import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentListener;
+import java.io.File;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.NoSuchElementException;
-import java.util.Set;
import javax.swing.Box;
-import javax.swing.JApplet;
import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFileChooser;
import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
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;
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.NodeVisualization.NodeFill;
-import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+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;
+import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
-
-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_CASE_SENSITIVE_LABEL = "Case Sensitive";
- static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";
- static final String DISPLAY_BRANCH_LENGTH_VALUES_LABEL = "Display Branch Length Values";
- static final String DISPLAY_SCALE_LABEL = "Display 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 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 = "Show External Node Shapes";
- static final String DISPLAY_NODE_BOXES_LABEL_INT = "Show Internal Node Shapes";
- static final String SHOW_OVERVIEW_LABEL = "Show 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 = "Show Domain Labels";
- 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 = "Show 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";
- 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;
+import org.forester.util.WindowsUtils;
+
+public abstract class MainFrame implements ActionListener {
+
+ public final static NHFilter nhfilter = new NHFilter();
+ public final static NHXFilter nhxfilter = new NHXFilter();
+ public final static XMLFilter xmlfilter = new XMLFilter();
+ public final static TolFilter tolfilter = new TolFilter();
+ public final static NexusFilter nexusfilter = new NexusFilter();
+ public final static PdfFilter pdffilter = new PdfFilter();
+ public final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
+ public final static MsaFileFilter msafilter = new MsaFileFilter();
+ public final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
+ public final static DefaultFilter defaultfilter = new DefaultFilter();
+ static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "rotate with mousewheel + Shift (or A and S), D toggles between horizontal and radial labels";
+ 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 = "Words";
+ static final String SEARCH_REGEX_LABEL = "Regex";
+ static final String SEARCH_CASE_SENSITIVE_LABEL = "Match Case";
+ static final String INVERSE_SEARCH_RESULT_LABEL = "Inverse";
+ 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 Cladogram";
+ 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 = "Lined Up Cladogram";
+ 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";
+
+ final AptxFrame _frame;
+ 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;
// 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 _collapse_below_threshold; //TODO implememt me
- 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 _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 _show_branch_length_values_cbmi;
- JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
- JCheckBoxMenuItem _show_overview_cbmi;
- JCheckBoxMenuItem _show_domain_labels;
- 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;
- JMenuItem _cycle_node_shape_mi;
- JMenuItem _cycle_node_fill_mi;
- JMenuItem _choose_node_size_mi;
- JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
- JCheckBoxMenuItem _show_confidence_stddev_cbmi;
+ JCheckBoxMenuItem _screen_antialias_cbmi;
+ JCheckBoxMenuItem _background_gradient_cbmi;
+ JRadioButtonMenuItem _non_lined_up_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 _collapsed_with_average_height_cbmi;
+ JCheckBoxMenuItem _show_abbreviated_labels_for_collapsed_nodes_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;
+ //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_yes_rbmi;
- JRadioButtonMenuItem _extract_taxonomy_pfam_rbmi;
- JCheckBoxMenuItem _replace_underscores_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;
+ JCheckBoxMenuItem _parse_beast_style_extended_nexus_tags_cbmi;
// _ search
- JCheckBoxMenuItem _search_case_senstive_cbmi;
- JCheckBoxMenuItem _search_whole_words_only_cbmi;
- JCheckBoxMenuItem _inverse_search_result_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 _aptxjs_website_item;
+ JMenuItem _mailing_list_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<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
- Configuration _configuration;
- JMenuItem _remove_branch_color_item;
- Options _options;
- InferenceManager _inference_manager;
- final ProcessPool _process_pool;
- private String _previous_node_annotation_ref;
+ JMenu _process_menu;
+ MainPanel _mainpanel;
+ Container _contentpane;
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;
+ Configuration _configuration;
+ Options _options;
+ private Phylogeny _species_tree;
+ InferenceManager _inference_manager;
+ final ProcessPool _process_pool;
+ private String _previous_node_annotation_ref;
MainFrame() {
+ this(false);
+ }
+ MainFrame(boolean embedded){
+ if (embedded) {
+ _frame = new EmbeddedFrame();
+ }
+ else {
+ _frame = new StandaloneFrame();
+ }
_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.
+ }
}
-
+ public void addComponentListener( ComponentListener componentListener ) {
+ _frame.addComponentListener( componentListener );
+
+ }
+
+ public void dispose() {
+ _frame.dispose();
+ }
+ public Container getContentPane() {
+ return _frame.getContentPane();
+ }
+
+ public void repaint() {
+ _frame.repaint();
+ }
+
+
+ public void addFrameListener(FrameListener frameListener) {
+ _frame.addFrameListener(frameListener);
+ }
+
+ public void setSize(int x, int y) {
+ _frame.setSize(x,y);
+ }
+ public Container getJMenuBar() {
+ return _frame.getJMenuBar();
+ }
+ public void setDefaultCloseOperation( int doNothingOnClose ) {
+ _frame.setDefaultCloseOperation(doNothingOnClose);
+
+ }
+ public Container getParent() {
+ return _frame.getParent();
+ }
+ public void setVisible(boolean visible) {
+ _frame.setVisible(visible);
+ }
+ public void requestFocusInWindow() {
+ _frame.requestFocusInWindow();
+ }
+ public void setJMenuBar( JMenuBar jmenubar ) {
+ _frame.setJMenuBar(jmenubar);
+ }
+ public void setLocationRelativeTo( Component component ) {
+ _frame.setLocationRelativeTo(component);
+ }
+ public void setTitle(String title) {
+ _frame.setTitle(title);
+ }
+
+ public Container getThisFrame() {
+ return _frame.getThisFrame();
+ }
+
+ public void validate() {
+ _frame.validate();
+ }
+
+
+
+
+
+
/**
* Action performed.
*/
@Override
public void actionPerformed( final ActionEvent e ) {
final Object o = e.getSource();
- boolean is_applet = false;
- JApplet applet = null;
- if ( getCurrentTreePanel() != null ) {
- is_applet = getCurrentTreePanel().isApplet();
- if ( is_applet ) {
- applet = getCurrentTreePanel().obtainApplet();
- }
+
+ if ( o == _exit_item ) {
+ close();
}
- if ( o == _open_url_item ) {
- readPhylogeniesFromURL();
+ else if ( o == _gsdi_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDI();
}
- else if ( o == _exit_item ) {
- close();
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
}
else if ( o == _taxcolor_item ) {
taxColor();
}
removeBranchColors();
}
+ else if ( o == _remove_visual_styles_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ removeVisualStyles();
+ }
else if ( o == _midpoint_root_item ) {
if ( isSubtreeDisplayed() ) {
return;
}
midpointRoot();
}
+ else if ( o == _delete_selected_nodes_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ deleteSelectedNodes( true );
+ }
+ else if ( o == _delete_not_selected_nodes_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ deleteSelectedNodes( false );
+ }
else if ( o == _annotate_item ) {
annotateSequences();
}
switchColors();
}
else if ( o == _display_basic_information_item ) {
- displayBasicInformation();
+ if ( getCurrentTreePanel() != null ) {
+ displayBasicInformation( getCurrentTreePanel().getTreeFile() );
+ }
}
else if ( o == _view_as_NH_item ) {
viewAsNH();
chooseMinimalConfidence();
}
else if ( o == _choose_node_size_mi ) {
- chooseNodeSize( getOptions(), this );
+ chooseNodeSize( getOptions(), _frame.getThisFrame() );
}
else if ( o == _overview_placment_mi ) {
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() );
else if ( o == _show_domain_labels ) {
updateOptions( getOptions() );
}
+ else if ( o == _show_annotation_ref_source ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _abbreviate_scientific_names ) {
updateOptions( getOptions() );
}
else if ( o == _show_default_node_shapes_external_cbmi ) {
updateOptions( getOptions() );
}
- else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
+ else if ( o == _show_default_node_shapes_for_marked_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _non_lined_up_cladograms_rbmi ) {
updateOptions( getOptions() );
showWhole();
}
- else if ( o == _uniform_cladograms_rbmi ) {
- updateOptions( getOptions() );
- showWhole();
- }
else if ( o == _ext_node_dependent_cladogram_rbmi ) {
updateOptions( getOptions() );
showWhole();
}
else if ( o == _search_case_senstive_cbmi ) {
+ if ( ( _search_with_regex_cbmi != null ) && _search_case_senstive_cbmi.isSelected() ) {
+ _search_with_regex_cbmi.setSelected( false );
+ }
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _search_whole_words_only_cbmi ) {
+ if ( ( _search_with_regex_cbmi != null ) && _search_whole_words_only_cbmi.isSelected() ) {
+ _search_with_regex_cbmi.setSelected( false );
+ }
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
}
else if ( o == _inverse_search_result_cbmi ) {
updateOptions( getOptions() );
- getMainPanel().getControlPanel().search();
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _search_with_regex_cbmi ) {
+ if ( ( _search_whole_words_only_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_whole_words_only_cbmi.setSelected( false );
+ }
+ if ( ( _search_case_senstive_cbmi != null ) && _search_with_regex_cbmi.isSelected() ) {
+ _search_case_senstive_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ getMainPanel().getControlPanel().search0();
+ getMainPanel().getControlPanel().search1();
+ }
+ else if ( o == _color_all_found_nodes_when_coloring_subtree_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _parse_beast_style_extended_nexus_tags_cbmi ) {
+ updateOptions( getOptions() );
}
else if ( o == _show_scale_cbmi ) {
updateOptions( getOptions() );
}
- else if ( o == _show_branch_length_values_cbmi ) {
+ else if ( o == _color_by_taxonomic_group_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _show_confidence_stddev_cbmi ) {
getCurrentTreePanel().updateOvSizes();
}
}
+ else if ( o == _line_up_renderable_data_cbmi ) {
+ if ( !_line_up_renderable_data_cbmi.isSelected() ) {
+ _right_line_up_domains_cbmi.setSelected( false );
+ }
+ updateOptions( getOptions() );
+ }
+
+ else if ( o == _collapsed_with_average_height_cbmi ) {
+ if ( _collapsed_with_average_height_cbmi.isSelected() ) {
+ _collapsed_with_average_height_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_abbreviated_labels_for_collapsed_nodes_cbmi ) {
+ if ( _show_abbreviated_labels_for_collapsed_nodes_cbmi.isSelected() ) {
+ _show_abbreviated_labels_for_collapsed_nodes_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
+ else if ( o == _right_line_up_domains_cbmi ) {
+ if ( _right_line_up_domains_cbmi.isSelected() ) {
+ _line_up_renderable_data_cbmi.setSelected( true );
+ }
+ updateOptions( getOptions() );
+ }
else if ( ( o == _rectangular_type_cbmi ) || ( o == _triangular_type_cbmi ) || ( o == _curved_type_cbmi )
|| ( o == _convex_type_cbmi ) || ( o == _euro_type_cbmi ) || ( o == _rounded_type_cbmi )
|| ( o == _unrooted_type_cbmi ) || ( o == _circular_type_cbmi ) ) {
about();
}
else if ( o == _help_item ) {
- help( getConfiguration().getWebLinks() );
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_DOC_SITE );
+ }
+ catch ( final IOException e1 ) {
+ 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);
}
catch ( final IOException e1 ) {
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _aptxjs_website_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_JS_WEB_SITE);;
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+ }
+ }
+ else if ( o == _mailing_list_item ) {
+ try {
+ AptxUtil.openWebsite( AptxConstants.APTX_MAILING_LIST );
+ }
+ catch ( final IOException e1 ) {
+ 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 );
}
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 );
}
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 );
}
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(),
+ getThisFrame() );
+ 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,
+ getThisFrame(),
+ 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,
+ getThisFrame(),
+ 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,
+ getThisFrame(),
+ 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,
+ getThisFrame(),
+ 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,
+ getThisFrame(),
+ getContentPane(),
+ _current_dir );
+ if ( new_dir != null ) {
+ setCurrentDir( new_dir );
+ }
+ }
+ else if ( o == _print_item ) {
+ print( getCurrentTreePanel(), getOptions(), _frame.getThisFrame() );
+ }
+ else if ( o == _save_item ) {
+ final File new_dir = writeToFile( _mainpanel.getCurrentPhylogeny(),
+ getMainPanel(),
+ _save_filechooser,
+ _current_dir,
+ getContentPane(),
+ _frame.getThisFrame() );
+ 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 == _choose_pdf_width_mi ) {
+ choosePdfWidth();
+ }
+ else if ( o == _lineage_inference ) {
+ if ( isSubtreeDisplayed() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Subtree is shown.",
+ "Cannot infer ancestral taxonomies",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ executeLineageInference();
+ }
else {
if ( _load_phylogeny_from_webservice_menu_items != null ) {
for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {
_contentpane.repaint();
}
+
public Configuration getConfiguration() {
return _configuration;
}
* 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() {
} );
}
- void activateSaveAllIfNeeded() {
- if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
- _save_all_item.setEnabled( true );
+ private void annotateSequences() {
+ if ( getCurrentTreePanel() != null ) {
+ List<PhylogenyNode> nodes = null;
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null )
+ || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
+ nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();
+ }
+ if ( ( nodes == null ) || nodes.isEmpty() ) {
+ JOptionPane
+ .showMessageDialog( getThisFrame(),
+ "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( getThisFrame(),
+ "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();
+ }
+ }
}
- else {
- _save_all_item.setEnabled( false );
+ }
+
+ private void chooseFont() {
+ final FontChooser fc = new FontChooser();
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ fc.showDialog( getThisFrame(), "Select the Base Font" );
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ if ( getMainPanel().getCurrentTreePanel() != null ) {
+ getMainPanel().getCurrentTreePanel().resetPreferredSize();
+ getMainPanel().getCurrentTreePanel().updateOvSizes();
}
+
+ repaint();
}
- void buildFileMenu() {
- _file_jmenu = createMenu( "File", getConfiguration() );
- _file_jmenu.add( _open_url_item = new JMenuItem( "Read tree from URL/webservice..." ) );
- _file_jmenu.addSeparator();
- _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
- customizeJMenuItem( _open_url_item );
- customizeJMenuItem( _exit_item );
- _jmenubar.add( _file_jmenu );
+ private void chooseMinimalConfidence() {
+ final String s = ( String ) JOptionPane
+ .showInputDialog( getThisFrame(),
+ "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 );
+ }
+ }
}
- void buildFontSizeMenu() {
- _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
- _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
- _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
- _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
- _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
- _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
- customizeJMenuItem( _super_tiny_fonts_item );
- customizeJMenuItem( _tiny_fonts_item );
- customizeJMenuItem( _small_fonts_item );
- customizeJMenuItem( _medium_fonts_item );
- customizeJMenuItem( _large_fonts_item );
- _jmenubar.add( _font_size_menu );
+ private void deleteSelectedNodes( final boolean delete ) {
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
+ if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> 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( getThisFrame(),
+ "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( getThisFrame(),
+ "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<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
+ 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();
+ }
}
- void buildHelpMenu() {
- _help_jmenu = createMenu( "Help", getConfiguration() );
- _help_jmenu.add( _help_item = new JMenuItem( "Help" ) );
- _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
- _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" );
- _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
- _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
- _help_jmenu.addSeparator();
- _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
- customizeJMenuItem( _help_item );
- customizeJMenuItem( _website_item );
- customizeJMenuItem( _phyloxml_website_item );
+ 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() );
+ }
+ }
+
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
+ _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( getThisFrame(),
+ 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( getThisFrame(),
+ "Failed to delete: " + file,
+ "Error",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ }
+ final int count = getMainPanel().getTabbedPane().getTabCount();
+ final List<Phylogeny> trees = new ArrayList<Phylogeny>();
+ 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( getThisFrame(),
+ "Failed to write to: " + file,
+ "Error",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ }
+ }
+
+ public void activateSaveAllIfNeeded() {
+ if ( ( getMainPanel().getTabbedPane() != null ) && ( getMainPanel().getTabbedPane().getTabCount() > 1 ) ) {
+ _save_all_item.setEnabled( true );
+ }
+ else {
+ _save_all_item.setEnabled( false );
+ }
+ }
+
+ void buildFileMenu() {
+ _file_jmenu = MainFrame.createMenu( "File", getConfiguration() );
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
+ _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
+ }
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
+ _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {
+ _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
+ }
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {
+ _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
+ }
+ _file_jmenu.addSeparator();
+ _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );
+ _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 );
+ }
+
+ void buildFontSizeMenu() {
+ _font_size_menu = createMenu( FONT_SIZE_MENU_LABEL, getConfiguration() );
+ _font_size_menu.add( _super_tiny_fonts_item = new JMenuItem( "Super Tiny Fonts" ) );
+ _font_size_menu.add( _tiny_fonts_item = new JMenuItem( "Tiny Fonts" ) );
+ _font_size_menu.add( _small_fonts_item = new JMenuItem( "Small Fonts" ) );
+ _font_size_menu.add( _medium_fonts_item = new JMenuItem( "Medium Fonts" ) );
+ _font_size_menu.add( _large_fonts_item = new JMenuItem( "Large Fonts" ) );
+ customizeJMenuItem( _super_tiny_fonts_item );
+ customizeJMenuItem( _tiny_fonts_item );
+ customizeJMenuItem( _small_fonts_item );
+ customizeJMenuItem( _medium_fonts_item );
+ customizeJMenuItem( _large_fonts_item );
+ _jmenubar.add( _font_size_menu );
+ }
+
+ void buildHelpMenu() {
+ _help_jmenu = createMenu( "Help", getConfiguration() );
+ _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
+ _help_jmenu.addSeparator();
+ _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
+ _help_jmenu.add( _aptxjs_website_item = new JMenuItem( "NEW! Archaeopteryx online version: Archaeopteryx.js" ) );
+ _help_jmenu.add( _mailing_list_item = new JMenuItem( "Mailing List" ) );
+ _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
+ _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
+ _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
+ _help_jmenu.addSeparator();
+ _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
+ customizeJMenuItem( _help_item );
+ customizeJMenuItem( _website_item );
+ customizeJMenuItem( _aptxjs_website_item );
+ customizeJMenuItem( _mailing_list_item );
+ customizeJMenuItem( _phyloxml_website_item );
customizeJMenuItem( _aptx_ref_item );
customizeJMenuItem( _phyloxml_ref_item );
customizeJMenuItem( _about_item );
customizeCheckBoxMenuItem( _convex_type_cbmi, false );
customizeCheckBoxMenuItem( _unrooted_type_cbmi, false );
customizeCheckBoxMenuItem( _circular_type_cbmi, false );
+ _triangular_type_cbmi.setToolTipText( "not suitable for phylograms" );
+ _curved_type_cbmi.setToolTipText( "not suitable for phylograms" );
_unrooted_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
_circular_type_cbmi.setToolTipText( MainFrame.USE_MOUSEWHEEL_SHIFT_TO_ROTATE );
initializeTypeMenu( getOptions() );
void buildViewMenu() {
_view_jmenu = createMenu( "View", getConfiguration() );
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
- _view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
- _view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
- _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
+ _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) );
+ _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) );
+ _view_jmenu.add( _view_as_nexus_item = new JMenuItem( "as Nexus" ) );
customizeJMenuItem( _display_basic_information_item );
customizeJMenuItem( _view_as_NH_item );
customizeJMenuItem( _view_as_XML_item );
}
}
+ void choosePdfWidth() {
+ final String s = ( String ) JOptionPane.showInputDialog( getThisFrame(),
+ "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 close() {
removeAllTextFrames();
if ( _mainpanel != null ) {
void colorRank() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
- final String[] ranks = AptxUtil.getAllPossibleRanks();
- final String rank = ( String ) JOptionPane
- .showInputDialog( this,
+ final Map<String, Integer> present_ranks = AptxUtil.getRankCounts( _mainpanel.getCurrentTreePanel().getPhylogeny());
+ final String[] ranks = AptxUtil.getAllPossibleRanks(present_ranks);
+ String rank = ( String ) JOptionPane
+ .showInputDialog( getThisFrame(),
"What rank should the colorization be based on",
"Rank Selection",
JOptionPane.QUESTION_MESSAGE,
ranks,
null );
if ( !ForesterUtil.isEmpty( rank ) ) {
+ if ( rank.indexOf( '(' ) > 0 ) {
+ rank = rank.substring( 0, rank.indexOf( '(' ) ).trim();
+ }
_mainpanel.getCurrentTreePanel().colorRank( rank );
}
}
}
}
- void displayBasicInformation() {
+ void displayBasicInformation( final File treefile ) {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "Basic Information";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ title = title + " for \"" + _mainpanel.getCurrentPhylogeny().getName() + "\"";
}
- showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny() ), title );
+ showTextFrame( AptxUtil.createBasicInformation( _mainpanel.getCurrentPhylogeny(), treefile ), title );
}
}
catch ( final Exception ex ) {
// Do nothing.
}
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
"Error during File|Open",
JOptionPane.ERROR_MESSAGE );
}
- void exceptionOccuredDuringSaveAs( final Exception e ) {
+ void executeGSDI() {
+ if ( !isOKforSDI( false, true ) ) {
+ return;
+ }
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Gene tree is not rooted.",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDI gsdi = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
}
- catch ( final Exception ex ) {
- // Do nothing.
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Error during GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ gene_tree.setRerootable( false );
+ gene_tree.clearHashIdToNodeMap();
+ gene_tree.recalculateNumberOfExternalDescendants( true );
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + 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 );
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + 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 );
+ }
+ }
+
+ void executeGSDIR() {
+ if ( !isOKforSDI( false, false ) ) {
+ return;
+ }
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
+ if ( ( p > 0 )
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDIR gsdir = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
+ try {
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
}
- JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ e.getLocalizedMessage(),
+ "Error during GSDIR",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
+ result_gene_tree.setRerootable( false );
+ result_gene_tree.clearHashIdToNodeMap();
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + 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 );
+ }
+ else {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + 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 );
+ }
+ }
+
+ void executeLineageInference() {
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
+ return;
+ }
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "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,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Gene tree and species tree have no species in common.",
"Error during SDI",
JOptionPane.ERROR_MESSAGE );
return false;
}
else if ( gene_tree.getNumberOfExternalNodes() < 2 ) {
- JOptionPane.showMessageDialog( this,
+ JOptionPane.showMessageDialog( getThisFrame(),
"Gene tree and species tree have only one species in common.",
"Error during SDI",
JOptionPane.ERROR_MESSAGE );
}
}
+ 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();
}
return _jmenubar;
}
- void help( final Map<String, WebLink> weblinks ) {
- final StringBuilder sb = new StringBuilder();
- sb.append( "Display options\n" );
- sb.append( "-------------------\n" );
- sb.append( "Use the checkboxes to select types of information to display on the tree.\n\n" );
- sb.append( "Clickable tree nodes\n" );
- sb.append( "--------------------\n" );
- sb.append( "Tree nodes can be clicked, the action is determined by the 'click on node to' menu\n" );
- sb.append( "or by right clicking:\n" );
- sb.append( "o Display Node Data -- display information for a node\n" );
- sb.append( "o Collapse/Uncollapse -- collapse and uncollapse subtree from clicked node\n" );
- sb.append( "o Root/Reroot -- change tree root to clicked node\n" );
- sb.append( "o Sub/Super Tree -- toggle between subtree from clicked node and whole tree\n" );
- sb.append( "o Swap Descendants -- switch descendant on either side of clicked node\n" );
- sb.append( "o Colorize Subtree -- color a subtree\n" );
- sb.append( "o Open Sequence Web -- launch a web browser to display sequence information\n" );
- sb.append( "o Open Taxonomy Web -- launch a web browser to display taxonomy information\n" );
- sb.append( "- there may be additional choices depending on this particular setup\n\n" );
- sb.append( "Right clicking on a node always displays the information of a node.\n\n" );
- sb.append( "Zooming\n" );
- sb.append( "---------\n" );
- sb.append( "The mouse wheel and the plus and minus keys control zooming.\n" );
- sb.append( "Mouse wheel+Ctrl changes the text size.\n" );
- sb.append( "Mouse wheel+Shift controls zooming in vertical direction only.\n" );
- sb.append( "Use the buttons on the control panel to zoom the tree in and out, horizontally or vertically.\n" );
- sb.append( "The entire tree can be fitted into the window by clicking the \"F\" button, or by pressing F, Delete, or Home.\n" );
- sb.append( "The up, down, left, and right keys can be used to move the visible part (if zoomed in).\n" );
- sb.append( "Up, down, left, and right+Shift can be used to control zooming horizontally and vertically.\n" );
- sb.append( "Plus and minus keys+Ctrl change the text size; F+Ctrl, Delete+Ctrl, or Home+Ctrl resets it.\n\n" );
- sb.append( "Quick tree manipulation:\n" );
- sb.append( "------------------------\n" );
- sb.append( "Order Subtrees -- order the tree by branch length\n" );
- sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
- sb.append( "Memory problems (Java heap space error)\n" );
- sb.append( "---------------------------------------\n" );
- sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
- sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
- sb.append( "the '-Xmx' Java command line option. For example:\n" );
- sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
- if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
- sb.append( "Active web links\n" );
- sb.append( "--------------------\n" );
- for( final String key : weblinks.keySet() ) {
- sb.append( " " + weblinks.get( key ).toString() + "\n" );
- }
- }
- // + "General remarks\n"
- // + "---------------\n"
- // +
- // "o The application version permits copying to the clipboard \n"
- // +
- // " in the \"View\"|\"View as ...\" frame (either by control-c or button press).\n"
- // +
- // "o Changes made to a subtree affect this subtree and its subtrees,\n"
- // + " but not any of its parent tree(s).\n"
- // +
- // "o Archaeopteryx tries to detect whether the numerical values in a NH tree\n"
- // +
- // " are likely to be bootstrap values instead of branch length values.\n\n"
- // +
- // " Remarks regarding SDI (Speciation Duplication Inference):\n"
- // +
- // "o Each external node of the gene tree (in display) needs to be associated with\n"
- // +
- // " a species: either directly through the \"Species\" field, or the species\n"
- // +
- // " is part of the sequence name in the form \"XXXX_SPECIES\"\n"
- // +
- // " (e.g. \"ACON_DROME\" or \"ACON_DROME/123-4489\" which is also acceptable).\n"
- // +
- // "o A species tree for each species of the gene tree needs to be loaded with\n"
- // +
- // " \"SDI\"|\"Load species tree\" prior the SDI execution.\n"
- // +
- // "o !External nodes of the gene tree associated with species not present in\n"
- // +
- // " the species tree are REMOVED prior to SDI execution!\n"
- // +
- // "o Both the gene tree and the species tree must be completely binary.\n"
- // +
- // "o Duplications and speciations are a function of the position of the root.\n"
- // +
- // " Hence, after each manual \"Root/Reroot\"ing some duplications will be\n"
- // + " incorrect and need to be inferred again\n"
- // +
- // " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
- sb.append( "\n" );
- sb.append( "phyloXML\n" );
- sb.append( "-------------------\n" );
- sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
- sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
- sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
- sb.append( "\n" );
- sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
- sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
- TextFrame.instantiate( sb.toString(), "Help", _textframes );
+ final Phylogeny getSpeciesTree() {
+ return _species_tree;
}
void initializeTypeMenu( final Options options ) {
}
}
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ return false;
+ }
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "No species tree loaded",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Species tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( getThisFrame(),
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else {
+ return true;
+ }
+ }
+
boolean isSubtreeDisplayed() {
if ( getCurrentTreePanel() != null ) {
if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
JOptionPane
- .showMessageDialog( this,
+ .showMessageDialog( getThisFrame(),
"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 );
}
}
- abstract void readPhylogeniesFromURL();
-
void readPhylogeniesFromWebservice( final int i ) {
final UrlTreeReader reader = new UrlTreeReader( this, i );
new Thread( reader ).start();
_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;
}
}
}
+ final void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
+
void setTypeMenuToAllUnselected() {
_convex_type_cbmi.setSelected( false );
_curved_type_cbmi.setSelected( false );
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
&& _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() );
options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
&& _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _show_default_node_shapes_internal_cbmi.isSelected() );
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
&& _show_default_node_shapes_external_cbmi.isSelected() );
- options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
- && _taxonomy_colorize_node_shapes_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );
}
- else if ( ( _uniform_cladograms_rbmi != null ) && ( _uniform_cladograms_rbmi.isSelected() ) ) {
- options.setCladogramType( CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
- }
else if ( ( _ext_node_dependent_cladogram_rbmi != null ) && ( _ext_node_dependent_cladogram_rbmi.isSelected() ) ) {
- options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
+ options.setCladogramType( CLADOGRAM_TYPE.LINED_UP );
}
options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )
&& _search_case_senstive_cbmi.isSelected() );
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )
&& _show_confidence_stddev_cbmi.isSelected() );
- if ( ( _show_branch_length_values_cbmi != null ) && _show_branch_length_values_cbmi.isEnabled() ) {
- options.setShowBranchLengthValues( _show_branch_length_values_cbmi.isSelected() );
+ 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() ) );
- options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );
options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );
if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )
&& _use_brackets_for_conf_in_nh_export_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() );
- if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE );
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
}
- else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ }
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
}
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
&& _replace_underscores_cbmi.isSelected() );
+ options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
&& _search_whole_words_only_cbmi.isSelected() );
+ options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )
&& _inverse_search_result_cbmi.isSelected() );
if ( _graphics_export_visible_only_cbmi != null ) {
- options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
- if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {
- _graphics_export_using_actual_size_cbmi.setSelected( true );
- _graphics_export_using_actual_size_cbmi.setEnabled( false );
- }
- else {
- _graphics_export_using_actual_size_cbmi.setEnabled( true );
- }
+ options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );
}
if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
else if ( ( _circular_type_cbmi != null ) && _circular_type_cbmi.isSelected() ) {
options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
}
+ if ( ( _right_line_up_domains_cbmi != null ) && _right_line_up_domains_cbmi.isEnabled() ) {
+ options.setRightLineUpDomains( _right_line_up_domains_cbmi.isSelected() );
+ }
+ if ( ( _line_up_renderable_data_cbmi != null ) && _line_up_renderable_data_cbmi.isEnabled() ) {
+ options.setLineUpRendarableNodeData( _line_up_renderable_data_cbmi.isSelected() );
+ }
+ if ( ( _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() );
+ }
+ if ( ( _parse_beast_style_extended_nexus_tags_cbmi != null ) && _parse_beast_style_extended_nexus_tags_cbmi.isEnabled() ) {
+ options.setParseBeastStyleExtendedNexusTags(_parse_beast_style_extended_nexus_tags_cbmi.isSelected() );
+ }
+ if ( ( _collapsed_with_average_height_cbmi != null ) && _collapsed_with_average_height_cbmi.isEnabled() ) {
+ options.setCollapsedWithAverageHeigh(_collapsed_with_average_height_cbmi.isSelected() );
+ }
+ if ( ( _show_abbreviated_labels_for_collapsed_nodes_cbmi != null ) && _show_abbreviated_labels_for_collapsed_nodes_cbmi.isEnabled() ) {
+ options.setShowAbbreviatedLabelsForCollapsedNodes(_show_abbreviated_labels_for_collapsed_nodes_cbmi.isSelected() );
+ }
+
}
void updateTypeCheckboxes( final Options options, final Object o ) {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "Nexus";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( _mainpanel.getCurrentPhylogeny().toNexus( getOptions().getNhConversionSupportValueStyle() ),
title );
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "New Hampshire";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
- showTextFrame( _mainpanel.getCurrentPhylogeny()
- .toNewHampshire( false, getOptions().getNhConversionSupportValueStyle() ),
+ showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()
+ .getNhConversionSupportValueStyle() ),
title );
}
}
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "phyloXML";
if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
+ title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;
}
showTextFrame( _mainpanel.getCurrentPhylogeny().toPhyloXML( 0 ), title );
}
}
- private void annotateSequences() {
- if ( getCurrentTreePanel() != null ) {
- final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
- 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 Long id : nodes ) {
- final PhylogenyNode n = phy.getNode( id );
- 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() );
+ 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) 2013 Christian M. Zmasek\n" );
+ void about() {
+ 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" );
+
+ if ( _configuration.isCouldReadConfigFile() ) {
+ about.append( "Using configuration file: " + _configuration.config_filename + "\n" );
+ }
+ else {
+ about.append( "Not using a configuration file\n" );
+ }
+
about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
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( "Comments: " + Constants.AUTHOR_EMAIL );
- JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );
+ about.append( AptxConstants.APTX_WEB_SITE + "\n" );
+ about.append( "Documentation:\n" );
+ 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 ) {
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 );
}
}
- 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 );
}
}
+ 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;
+ }
+ 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 ) {
+
+ String pdf_written_to = "";
+ boolean error = false;
+ try {
+ if ( opts.isPrintUsingActualSize() ) {
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, tp, tp.getWidth() , tp.getHeight() );
+ }
+ else {
+ // Never false.
+ }
+ }
+ 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: "
static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {
if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {
- mi.setText( "Select Colors... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() + ")" );
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()
+ + ")" );
}
else {
- mi.setText( "Select Colors..." );
+ mi.setText( "Select Color Scheme..." );
}
}
static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {
- mi.setText( "Select Font... (current: " + font_desc + ")" );
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );
+ }
+
+ 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 ) {
mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );
}
- static void updateOptionsMenuDependingOnPhylogenyType( final MainPanel main_panel,
- final JCheckBoxMenuItem scale,
- final JCheckBoxMenuItem branch_lengths,
- final JRadioButtonMenuItem non_lined_up,
- final JRadioButtonMenuItem uniform_clado,
- final JRadioButtonMenuItem nonuniform_clado,
- final JCheckBoxMenuItem label_direction_cbmi ) {
- final TreePanel tree_panel = main_panel.getCurrentTreePanel();
- final ControlPanel control = main_panel.getControlPanel();
- final Options options = main_panel.getOptions();
- scale.setSelected( options.isShowScale() );
- branch_lengths.setSelected( options.isShowBranchLengthValues() );
- // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
- if ( ( tree_panel != null ) && ( !tree_panel.isPhyHasBranchLengths() ) ) {
- scale.setSelected( false );
- scale.setEnabled( false );
- branch_lengths.setSelected( false );
- branch_lengths.setEnabled( false );
- }
- else if ( ( tree_panel != null ) && !control.isDrawPhylogram() ) {
- scale.setSelected( false );
- scale.setEnabled( false );
- branch_lengths.setEnabled( true );
+ static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
+ for( final TreePanel tree_panel : treepanels ) {
+ tree_panel.setTextAntialias();
}
- else {
- scale.setEnabled( true );
- branch_lengths.setEnabled( true );
+ }
+
+ 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 );
}
- if ( ( tree_panel != null )
- && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
- && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
- .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
- branch_lengths.setSelected( false );
- branch_lengths.setEnabled( false );
+ catch ( final Exception e ) {
+ exception = true;
+ exceptionOccuredDuringSaveAs( e, tp, tp );
}
- if ( tree_panel != null ) {
- if ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR )
- || ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
- non_lined_up.setEnabled( false );
- uniform_clado.setEnabled( false );
- nonuniform_clado.setEnabled( false );
+ 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 {
- non_lined_up.setEnabled( true );
- uniform_clado.setEnabled( true );
- nonuniform_clado.setEnabled( true );
+ 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 {
- if ( ( tree_panel != null )
- && ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) && ( tree_panel
- .getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) ) ) {
- branch_lengths.setSelected( false );
- branch_lengths.setEnabled( false );
+ 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 );
}
- if ( ( tree_panel != null )
- && ( ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) || ( tree_panel
- .getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) ) {
- non_lined_up.setEnabled( false );
+ 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 {
- // non_lined_up.setSelected( options.isNonLinedUpCladogram() );
- non_lined_up.setEnabled( true );
+ 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 );
}
}
- label_direction_cbmi.setEnabled( true );
- if ( tree_panel != null ) {
- if ( ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
- && ( tree_panel.getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
- label_direction_cbmi.setEnabled( 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 ( tree_panel.getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
- scale.setSelected( false );
- scale.setEnabled( false );
+ 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;
}
+
- static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {
- for( final TreePanel tree_panel : treepanels ) {
- tree_panel.setTextAntialias();
- }
+}
+
+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
git://source.jalview.org / jalview.git / blobdiff