanel(); + my_panel.add( new JLabel( "Reference " ) ); + my_panel.add( ref_field ); + my_panel.add( Box.createHorizontalStrut( 15 ) ); + my_panel.add( new JLabel( "Description " ) ); + my_panel.add( desc_filed ); + final int result = JOptionPane.showConfirmDialog( null, + my_panel, + "Enter the sequence annotation(s) for the " + + nodes.size() + " selected nodes", + JOptionPane.OK_CANCEL_OPTION ); + if ( result == JOptionPane.OK_OPTION ) { + String ref = ref_field.getText(); + String desc = desc_filed.getText(); + if ( !ForesterUtil.isEmpty( ref ) ) { + ref = ref.trim(); + ref = ref.replaceAll( "\\s+", " " ); + if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) ) + || ( ref.length() < 3 ) ) { + JOptionPane.showMessageDialog( this, + "Reference needs to be in the form of \"GO:1234567\"", + "Illegal Format for Annotation Reference", + JOptionPane.ERROR_MESSAGE ); + return; + } + } + if ( ref != null ) { + setPreviousNodeAnnotationReference( ref ); + } + if ( desc != null ) { + desc = desc.trim(); + desc = desc.replaceAll( "\\s+", " " ); + } + if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) { + for( final PhylogenyNode n : nodes ) { + ForesterUtil.ensurePresenceOfSequence( n ); + final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() + : new Annotation( ref ); + if ( !ForesterUtil.isEmpty( desc ) ) { + ann.setDesc( desc ); + } + n.getNodeData().getSequence().addAnnotation( ann ); + } + } + getMainPanel().getControlPanel().showAnnotations(); + } + } + } + } + + 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 enter 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 deleteSelectedNodes( final boolean delete ) { final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) { @@ -605,10 +949,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { } if ( ( nodes == null ) || nodes.isEmpty() ) { JOptionPane - .showMessageDialog( this, - "Need to select external nodes, either via direct selection or via the \"Search\" function", - "No external nodes selected to " + function.toLowerCase(), - JOptionPane.ERROR_MESSAGE ); + .showMessageDialog( this, + "Need to select external nodes, either via direct selection or via the \"Search\" function", + "No external nodes selected to " + function.toLowerCase(), + JOptionPane.ERROR_MESSAGE ); return; } final int todo = nodes.size(); @@ -625,8 +969,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { return; } final int result = JOptionPane.showConfirmDialog( null, function + " " + todo - + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res - + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION ); + + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res + + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION ); if ( result == JOptionPane.OK_OPTION ) { if ( !delete ) { final List to_delete = new ArrayList(); @@ -656,80 +1000,108 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void resetSearch() { - getMainPanel().getCurrentTreePanel().setFoundNodes0( null ); - getMainPanel().getCurrentTreePanel().setFoundNodes1( null ); - getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 ); - getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false ); - getMainPanel().getControlPanel().getSearchTextField0().setText( "" ); - getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false ); - getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false ); - getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 ); - getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false ); - getMainPanel().getControlPanel().getSearchTextField1().setText( "" ); - getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false ); - getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false ); - } - - public Configuration getConfiguration() { - return _configuration; - } - - /** - * This method returns the current external node data which - * has been selected by the user by clicking the "Return ..." - * menu item. This method is expected to be called from Javascript or - * something like it. - * - * @return current external node data as String - */ - public String getCurrentExternalNodesDataBuffer() { - return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString(); - } - - public int getCurrentExternalNodesDataBufferChangeCounter() { - return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter(); + private void doUpdateProcessMenu() { + if ( _process_pool.size() > 0 ) { + if ( _process_menu == null ) { + _process_menu = createMenu( "", getConfiguration() ); + _process_menu.setForeground( Color.RED ); + } + _process_menu.removeAll(); + final String text = "processes running: " + _process_pool.size(); + _process_menu.setText( text ); + _jmenubar.add( _process_menu ); + for( int i = 0; i < _process_pool.size(); ++i ) { + final ProcessRunning p = _process_pool.getProcessByIndex( i ); + _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) ); + } + } + else { + if ( _process_menu != null ) { + _process_menu.removeAll(); + _jmenubar.remove( _process_menu ); + } + } + _jmenubar.validate(); + _jmenubar.repaint(); + repaint(); } - public int getCurrentExternalNodesDataBufferLength() { - return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length(); + private String getPreviousNodeAnnotationReference() { + return _previous_node_annotation_ref; } - public InferenceManager getInferenceManager() { - return _inference_manager; + private void removeBranchColors() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); + } } - public MainPanel getMainPanel() { - return _mainpanel; + private void removeVisualStyles() { + if ( getMainPanel().getCurrentPhylogeny() != null ) { + AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); + } } - public Options getOptions() { - return _options; + private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) { + _previous_node_annotation_ref = previous_node_annotation_ref; } - public ProcessPool getProcessPool() { - return _process_pool; - } - - public void showTextFrame( final String s, final String title ) { - checkTextFrames(); - _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) ); - } - - public void showWhole() { - _mainpanel.getControlPanel().showWhole(); - } - - public void updateProcessMenu() { - // In general Swing is not thread safe. - // See "Swing's Threading Policy". - SwingUtilities.invokeLater( new Runnable() { - - @Override - public void run() { - doUpdateProcessMenu(); + private void writeAllToFile() { + if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) { + return; + } + final File my_dir = getCurrentDir(); + if ( my_dir != null ) { + _save_filechooser.setCurrentDirectory( my_dir ); + } + _save_filechooser.setSelectedFile( new File( "" ) ); + final int result = _save_filechooser.showSaveDialog( _contentpane ); + final File file = _save_filechooser.getSelectedFile(); + setCurrentDir( _save_filechooser.getCurrentDirectory() ); + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( file.exists() ) { + final int i = JOptionPane.showConfirmDialog( this, + file + " already exists. Overwrite?", + "Warning", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.WARNING_MESSAGE ); + if ( i != JOptionPane.OK_OPTION ) { + return; + } + else { + try { + file.delete(); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( this, + "Failed to delete: " + file, + "Error", + JOptionPane.WARNING_MESSAGE ); + } + } } - } ); + final int count = getMainPanel().getTabbedPane().getTabCount(); + final List trees = new ArrayList(); + for( int i = 0; i < count; ++i ) { + final Phylogeny phy = getMainPanel().getPhylogeny( i ); + if ( ForesterUtil.isEmpty( phy.getName() ) + && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) { + phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) ); + } + trees.add( phy ); + getMainPanel().getTreePanels().get( i ).setEdited( false ); + } + final PhylogenyWriter writer = new PhylogenyWriter(); + try { + writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR ); + } + catch ( final IOException e ) { + JOptionPane.showMessageDialog( this, + "Failed to write to: " + file, + "Error", + JOptionPane.WARNING_MESSAGE ); + } + } } void activateSaveAllIfNeeded() { @@ -742,8 +1114,33 @@ public abstract class MainFrame extends JFrame implements ActionListener { } void buildFileMenu() { - _file_jmenu = createMenu( "File", getConfiguration() ); + _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..." ) ); + _file_jmenu.addSeparator(); _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); + 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 ); customizeJMenuItem( _exit_item ); _jmenubar.add( _file_jmenu ); } @@ -838,6 +1235,84 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + 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 ); + } + } + } + + 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: " + AptxConstants.A4_SIZE_X + ", " + + AptxConstants.A4_SIZE_Y + "]\n" + "[US Letter: " + + AptxConstants.US_LETTER_SIZE_X + ", " + + AptxConstants.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 ); + } + } + } + void close() { removeAllTextFrames(); if ( _mainpanel != null ) { @@ -932,16 +1407,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { JOptionPane.ERROR_MESSAGE ); } - void exceptionOccuredDuringSaveAs( final Exception e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } - JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE ); - } - void executeGSDI() { if ( !isOKforSDI( false, true ) ) { return; @@ -995,8 +1460,8 @@ public abstract class MainFrame extends JFrame 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, @@ -1008,8 +1473,8 @@ public abstract class MainFrame extends JFrame 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 ); } } @@ -1068,8 +1533,8 @@ public abstract class MainFrame extends JFrame 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, @@ -1079,11 +1544,29 @@ public abstract class MainFrame extends JFrame 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 ); } } + void executeLineageInference() { + if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) { + return; + } + if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { + JOptionPane.showMessageDialog( this, + "Phylogeny is not rooted.", + "Cannot infer ancestral taxonomies", + JOptionPane.ERROR_MESSAGE ); + return; + } + final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this, + _mainpanel.getCurrentTreePanel(), + _mainpanel.getCurrentPhylogeny() + .copy() ); + new Thread( inferrer ).start(); + } + boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) { if ( ( gene_tree == null ) || gene_tree.isEmpty() ) { JOptionPane.showMessageDialog( this, @@ -1104,6 +1587,32 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + ControlPanel getControlPanel() { + return getMainPanel().getControlPanel(); + } + + 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(); } @@ -1188,10 +1697,10 @@ public abstract class MainFrame extends JFrame 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; } } @@ -1218,10 +1727,29 @@ public abstract class MainFrame extends JFrame implements ActionListener { _textframes.clear(); } + void resetSearch() { + getMainPanel().getCurrentTreePanel().setFoundNodes0( null ); + getMainPanel().getCurrentTreePanel().setFoundNodes1( null ); + getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 ); + getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false ); + getMainPanel().getControlPanel().getSearchTextField0().setText( "" ); + getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false ); + getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false ); + getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 ); + getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false ); + getMainPanel().getControlPanel().getSearchTextField1().setText( "" ); + getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false ); + getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false ); + } + void setConfiguration( final Configuration configuration ) { _configuration = configuration; } + void setCurrentDir( final File current_dir ) { + _current_dir = current_dir; + } + void setInferenceManager( final InferenceManager i ) { _inference_manager = i; } @@ -1323,20 +1851,20 @@ public abstract class MainFrame extends JFrame 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 ); } @@ -1347,7 +1875,7 @@ public abstract class MainFrame extends JFrame 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() ); } @@ -1361,14 +1889,14 @@ public abstract class MainFrame extends JFrame 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() ); if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); } options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null ) - && ( _print_using_actual_size_cbmi.isSelected() ) ); + && ( _print_using_actual_size_cbmi.isSelected() ) ); options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null ) - && ( _graphics_export_using_actual_size_cbmi.isSelected() ) ); + && ( _graphics_export_using_actual_size_cbmi.isSelected() ) ); options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null ) && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { @@ -1382,9 +1910,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ); } options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) - && _print_black_and_white_cbmi.isSelected() ); + && _print_black_and_white_cbmi.isSelected() ); options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) - && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); + && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) { options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); } @@ -1398,14 +1926,14 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) - && _replace_underscores_cbmi.isSelected() ); + && _replace_underscores_cbmi.isSelected() ); options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null ) - && _allow_errors_in_distance_to_parent_cbmi.isSelected() ); + && _allow_errors_in_distance_to_parent_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() ); 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 ) ) { @@ -1446,6 +1974,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) { options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() ); } + if ( ( _color_all_found_nodes_when_coloring_subtree_cbmi != null ) && _color_all_found_nodes_when_coloring_subtree_cbmi.isEnabled() ) { + options.setColorAllFoundNodesWhenColoringSubtree( _color_all_found_nodes_when_coloring_subtree_cbmi.isSelected() ); + } } void updateTypeCheckboxes( final Options options, final Object o ) { @@ -1471,8 +2002,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions() - .getNhConversionSupportValueStyle() ), - title ); + .getNhConversionSupportValueStyle() ), + title ); } } @@ -1486,170 +2017,50 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - private void annotateSequences() { - if ( getCurrentTreePanel() != null ) { - List nodes = null; - if ( ( getCurrentTreePanel().getFoundNodes0() != null ) - || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { - nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); - } - if ( ( nodes == null ) || nodes.isEmpty() ) { - JOptionPane - .showMessageDialog( this, - "Need to select nodes, either via direct selection or via the \"Search\" function", - "No nodes selected for annotation", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final JTextField ref_field = new JTextField( 10 ); - final JTextField desc_filed = new JTextField( 20 ); - ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? "" - : getPreviousNodeAnnotationReference() ); - final JPanel my_panel = new JPanel(); - my_panel.add( new JLabel( "Reference " ) ); - my_panel.add( ref_field ); - my_panel.add( Box.createHorizontalStrut( 15 ) ); - my_panel.add( new JLabel( "Description " ) ); - my_panel.add( desc_filed ); - final int result = JOptionPane.showConfirmDialog( null, - my_panel, - "Enter the sequence annotation(s) for the " - + nodes.size() + " selected nodes", - JOptionPane.OK_CANCEL_OPTION ); - if ( result == JOptionPane.OK_OPTION ) { - String ref = ref_field.getText(); - String desc = desc_filed.getText(); - if ( !ForesterUtil.isEmpty( ref ) ) { - ref = ref.trim(); - ref = ref.replaceAll( "\\s+", " " ); - if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) ) - || ( ref.length() < 3 ) ) { - JOptionPane.showMessageDialog( this, - "Reference needs to be in the form of \"GO:1234567\"", - "Illegal Format for Annotation Reference", - JOptionPane.ERROR_MESSAGE ); - return; - } - } - if ( ref != null ) { - setPreviousNodeAnnotationReference( ref ); - } - if ( desc != null ) { - desc = desc.trim(); - desc = desc.replaceAll( "\\s+", " " ); - } - if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) { - for( final PhylogenyNode n : nodes ) { - ForesterUtil.ensurePresenceOfSequence( n ); - final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() - : new Annotation( ref ); - if ( !ForesterUtil.isEmpty( desc ) ) { - ann.setDesc( desc ); - } - n.getNodeData().getSequence().addAnnotation( ann ); - } - } - getMainPanel().getControlPanel().showAnnotations(); - } - } - } - } - - 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 enter 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 ); + private static void cycleNodeDataReturn( final Options op, final Configuration conf ) { + switch ( op.getExtDescNodeDataToReturn() ) { + case UNKNOWN: + op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL ); + break; + case DOMAINS_ALL: + op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ); + break; + case DOMAINS_COLLAPSED_PER_PROTEIN: + op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS ); + break; + case SEQ_ANNOTATIONS: + op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); + break; + case GO_TERM_IDS: + op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); + break; + case SEQUENCE_MOL_SEQ_FASTA: + if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS ) + && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) { + op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() ); } - catch ( final Exception ex ) { - success = false; + else { + op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); } - } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - getOptions().setMinConfidenceValue( m ); - } - } - } - - private void doUpdateProcessMenu() { - if ( _process_pool.size() > 0 ) { - if ( _process_menu == null ) { - _process_menu = createMenu( "", getConfiguration() ); - _process_menu.setForeground( Color.RED ); - } - _process_menu.removeAll(); - final String text = "processes running: " + _process_pool.size(); - _process_menu.setText( text ); - _jmenubar.add( _process_menu ); - for( int i = 0; i < _process_pool.size(); ++i ) { - final ProcessRunning p = _process_pool.getProcessByIndex( i ); - _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) ); - } - } - else { - if ( _process_menu != null ) { - _process_menu.removeAll(); - _jmenubar.remove( _process_menu ); - } - } - _jmenubar.validate(); - _jmenubar.repaint(); - repaint(); - } - - private String getPreviousNodeAnnotationReference() { - return _previous_node_annotation_ref; - } - - private void removeBranchColors() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); - } - } - - private void removeVisualStyles() { - if ( getMainPanel().getCurrentPhylogeny() != null ) { - AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() ); + break; + default: + op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); } } - private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) { - _previous_node_annotation_ref = previous_node_annotation_ref; - } - /** * Display the about box. */ static void about() { - final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" ); - about.append( "Copyright (C) 2014 Christian M Zmasek\n" ); + final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + AptxConstants.VERSION + "\n" ); + about.append( "Copyright (C) 2016 Christian M Zmasek\n" ); about.append( "All Rights Reserved\n" ); about.append( "License: GNU Lesser General Public License (LGPL)\n" ); - about.append( "Last modified: " + Constants.PRG_DATE + "\n" ); + about.append( "Last modified: " + AptxConstants.PRG_DATE + "\n" ); about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" ); about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" ); about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" ); @@ -1667,13 +2078,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" ); about.append( "[locale: " + Locale.getDefault() + "]\n" ); about.append( "References:\n" ); - about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" ); + about.append( AptxConstants.PHYLOXML_REFERENCE_SHORT + "\n" ); about.append( "For more information & download:\n" ); - about.append( Constants.APTX_WEB_SITE + "\n" ); + about.append( AptxConstants.APTX_WEB_SITE + "\n" ); about.append( "Documentation:\n" ); - about.append( Constants.APTX_DOC_SITE + "\n" ); - about.append( "Comments: " + Constants.AUTHOR_EMAIL ); - JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE ); + about.append( AptxConstants.APTX_DOC_SITE + "\n" ); + about.append( "Comments: " + AptxConstants.AUTHOR_EMAIL ); + JOptionPane.showMessageDialog( null, about, AptxConstants.PRG_NAME, JOptionPane.PLAIN_MESSAGE ); } static void chooseNodeSize( final Options options, final Component parent ) { @@ -1681,11 +2092,11 @@ public abstract class MainFrame extends JFrame implements ActionListener { "Please enter the default size for node shapes.\n" + "[current value: " + options.getDefaultNodeShapeSize() + "]\n", - "Node Shape Size", - JOptionPane.QUESTION_MESSAGE, - null, - null, - options.getDefaultNodeShapeSize() ); + "Node Shape Size", + JOptionPane.QUESTION_MESSAGE, + null, + null, + options.getDefaultNodeShapeSize() ); if ( !ForesterUtil.isEmpty( s ) ) { boolean success = true; double m = 0.0; @@ -1765,42 +2176,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - private static void cycleNodeDataReturn( final Options op, Configuration conf ) { - switch ( op.getExtDescNodeDataToReturn() ) { - case UNKNOWN: - op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL ); - break; - case DOMAINS_ALL: - op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ); - break; - case DOMAINS_COLLAPSED_PER_PROTEIN: - op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS ); - break; - case SEQ_ANNOTATIONS: - op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); - break; - case GO_TERM_IDS: - op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA ); - break; - case SEQUENCE_MOL_SEQ_FASTA: - if ( conf != null && conf.getExtDescNodeDataToReturn() != null - && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL - && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN - && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS - && conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS - && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA - ) { - op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() ); - } - else { - op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); - } - break; - default: - op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); - } - } - static void cycleOverview( final Options op, final TreePanel tree_panel ) { switch ( op.getOvPlacement() ) { case LOWER_LEFT: @@ -1823,6 +2198,102 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + static void exceptionOccuredDuringSaveAs( final Exception e, final TreePanel tp, final Component comp ) { + try { + tp.setArrowCursor(); + } + catch ( final Exception ex ) { + // Do nothing. + } + JOptionPane.showMessageDialog( comp, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE ); + } + + static void print( final TreePanel tp, final Options op, final Component c ) { + if ( ( tp == null ) || ( tp.getPhylogeny() == null ) || tp.getPhylogeny().isEmpty() ) { + return; + } + if ( !op.isPrintUsingActualSize() ) { + tp.calcParametersForPainting( op.getPrintSizeX() - 80, op.getPrintSizeY() - 140 ); + tp.resetPreferredSize(); + tp.repaint(); + } + final String job_name = AptxConstants.PRG_NAME; + boolean error = false; + String printer_name = null; + try { + printer_name = Printer.print( tp, job_name ); + } + catch ( final Exception e ) { + error = true; + JOptionPane.showMessageDialog( c, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE ); + } + if ( !error && ( printer_name != null ) ) { + String msg = "Printing data sent to printer"; + if ( printer_name.length() > 1 ) { + msg += " [" + printer_name + "]"; + } + JOptionPane.showMessageDialog( c, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE ); + } + if ( !op.isPrintUsingActualSize() ) { + tp.getControlPanel().showWhole(); + } + } + + static void printPhylogenyToPdf( final String file_name, + final Options opts, + final TreePanel tp, + final Component comp ) { + if ( !opts.isPrintUsingActualSize() ) { + tp.calcParametersForPainting( opts.getPrintSizeX(), opts.getPrintSizeY() ); + tp.resetPreferredSize(); + tp.repaint(); + } + String pdf_written_to = ""; + boolean error = false; + try { + if ( opts.isPrintUsingActualSize() ) { + pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth(), tp.getHeight() ); + } + else { + pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, + tp, + opts.getPrintSizeX(), + opts.getPrintSizeY() ); + } + } + catch ( final IOException e ) { + error = true; + JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); + } + if ( !error ) { + if ( !ForesterUtil.isEmpty( pdf_written_to ) ) { + JOptionPane.showMessageDialog( comp, + "Wrote PDF to: " + pdf_written_to, + "Information", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( comp, + "There was an unknown problem when attempting to write to PDF file: \"" + + file_name + "\"", + "Error", + JOptionPane.ERROR_MESSAGE ); + } + } + if ( !opts.isPrintUsingActualSize() ) { + tp.getControlPanel().showWhole(); + } + } + + static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) { + if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) { + mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" ); + } + else { + mi.setText( "Cycle Node Return Data..." ); + } + } + static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) { if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) { mi.setText( "Cycle Node Shape Fill Type... (current: " @@ -1843,16 +2314,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) { - if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) { - mi.setText( "Cycle Node Return Data... (current: " - + options.getExtDescNodeDataToReturn().toString() + ")" ); - } - else { - mi.setText( "Cycle Node Return Data..." ); - } - } - static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) { if ( ( options != null ) && ( options.getOvPlacement() != null ) ) { mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" ); @@ -1865,7 +2326,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) { if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) { mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() - + ")" ); + + ")" ); } else { mi.setText( "Select Color Scheme..." ); @@ -1876,6 +2337,15 @@ public abstract class MainFrame extends JFrame implements ActionListener { mi.setText( "Select Default Font... (current: " + font_desc + ")" ); } + 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 setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) { if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) { mi.setEnabled( true ); @@ -1898,4 +2368,436 @@ public abstract class MainFrame extends JFrame implements ActionListener { tree_panel.setTextAntialias(); } } + + static boolean writeAsNewHampshire( final TreePanel tp, final Options op, boolean exception, final File file ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toNewHampshire( tp.getPhylogeny(), true, op.getNhConversionSupportValueStyle(), file ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringSaveAs( e, tp, tp ); + } + return exception; + } + + static boolean writeAsNexus( final TreePanel tp, final Options op, boolean exception, final File file ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toNexus( file, tp.getPhylogeny(), op.getNhConversionSupportValueStyle() ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringSaveAs( e, tp, tp ); + } + return exception; + } + + static boolean writeAsPhyloXml( final TreePanel tp, final Options op, boolean exception, final File file ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toPhyloXML( file, tp.getPhylogeny(), 0 ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringSaveAs( e, tp, tp ); + } + return exception; + } + + static void writePhylogenyToGraphicsFile( final String file_name, + final GraphicsExportType type, + final MainPanel mp, + final Component comp, + final Container contentpane ) { + mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(), + mp.getCurrentTreePanel().getHeight() ); + String file_written_to = ""; + boolean error = false; + try { + file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name, + mp.getCurrentTreePanel().getWidth(), + mp.getCurrentTreePanel().getHeight(), + mp.getCurrentTreePanel(), + mp.getControlPanel(), + type, + mp.getOptions() ); + } + catch ( final IOException e ) { + error = true; + JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); + } + if ( !error ) { + if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) { + JOptionPane.showMessageDialog( comp, + "Wrote image to: " + file_written_to, + "Graphics Export", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( comp, + "There was an unknown problem when attempting to write to an image file: \"" + + file_name + "\"", + "Error", + JOptionPane.ERROR_MESSAGE ); + } + } + contentpane.repaint(); + } + + static File writeToFile( final Phylogeny t, + final MainPanel mp, + final JFileChooser save_filechooser, + final File current_dir, + final Container contentpane, + final Component comp ) { + File new_file = null; + if ( t == null ) { + return null; + } + String initial_filename = null; + if ( mp.getCurrentTreePanel().getTreeFile() != null ) { + try { + initial_filename = mp.getCurrentTreePanel().getTreeFile().getCanonicalPath(); + } + catch ( final IOException e ) { + initial_filename = null; + } + } + if ( !ForesterUtil.isEmpty( initial_filename ) ) { + save_filechooser.setSelectedFile( new File( initial_filename ) ); + } + else { + save_filechooser.setSelectedFile( new File( "" ) ); + } + final File my_dir = current_dir; + if ( my_dir != null ) { + save_filechooser.setCurrentDirectory( my_dir ); + } + final int result = save_filechooser.showSaveDialog( contentpane ); + final File file = save_filechooser.getSelectedFile(); + new_file = save_filechooser.getCurrentDirectory(); + boolean exception = false; + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( file.exists() ) { + final int i = JOptionPane.showConfirmDialog( comp, + file + " already exists.\nOverwrite?", + "Overwrite?", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.QUESTION_MESSAGE ); + if ( i != JOptionPane.OK_OPTION ) { + return null; + } + else { + final File to = new File( file.getAbsoluteFile().toString() + AptxConstants.BACKUP_FILE_SUFFIX ); + try { + ForesterUtil.copyFile( file, to ); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( comp, + "Failed to create backup copy " + to, + "Failed to Create Backup Copy", + JOptionPane.WARNING_MESSAGE ); + } + try { + file.delete(); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( comp, + "Failed to delete: " + file, + "Failed to Delete", + JOptionPane.WARNING_MESSAGE ); + } + } + } + if ( save_filechooser.getFileFilter() == MainFrame.nhfilter ) { + exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + else if ( save_filechooser.getFileFilter() == MainFrame.xmlfilter ) { + exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + else if ( save_filechooser.getFileFilter() == MainFrame.nexusfilter ) { + exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + // "*.*": + else { + final String file_name = file.getName().trim().toLowerCase(); + if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) + || file_name.endsWith( ".tree" ) ) { + exception = writeAsNewHampshire( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) { + exception = writeAsNexus( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + // XML is default: + else { + exception = writeAsPhyloXml( mp.getCurrentTreePanel(), mp.getOptions(), exception, file ); + } + } + if ( !exception ) { + mp.setTitleOfSelectedTab( file.getName() ); + mp.getCurrentTreePanel().setTreeFile( file ); + mp.getCurrentTreePanel().setEdited( false ); + } + } + return new_file; + } + + static File writeToGraphicsFile( final Phylogeny t, + final GraphicsExportType type, + final MainPanel mp, + final JFileChooser writetographics_filechooser, + final Component component, + final Container contentpane, + final File current_dir ) { + File new_dir = null; + if ( ( t == null ) || t.isEmpty() ) { + return null; + } + String initial_filename = ""; + if ( mp.getCurrentTreePanel().getTreeFile() != null ) { + initial_filename = mp.getCurrentTreePanel().getTreeFile().toString(); + } + if ( initial_filename.indexOf( '.' ) > 0 ) { + initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); + } + initial_filename = initial_filename + "." + type; + writetographics_filechooser.setSelectedFile( new File( initial_filename ) ); + final File my_dir = current_dir; + if ( my_dir != null ) { + writetographics_filechooser.setCurrentDirectory( my_dir ); + } + final int result = writetographics_filechooser.showSaveDialog( contentpane ); + File file = writetographics_filechooser.getSelectedFile(); + //setCurrentDir( writetographics_filechooser.getCurrentDirectory() ); + new_dir = writetographics_filechooser.getCurrentDirectory(); + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) { + file = new File( file.toString() + "." + type ); + } + if ( file.exists() ) { + final int i = JOptionPane.showConfirmDialog( component, + file + " already exists. Overwrite?", + "Warning", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.WARNING_MESSAGE ); + if ( i != JOptionPane.OK_OPTION ) { + return null; + } + else { + try { + file.delete(); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( component, + "Failed to delete: " + file, + "Error", + JOptionPane.WARNING_MESSAGE ); + } + } + } + writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane ); + } + return new_dir; + } + + static File writeToPdf( final Phylogeny t, + final MainPanel mp, + final JFileChooser writetopdf_filechooser, + final File curr_dir, + final Container contentpane, + final Component component ) { + if ( ( t == null ) || t.isEmpty() ) { + return null; + } + String initial_filename = ""; + if ( mp.getCurrentTreePanel().getTreeFile() != null ) { + initial_filename = mp.getCurrentTreePanel().getTreeFile().toString(); + } + if ( initial_filename.indexOf( '.' ) > 0 ) { + initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); + } + initial_filename = initial_filename + ".pdf"; + writetopdf_filechooser.setSelectedFile( new File( initial_filename ) ); + final File my_dir = curr_dir; + if ( my_dir != null ) { + writetopdf_filechooser.setCurrentDirectory( my_dir ); + } + final int result = writetopdf_filechooser.showSaveDialog( contentpane ); + File file = writetopdf_filechooser.getSelectedFile(); + // setCurrentDir( writetopdf_filechooser.getCurrentDirectory() ); + final File new_current_dir = writetopdf_filechooser.getCurrentDirectory(); + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) { + file = new File( file.toString() + ".pdf" ); + } + if ( file.exists() ) { + final int i = JOptionPane.showConfirmDialog( component, + file + " already exists. Overwrite?", + "WARNING", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.WARNING_MESSAGE ); + if ( i != JOptionPane.OK_OPTION ) { + return null; + } + } + printPhylogenyToPdf( file.toString(), mp.getOptions(), mp.getCurrentTreePanel(), component ); + } + return new_current_dir; + } +} + +class DefaultFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) + || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" ) + || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" ) + || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) + || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" ) + || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" ) + || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) + || file_name.endsWith( ".con" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)"; + } +} + +class GraphicsFileFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" ) + || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)"; + } +} + +class MsaFileFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" ) + || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)"; + } } + +class NexusFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" ) + || file_name.endsWith( ".tre" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "Nexus files (*.nex, *.nexus, *.nx, *.tre)"; + } +} // NexusFilter + +class NHFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) + || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" ) + || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" ) + || f.isDirectory(); + } + + @Override + public String getDescription() { + return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)"; + } +} // NHFilter + +class NHXFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".nhx" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "NHX files (*.nhx) [deprecated]"; + } +} + +class PdfFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "PDF files (*.pdf)"; + } +} // PdfFilter + +class SequencesFileFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" ) + || file_name.endsWith( ".seqs" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )"; + } +} + +class TolFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f + .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) ); + } + + @Override + public String getDescription() { + return "Tree of Life files (*.tol, *.tolxml)"; + } +} // TolFilter + +class XMLFilter extends FileFilter { + + @Override + public boolean accept( final File f ) { + final String file_name = f.getName().trim().toLowerCase(); + return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" ) + || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory(); + } + + @Override + public String getDescription() { + return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)"; + } +} // XMLFilter