X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrame.java;h=7ab7ce7c4f96314279a085223e49d66befb9cc02;hb=8d6e81da091d432309f2f7034cf93dbc5ba5e82a;hp=aa4b40e7c8643b6717c120a11694c6072659f7cf;hpb=5c4dc1fb4a38c45f03ef67541592bac5113a2a6f;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index aa4b40e..7ab7ce7 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; @@ -51,7 +52,9 @@ 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; @@ -59,12 +62,14 @@ 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; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; import org.forester.phylogeny.data.Annotation; +import org.forester.phylogeny.data.NodeDataField; import org.forester.phylogeny.data.NodeVisualData.NodeFill; import org.forester.phylogeny.data.NodeVisualData.NodeShape; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; @@ -73,196 +78,230 @@ 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 style). 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 = 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; // 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; - 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; // 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; + // + JFileChooser _writetopdf_filechooser; + File _current_dir; + JFileChooser _save_filechooser; + JFileChooser _writetographics_filechooser; // process menu: - JMenu _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; + 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(); + _save_filechooser = new JFileChooser(); + _save_filechooser.setCurrentDirectory( new File( "." ) ); + _save_filechooser.setMultiSelectionEnabled( false ); + _save_filechooser.setFileFilter( MainFrame.xmlfilter ); + _save_filechooser.addChoosableFileFilter( nhfilter ); + _save_filechooser.addChoosableFileFilter( nexusfilter ); + _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); + _writetographics_filechooser = new JFileChooser(); + _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter ); } /** @@ -404,10 +443,13 @@ public abstract class MainFrame extends JFrame implements ActionListener { MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() ); } else if ( o == _cycle_node_fill_mi ) { - MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() ); + MainFrame.cycleNodeFill( getOptions() ); } else if ( o == _cycle_node_shape_mi ) { - MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() ); + MainFrame.cycleNodeShape( getOptions() ); + } + else if ( o == _cycle_data_return ) { + MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() ); } else if ( o == _screen_antialias_cbmi ) { updateOptions( getOptions() ); @@ -568,102 +610,67 @@ public abstract class MainFrame extends JFrame implements ActionListener { ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() ); } } - else { - if ( _load_phylogeny_from_webservice_menu_items != null ) { - for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) { - if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) { - readPhylogeniesFromWebservice( i ); - } - } - } + else if ( o == _write_to_pdf_item ) { + writeToPdf( _mainpanel.getCurrentPhylogeny() ); } - _contentpane.repaint(); - } - - private void deleteSelectedNodes( final boolean delete ) { - final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); - if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) { - return; + else if ( o == _save_all_item ) { + writeAllToFile(); } - final List nodes = new ArrayList(); - if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { - final List all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); - for( final PhylogenyNode n : all_selected_nodes ) { - if ( n.isExternal() ) { - nodes.add( n ); - } - } + else if ( o == _write_to_jpg_item ) { + writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG ); } - String function = "Retain"; - if ( delete ) { - function = "Delete"; + else if ( o == _write_to_gif_item ) { + writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF ); } - 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 ); - return; + else if ( o == _write_to_tif_item ) { + writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF ); } - final int todo = nodes.size(); - final int ext = phy.getNumberOfExternalNodes(); - int res = todo; - if ( delete ) { - res = ext - todo; + else if ( o == _write_to_bmp_item ) { + writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP ); } - if ( res < 1 ) { - JOptionPane.showMessageDialog( this, - "Cannot delete all nodes", - "Attempt to delete all nodes ", - JOptionPane.ERROR_MESSAGE ); - return; + else if ( o == _print_item ) { + print( getCurrentTreePanel(), + getOptions(), + + this ); } - 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 ); - if ( result == JOptionPane.OK_OPTION ) { - if ( !delete ) { - final List to_delete = new ArrayList(); - for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( !nodes.contains( n ) ) { - to_delete.add( n ); + else if ( o == _save_item ) { + writeToFile( _mainpanel.getCurrentPhylogeny() ); + } + else if ( o == _write_to_png_item ) { + writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG ); + } + 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 ( _load_phylogeny_from_webservice_menu_items != null ) { + for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) { + if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) { + readPhylogeniesFromWebservice( i ); } } - for( final PhylogenyNode n : to_delete ) { - phy.deleteSubtree( n, true ); - } - } - else { - for( final PhylogenyNode n : nodes ) { - phy.deleteSubtree( n, true ); - } } - resetSearch(); - getCurrentTreePanel().setNodeInPreorderToNull(); - phy.externalNodesHaveChanged(); - phy.clearHashIdToNodeMap(); - phy.recalculateNumberOfExternalDescendants( true ); - getCurrentTreePanel().resetNodeIdToDistToLeafMap(); - getCurrentTreePanel().setEdited( true ); - repaint(); } - } - - 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 ); + _contentpane.repaint(); } public Configuration getConfiguration() { @@ -675,7 +682,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { * 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() { @@ -737,8 +744,33 @@ 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 ); } @@ -833,6 +865,84 @@ 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: " + 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 ); + } + } + } + void close() { removeAllTextFrames(); if ( _mainpanel != null ) { @@ -1099,6 +1209,32 @@ 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(); } @@ -1199,6 +1335,51 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + void static printPhylogenyToPdf( final String file_name ) { + if ( !getOptions().isPrintUsingActualSize() ) { + getCurrentTreePanel() + .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() ); + getCurrentTreePanel().resetPreferredSize(); + getCurrentTreePanel().repaint(); + } + String pdf_written_to = ""; + boolean error = false; + try { + if ( getOptions().isPrintUsingActualSize() ) { + pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, + getCurrentTreePanel(), + getCurrentTreePanel().getWidth(), + getCurrentTreePanel().getHeight() ); + } + else { + pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions() + .getPrintSizeX(), getOptions().getPrintSizeY() ); + } + } + catch ( final IOException e ) { + error = true; + JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); + } + if ( !error ) { + if ( !ForesterUtil.isEmpty( pdf_written_to ) ) { + JOptionPane.showMessageDialog( this, + "Wrote PDF to: " + pdf_written_to, + "Information", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "There was an unknown problem when attempting to write to PDF file: \"" + + file_name + "\"", + "Error", + JOptionPane.ERROR_MESSAGE ); + } + } + if ( !getOptions().isPrintUsingActualSize() ) { + getControlPanel().showWhole(); + } + } + void readPhylogeniesFromWebservice( final int i ) { final UrlTreeReader reader = new UrlTreeReader( this, i ); new Thread( reader ).start(); @@ -1213,10 +1394,29 @@ 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; } @@ -1481,6 +1681,263 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringSaveAs( e ); + } + return exception; + } + + boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringSaveAs( e ); + } + return exception; + } + + boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) { + try { + final PhylogenyWriter writer = new PhylogenyWriter(); + writer.toPhyloXML( file, t, 0 ); + } + catch ( final Exception e ) { + exception = true; + exceptionOccuredDuringSaveAs( e ); + } + return exception; + } + + void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) { + _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), + _mainpanel.getCurrentTreePanel().getHeight() ); + String file_written_to = ""; + boolean error = false; + try { + file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name, + _mainpanel.getCurrentTreePanel().getWidth(), + _mainpanel.getCurrentTreePanel().getHeight(), + _mainpanel.getCurrentTreePanel(), + _mainpanel.getControlPanel(), + type, + getOptions() ); + } + catch ( final IOException e ) { + error = true; + JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); + } + if ( !error ) { + if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) { + JOptionPane.showMessageDialog( this, + "Wrote image to: " + file_written_to, + "Graphics Export", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, + "There was an unknown problem when attempting to write to an image file: \"" + + file_name + "\"", + "Error", + JOptionPane.ERROR_MESSAGE ); + } + } + _contentpane.repaint(); + } + + void writeToFile( final Phylogeny t ) { + if ( t == null ) { + return; + } + String initial_filename = null; + if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { + try { + initial_filename = getMainPanel().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 = getCurrentDir(); + if ( my_dir != null ) { + _save_filechooser.setCurrentDirectory( my_dir ); + } + final int result = _save_filechooser.showSaveDialog( _contentpane ); + final File file = _save_filechooser.getSelectedFile(); + setCurrentDir( _save_filechooser.getCurrentDirectory() ); + boolean exception = false; + if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + if ( file.exists() ) { + final int i = JOptionPane.showConfirmDialog( this, + file + " already exists.\nOverwrite?", + "Overwrite?", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.QUESTION_MESSAGE ); + if ( i != JOptionPane.OK_OPTION ) { + return; + } + else { + final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX ); + try { + ForesterUtil.copyFile( file, to ); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( this, + "Failed to create backup copy " + to, + "Failed to Create Backup Copy", + JOptionPane.WARNING_MESSAGE ); + } + try { + file.delete(); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( this, + "Failed to delete: " + file, + "Failed to Delete", + JOptionPane.WARNING_MESSAGE ); + } + } + } + if ( _save_filechooser.getFileFilter() == MainFrame.nhfilter ) { + exception = writeAsNewHampshire( t, exception, file ); + } + else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) { + exception = writeAsPhyloXml( t, exception, file ); + } + else if ( _save_filechooser.getFileFilter() == MainFrame.nexusfilter ) { + exception = writeAsNexus( t, 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( t, exception, file ); + } + else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) { + exception = writeAsNexus( t, exception, file ); + } + // XML is default: + else { + exception = writeAsPhyloXml( t, exception, file ); + } + } + if ( !exception ) { + getMainPanel().setTitleOfSelectedTab( file.getName() ); + getMainPanel().getCurrentTreePanel().setTreeFile( file ); + getMainPanel().getCurrentTreePanel().setEdited( false ); + } + } + } + + void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) { + if ( ( t == null ) || t.isEmpty() ) { + return; + } + String initial_filename = ""; + if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { + initial_filename = getMainPanel().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 = getCurrentDir(); + 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() ); + 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( 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 ); + } + } + } + writePhylogenyToGraphicsFile( file.toString(), type ); + } + } + + static File writeToPdf( final Phylogeny t, + final MainPanel mp, + JFileChooser writetopdf_filechooser, + File curr_dir, + Container contentpane , + 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() ); + } + return new_current_dir; + } + private void annotateSequences() { if ( getCurrentTreePanel() != null ) { List nodes = null; @@ -1590,6 +2047,77 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } + private void deleteSelectedNodes( final boolean delete ) { + final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); + if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) { + return; + } + final List nodes = new ArrayList(); + if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) { + final List all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes(); + for( final PhylogenyNode n : all_selected_nodes ) { + if ( n.isExternal() ) { + nodes.add( n ); + } + } + } + String function = "Retain"; + if ( delete ) { + function = "Delete"; + } + 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 ); + return; + } + final int todo = nodes.size(); + final int ext = phy.getNumberOfExternalNodes(); + int res = todo; + if ( delete ) { + res = ext - todo; + } + if ( res < 1 ) { + JOptionPane.showMessageDialog( this, + "Cannot delete all nodes", + "Attempt to delete all nodes ", + JOptionPane.ERROR_MESSAGE ); + 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 ); + if ( result == JOptionPane.OK_OPTION ) { + if ( !delete ) { + final List to_delete = new ArrayList(); + for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + if ( !nodes.contains( n ) ) { + to_delete.add( n ); + } + } + for( final PhylogenyNode n : to_delete ) { + phy.deleteSubtree( n, true ); + } + } + else { + for( final PhylogenyNode n : nodes ) { + phy.deleteSubtree( n, true ); + } + } + resetSearch(); + getCurrentTreePanel().setNodeInPreorderToNull(); + phy.externalNodesHaveChanged(); + phy.clearHashIdToNodeMap(); + phy.recalculateNumberOfExternalDescendants( true ); + getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + getCurrentTreePanel().setEdited( true ); + repaint(); + } + } + private void doUpdateProcessMenu() { if ( _process_pool.size() > 0 ) { if ( _process_menu == null ) { @@ -1620,6 +2148,43 @@ public abstract class MainFrame extends JFrame implements ActionListener { return _previous_node_annotation_ref; } + 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 = Constants.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(); + } + } + private void removeBranchColors() { if ( getMainPanel().getCurrentPhylogeny() != null ) { AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() ); @@ -1636,6 +2201,64 @@ public abstract class MainFrame extends JFrame implements ActionListener { _previous_node_annotation_ref = previous_node_annotation_ref; } + 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 ); + } + } + } + /** * Display the about box. */ @@ -1731,7 +2354,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { return label; } - static void cycleNodeFill( final Options op, final TreePanel tree_panel ) { + static void cycleNodeFill( final Options op ) { switch ( op.getDefaultNodeFill() ) { case GRADIENT: op.setDefaultNodeFill( NodeFill.SOLID ); @@ -1747,7 +2370,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - static void cycleNodeShape( final Options op, final TreePanel tree_panel ) { + static void cycleNodeShape( final Options op ) { switch ( op.getDefaultNodeShape() ) { case CIRCLE: op.setDefaultNodeShape( NodeShape.RECTANGLE ); @@ -1782,6 +2405,15 @@ 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 setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) { if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) { mi.setText( "Cycle Node Shape Fill Type... (current: " @@ -1825,6 +2457,15 @@ 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 ); @@ -1847,4 +2488,194 @@ public abstract class MainFrame extends JFrame implements ActionListener { tree_panel.setTextAntialias(); } } + + 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() ); + } + else { + op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); + } + break; + default: + op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN ); + } + } +} + +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