import javax.swing.JRadioButtonMenuItem;\r
import javax.swing.JTextField;\r
import javax.swing.SwingUtilities;\r
+import javax.swing.filechooser.FileFilter;\r
\r
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;\r
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;\r
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;\r
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;\r
import org.forester.archaeopteryx.tools.InferenceManager;\r
import org.forester.archaeopteryx.tools.ProcessPool;\r
import org.forester.archaeopteryx.tools.ProcessRunning;\r
-import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;\r
-import org.forester.archaeopteryx.webservices.WebservicesManager;\r
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;\r
+import org.forester.io.writers.PhylogenyWriter;\r
import org.forester.phylogeny.Phylogeny;\r
import org.forester.phylogeny.PhylogenyMethods;\r
import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;\r
import org.forester.util.ForesterUtil;\r
import org.forester.util.WindowsUtils;\r
\r
+class DefaultFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )\r
+ || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )\r
+ || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )\r
+ || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )\r
+ || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )\r
+ || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )\r
+ || file_name.endsWith( ".con" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";\r
+ }\r
+}\r
+\r
+class GraphicsFileFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )\r
+ || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();\r
+ }\r
+\r
+ @Override\r
+ public String getDescription() {\r
+ return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";\r
+ }\r
+}\r
+\r
public abstract class MainFrame extends JFrame implements ActionListener {\r
\r
- static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
- static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME\r
- static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;\r
- private static final long serialVersionUID = 3655000897845508358L;\r
- final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),\r
- Font.PLAIN,\r
- 10 );\r
- static final String TYPE_MENU_HEADER = "Type";\r
- static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";\r
- static final String EURO_TYPE_CBMI_LABEL = "Euro Type";\r
- static final String CURVED_TYPE_CBMI_LABEL = "Curved";\r
- static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";\r
- static final String CONVEX_TYPE_CBMI_LABEL = "Convex";\r
- static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";\r
- static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO\r
- static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO\r
- static final String OPTIONS_HEADER = "Options";\r
- static final String SEARCH_SUBHEADER = "Search:";\r
- static final String DISPLAY_SUBHEADER = "Display:";\r
- static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";\r
- static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";\r
- static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";\r
- static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";\r
- static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";\r
- static final String DISPLAY_SCALE_LABEL = "Scale";\r
- static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";\r
- static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";\r
- static final String LABEL_DIRECTION_LABEL = "Radial Labels";\r
- static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";\r
- 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.";\r
- static final String SCREEN_ANTIALIAS_LABEL = "Antialias";\r
- static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";\r
- static final String BG_GRAD_LABEL = "Background Color Gradient";\r
- static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";\r
- static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";\r
- static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";\r
- static final String SHOW_OVERVIEW_LABEL = "Overview";\r
- static final String FONT_SIZE_MENU_LABEL = "Font Size";\r
- static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";\r
- static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";\r
- static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";\r
- 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";\r
- static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";\r
- static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";\r
- static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";\r
- static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";\r
- static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";\r
- static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";\r
- static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";\r
- static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
- static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";\r
- static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\r
- static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";\r
- JMenuBar _jmenubar;\r
- JMenu _file_jmenu;\r
- JMenu _tools_menu;\r
- JMenu _view_jmenu;\r
- JMenu _options_jmenu;\r
- JMenu _font_size_menu;\r
- JMenu _help_jmenu;\r
- JMenuItem[] _load_phylogeny_from_webservice_menu_items;\r
+ /**\r
+ * Display the about box.\r
+ */\r
+ static void about() {\r
+ final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
+ about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
+ about.append( "All Rights Reserved\n" );\r
+ about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
+ about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
+ about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
+ about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
+ about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
+ if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
+ about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
+ && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
+ about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
+ + ForesterUtil.OS_VERSION + "]\n" );\r
+ }\r
+ final Runtime rt = java.lang.Runtime.getRuntime();\r
+ final long free_memory = rt.freeMemory() / 1000000;\r
+ final long total_memory = rt.totalMemory() / 1000000;\r
+ about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
+ about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
+ about.append( "References:\n" );\r
+ about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
+ about.append( "For more information & download:\n" );\r
+ about.append( Constants.APTX_WEB_SITE + "\n" );\r
+ about.append( "Documentation:\n" );\r
+ about.append( Constants.APTX_DOC_SITE + "\n" );\r
+ about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
+ JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
+ }\r
+\r
+ static void chooseNodeSize( final Options options, final Component parent ) {\r
+ final String s = ( String ) JOptionPane.showInputDialog( parent,\r
+ "Please enter the default size for node shapes.\n"\r
+ + "[current value: "\r
+ + options.getDefaultNodeShapeSize() + "]\n",\r
+ "Node Shape Size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ options.getDefaultNodeShapeSize() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ final short size = ForesterUtil.roundToShort( m );\r
+ if ( size >= 0.0 ) {\r
+ options.setDefaultNodeShapeSize( size );\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
+ return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
+ }\r
+\r
+ static JMenu createMenu( final String title, final Configuration conf ) {\r
+ final JMenu jmenu = new JMenu( title );\r
+ if ( !conf.isUseNativeUI() ) {\r
+ jmenu.setFont( MainFrame.menu_font );\r
+ jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
+ jmenu.setForeground( conf.getGuiMenuTextColor() );\r
+ }\r
+ return jmenu;\r
+ }\r
+\r
+ static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
+ label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
+ if ( !configuration.isUseNativeUI() ) {\r
+ label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
+ label.setForeground( configuration.getGuiMenuTextColor() );\r
+ label.setOpaque( true );\r
+ }\r
+ label.setSelected( false );\r
+ label.setEnabled( false );\r
+ return label;\r
+ }\r
+\r
+ private static void cycleNodeDataReturn( final Options op, final Configuration conf ) {\r
+ switch ( op.getExtDescNodeDataToReturn() ) {\r
+ case UNKNOWN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
+ break;\r
+ case DOMAINS_ALL:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
+ break;\r
+ case DOMAINS_COLLAPSED_PER_PROTEIN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
+ break;\r
+ case SEQ_ANNOTATIONS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
+ break;\r
+ case GO_TERM_IDS:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
+ break;\r
+ case SEQUENCE_MOL_SEQ_FASTA:\r
+ if ( ( conf != null ) && ( conf.getExtDescNodeDataToReturn() != null )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS )\r
+ && ( conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA ) ) {\r
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
+ }\r
+ else {\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ break;\r
+ default:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ }\r
+\r
+ static void cycleNodeFill( final Options op ) {\r
+ switch ( op.getDefaultNodeFill() ) {\r
+ case GRADIENT:\r
+ op.setDefaultNodeFill( NodeFill.SOLID );\r
+ break;\r
+ case NONE:\r
+ op.setDefaultNodeFill( NodeFill.GRADIENT );\r
+ break;\r
+ case SOLID:\r
+ op.setDefaultNodeFill( NodeFill.NONE );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
+ }\r
+ }\r
+\r
+ static void cycleNodeShape( final Options op ) {\r
+ switch ( op.getDefaultNodeShape() ) {\r
+ case CIRCLE:\r
+ op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
+ break;\r
+ case RECTANGLE:\r
+ op.setDefaultNodeShape( NodeShape.CIRCLE );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
+ }\r
+ }\r
+\r
+ static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
+ switch ( op.getOvPlacement() ) {\r
+ case LOWER_LEFT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
+ break;\r
+ case LOWER_RIGHT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
+ break;\r
+ case UPPER_LEFT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
+ break;\r
+ case UPPER_RIGHT:\r
+ op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
+ break;\r
+ default:\r
+ throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
+ }\r
+ if ( tree_panel != null ) {\r
+ tree_panel.updateOvSettings();\r
+ }\r
+ }\r
+\r
+ static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
+ mi.setText( "Cycle Node Return Data... (current: " + options.getExtDescNodeDataToReturn().toString() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Return Data..." );\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
+ mi.setText( "Cycle Node Shape Fill Type... (current: "\r
+ + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Node Shape Fill Type..." );\r
+ }\r
+ }\r
+\r
+ static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
+ if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
+ mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Cycle Overview Placement..." );\r
+ }\r
+ }\r
+\r
+ static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
+ if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
+ mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
+ + ")" );\r
+ }\r
+ else {\r
+ mi.setText( "Select Color Scheme..." );\r
+ }\r
+ }\r
+\r
+ static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
+ mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
+ }\r
+\r
+ static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
+ + o.getPrintSizeY() + ")" );\r
+ }\r
+\r
+ static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
+ mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
+ }\r
+\r
+ static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
+ if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
+ mi.setEnabled( true );\r
+ }\r
+ else {\r
+ mi.setEnabled( false );\r
+ }\r
+ mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
+ }\r
+\r
+ static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
+ mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
+ }\r
+\r
+ static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
+ for( final TreePanel tree_panel : treepanels ) {\r
+ tree_panel.setTextAntialias();\r
+ }\r
+ }\r
+ final static NHFilter nhfilter = new NHFilter();\r
+ final static NHXFilter nhxfilter = new NHXFilter();\r
+ final static XMLFilter xmlfilter = new XMLFilter();\r
+ final static TolFilter tolfilter = new TolFilter();\r
+ final static NexusFilter nexusfilter = new NexusFilter();\r
+ final static PdfFilter pdffilter = new PdfFilter();\r
+ final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();\r
+ final static MsaFileFilter msafilter = new MsaFileFilter();\r
+ final static SequencesFileFilter seqsfilter = new SequencesFileFilter();\r
+ final static DefaultFilter defaultfilter = new DefaultFilter();\r
+ static final String USE_MOUSEWHEEL_SHIFT_TO_ROTATE = "In this display type, use mousewheel + Shift to rotate [or A and S]";\r
+ static final String PHYLOXML_REF_TOOL_TIP = Constants.PHYLOXML_REFERENCE; //TODO //FIXME\r
+ static final String APTX_REF_TOOL_TIP = Constants.APTX_REFERENCE;\r
+ private static final long serialVersionUID = 3655000897845508358L;\r
+ final static Font menu_font = new Font( Configuration.getDefaultFontFamilyName(),\r
+ Font.PLAIN,\r
+ 10 );\r
+ static final String TYPE_MENU_HEADER = "Type";\r
+ static final String RECTANGULAR_TYPE_CBMI_LABEL = "Rectangular";\r
+ static final String EURO_TYPE_CBMI_LABEL = "Euro Type";\r
+ static final String CURVED_TYPE_CBMI_LABEL = "Curved";\r
+ static final String TRIANGULAR_TYPE_CBMI_LABEL = "Triangular";\r
+ static final String CONVEX_TYPE_CBMI_LABEL = "Convex";\r
+ static final String ROUNDED_TYPE_CBMI_LABEL = "Rounded";\r
+ static final String UNROOTED_TYPE_CBMI_LABEL = "Unrooted (alpha)"; //TODO\r
+ static final String CIRCULAR_TYPE_CBMI_LABEL = "Circular (alpha)"; //TODO\r
+ static final String OPTIONS_HEADER = "Options";\r
+ static final String SEARCH_SUBHEADER = "Search:";\r
+ static final String DISPLAY_SUBHEADER = "Display:";\r
+ static final String SEARCH_TERMS_ONLY_LABEL = "Match Complete Terms Only";\r
+ static final String SEARCH_REGEX_LABEL = "Search with Regular Expressions";\r
+ static final String SEARCH_CASE_SENSITIVE_LABEL = "Case Sensitive";\r
+ static final String INVERSE_SEARCH_RESULT_LABEL = "Negate Result";\r
+ static final String COLOR_BY_TAXONOMIC_GROUP = "Colorize by Taxonomic Group";\r
+ static final String DISPLAY_SCALE_LABEL = "Scale";\r
+ static final String NON_LINED_UP_CLADOGRAMS_LABEL = "Non-Lined Up Cladograms";\r
+ static final String UNIFORM_CLADOGRAMS_LABEL = "Total Node Sum Dependent Cladograms";\r
+ static final String LABEL_DIRECTION_LABEL = "Radial Labels";\r
+ static final String LABEL_DIRECTION_TIP = "To use radial node labels in radial and unrooted display types";\r
+ 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.";\r
+ static final String SCREEN_ANTIALIAS_LABEL = "Antialias";\r
+ static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";\r
+ static final String BG_GRAD_LABEL = "Background Color Gradient";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Shapes for External Nodes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Shapes for Internal Nodes";\r
+ static final String DISPLAY_NODE_BOXES_LABEL_MARKED = "Shapes for Nodes with Visual Data";\r
+ static final String SHOW_OVERVIEW_LABEL = "Overview";\r
+ static final String FONT_SIZE_MENU_LABEL = "Font Size";\r
+ static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";\r
+ static final String SHOW_DOMAIN_LABELS_LABEL = "Domain Labels";\r
+ static final String SHOW_ANN_REF_SOURCE_LABEL = "Seq Annotation Ref Sources";\r
+ 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";\r
+ static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";\r
+ static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";\r
+ static final String CYCLE_NODE_SHAPE_LABEL = "Cycle Node Shapes";\r
+ static final String CYCLE_NODE_FILL_LABEL = "Cycle Node Fill Type";\r
+ static final String CHOOSE_NODE_SIZE_LABEL = "Choose Node Shape Size";\r
+ static final String SHOW_CONF_STDDEV_LABEL = "Confidence Standard Deviations";\r
+ static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";\r
+ static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";\r
+ static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Basic Tree Information";\r
+ static final String RIGHT_LINE_UP_DOMAINS = "Right-align Domain Architectures";\r
+ static final String LINE_UP_RENDERABLE_DATA = "Line Up Diagrams (such as Domain Architectures)";\r
+ JMenuBar _jmenubar;\r
+ JMenu _file_jmenu;\r
+ JMenu _tools_menu;\r
+ JMenu _view_jmenu;\r
+ JMenu _options_jmenu;\r
+ JMenu _font_size_menu;\r
+ JMenu _help_jmenu;\r
+ JMenuItem[] _load_phylogeny_from_webservice_menu_items;\r
// Analysis menu\r
- JMenu _analysis_menu;\r
- JMenuItem _load_species_tree_item;\r
- JMenuItem _gsdi_item;\r
- JMenuItem _gsdir_item;\r
- JMenuItem _lineage_inference;\r
+ JMenu _analysis_menu;\r
+ JMenuItem _load_species_tree_item;\r
+ JMenuItem _gsdi_item;\r
+ JMenuItem _gsdir_item;\r
+ JMenuItem _lineage_inference;\r
// file menu:\r
- JMenuItem _open_item;\r
- JMenuItem _open_url_item;\r
- JMenuItem _save_item;\r
- JMenuItem _save_all_item;\r
- JMenuItem _close_item;\r
- JMenuItem _exit_item;\r
- JMenuItem _new_item;\r
- JMenuItem _print_item;\r
+ JMenuItem _open_item;\r
+ JMenuItem _open_url_item;\r
+ JMenuItem _save_item;\r
+ JMenuItem _save_all_item;\r
+ JMenuItem _close_item;\r
+ JMenuItem _exit_item;\r
+ JMenuItem _new_item;\r
+ JMenuItem _print_item;\r
JMenuItem _write_to_pdf_item;\r
JMenuItem _write_to_jpg_item;\r
JMenuItem _write_to_gif_item;\r
JMenuItem _write_to_tif_item;\r
- JMenuItem _write_to_png_item;\r
+ JMenuItem _write_to_png_item;\r
JMenuItem _write_to_bmp_item;\r
// tools menu:\r
- JMenuItem _midpoint_root_item;\r
- JMenuItem _taxcolor_item;\r
- JMenuItem _confcolor_item;\r
- JMenuItem _color_rank_jmi;\r
- JMenuItem _collapse_species_specific_subtrees;\r
- JMenuItem _obtain_detailed_taxonomic_information_jmi;\r
- JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;\r
- JMenuItem _obtain_seq_information_jmi;\r
- JMenuItem _move_node_names_to_tax_sn_jmi;\r
- JMenuItem _move_node_names_to_seq_names_jmi;\r
- JMenuItem _extract_tax_code_from_node_names_jmi;\r
- JMenuItem _annotate_item;\r
- JMenuItem _remove_branch_color_item;\r
- JMenuItem _remove_visual_styles_item;\r
- JMenuItem _delete_selected_nodes_item;\r
- JMenuItem _delete_not_selected_nodes_item;\r
+ JMenuItem _midpoint_root_item;\r
+ JMenuItem _taxcolor_item;\r
+ JMenuItem _confcolor_item;\r
+ JMenuItem _color_rank_jmi;\r
+ JMenuItem _collapse_species_specific_subtrees;\r
+ JMenuItem _obtain_detailed_taxonomic_information_jmi;\r
+ JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;\r
+ JMenuItem _obtain_seq_information_jmi;\r
+ JMenuItem _move_node_names_to_tax_sn_jmi;\r
+ JMenuItem _move_node_names_to_seq_names_jmi;\r
+ JMenuItem _extract_tax_code_from_node_names_jmi;\r
+ JMenuItem _annotate_item;\r
+ JMenuItem _remove_branch_color_item;\r
+ JMenuItem _remove_visual_styles_item;\r
+ JMenuItem _delete_selected_nodes_item;\r
+ JMenuItem _delete_not_selected_nodes_item;\r
// font size menu:\r
- JMenuItem _super_tiny_fonts_item;\r
- JMenuItem _tiny_fonts_item;\r
- JMenuItem _small_fonts_item;\r
- JMenuItem _medium_fonts_item;\r
- JMenuItem _large_fonts_item;\r
+ JMenuItem _super_tiny_fonts_item;\r
+ JMenuItem _tiny_fonts_item;\r
+ JMenuItem _small_fonts_item;\r
+ JMenuItem _medium_fonts_item;\r
+ JMenuItem _large_fonts_item;\r
// options menu:\r
// _ screen and print\r
- JMenuItem _choose_font_mi;\r
- JMenuItem _switch_colors_mi;\r
- JCheckBoxMenuItem _label_direction_cbmi;\r
+ JMenuItem _choose_font_mi;\r
+ JMenuItem _switch_colors_mi;\r
+ JCheckBoxMenuItem _label_direction_cbmi;\r
// _ screen display\r
- JCheckBoxMenuItem _screen_antialias_cbmi;\r
- JCheckBoxMenuItem _background_gradient_cbmi;\r
- JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;\r
- JRadioButtonMenuItem _uniform_cladograms_rbmi;\r
- JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;\r
- JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;\r
- JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me\r
- JCheckBoxMenuItem _show_overview_cbmi;\r
- JCheckBoxMenuItem _show_domain_labels;\r
- JCheckBoxMenuItem _show_annotation_ref_source;\r
- JCheckBoxMenuItem _abbreviate_scientific_names;\r
- JCheckBoxMenuItem _color_labels_same_as_parent_branch;\r
- JMenuItem _overview_placment_mi;\r
- JMenuItem _choose_minimal_confidence_mi;\r
- JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;\r
- JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;\r
- JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;\r
- JMenuItem _cycle_node_shape_mi;\r
- JMenuItem _cycle_node_fill_mi;\r
- JMenuItem _choose_node_size_mi;\r
- JMenuItem _cycle_data_return;\r
- JCheckBoxMenuItem _show_confidence_stddev_cbmi;\r
- JCheckBoxMenuItem _right_line_up_domains_cbmi;\r
- JCheckBoxMenuItem _line_up_renderable_data_cbmi;\r
+ JCheckBoxMenuItem _screen_antialias_cbmi;\r
+ JCheckBoxMenuItem _background_gradient_cbmi;\r
+ JRadioButtonMenuItem _non_lined_up_cladograms_rbmi;\r
+ JRadioButtonMenuItem _uniform_cladograms_rbmi;\r
+ JRadioButtonMenuItem _ext_node_dependent_cladogram_rbmi;\r
+ JCheckBoxMenuItem _color_by_taxonomic_group_cbmi;\r
+ JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me\r
+ JCheckBoxMenuItem _show_overview_cbmi;\r
+ JCheckBoxMenuItem _show_domain_labels;\r
+ JCheckBoxMenuItem _show_annotation_ref_source;\r
+ JCheckBoxMenuItem _abbreviate_scientific_names;\r
+ JCheckBoxMenuItem _color_labels_same_as_parent_branch;\r
+ JMenuItem _overview_placment_mi;\r
+ JMenuItem _choose_minimal_confidence_mi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;\r
+ JCheckBoxMenuItem _show_default_node_shapes_for_marked_cbmi;\r
+ JMenuItem _cycle_node_shape_mi;\r
+ JMenuItem _cycle_node_fill_mi;\r
+ JMenuItem _choose_node_size_mi;\r
+ JMenuItem _cycle_data_return;\r
+ JCheckBoxMenuItem _show_confidence_stddev_cbmi;\r
+ JCheckBoxMenuItem _right_line_up_domains_cbmi;\r
+ JCheckBoxMenuItem _line_up_renderable_data_cbmi;\r
// _ print\r
- JCheckBoxMenuItem _graphics_export_visible_only_cbmi;\r
- JCheckBoxMenuItem _antialias_print_cbmi;\r
- JCheckBoxMenuItem _print_black_and_white_cbmi;\r
- JCheckBoxMenuItem _print_using_actual_size_cbmi;\r
- JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;\r
- JMenuItem _print_size_mi;\r
- JMenuItem _choose_pdf_width_mi;\r
+ JCheckBoxMenuItem _graphics_export_visible_only_cbmi;\r
+ JCheckBoxMenuItem _antialias_print_cbmi;\r
+ JCheckBoxMenuItem _print_black_and_white_cbmi;\r
+ JCheckBoxMenuItem _print_using_actual_size_cbmi;\r
+ JCheckBoxMenuItem _graphics_export_using_actual_size_cbmi;\r
+ JMenuItem _print_size_mi;\r
+ JMenuItem _choose_pdf_width_mi;\r
// _ parsing\r
- JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;\r
- JRadioButtonMenuItem _extract_taxonomy_no_rbmi;\r
- JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;\r
- JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;\r
- JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;\r
- JCheckBoxMenuItem _replace_underscores_cbmi;\r
- JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;\r
- JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;\r
- JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;\r
+ JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_no_rbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;\r
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;\r
+ JCheckBoxMenuItem _replace_underscores_cbmi;\r
+ JCheckBoxMenuItem _allow_errors_in_distance_to_parent_cbmi;\r
+ JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;\r
+ JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;\r
// _ search\r
- JCheckBoxMenuItem _search_case_senstive_cbmi;\r
- JCheckBoxMenuItem _search_whole_words_only_cbmi;\r
- JCheckBoxMenuItem _inverse_search_result_cbmi;\r
- JCheckBoxMenuItem _search_with_regex_cbmi;\r
+ JCheckBoxMenuItem _search_case_senstive_cbmi;\r
+ JCheckBoxMenuItem _search_whole_words_only_cbmi;\r
+ JCheckBoxMenuItem _inverse_search_result_cbmi;\r
+ JCheckBoxMenuItem _search_with_regex_cbmi;\r
// type menu:\r
- JMenu _type_menu;\r
- JCheckBoxMenuItem _rectangular_type_cbmi;\r
- JCheckBoxMenuItem _triangular_type_cbmi;\r
- JCheckBoxMenuItem _curved_type_cbmi;\r
- JCheckBoxMenuItem _convex_type_cbmi;\r
- JCheckBoxMenuItem _euro_type_cbmi;\r
- JCheckBoxMenuItem _rounded_type_cbmi;\r
- JCheckBoxMenuItem _unrooted_type_cbmi;\r
- JCheckBoxMenuItem _circular_type_cbmi;\r
+ JMenu _type_menu;\r
+ JCheckBoxMenuItem _rectangular_type_cbmi;\r
+ JCheckBoxMenuItem _triangular_type_cbmi;\r
+ JCheckBoxMenuItem _curved_type_cbmi;\r
+ JCheckBoxMenuItem _convex_type_cbmi;\r
+ JCheckBoxMenuItem _euro_type_cbmi;\r
+ JCheckBoxMenuItem _rounded_type_cbmi; ;\r
+ JCheckBoxMenuItem _unrooted_type_cbmi;\r
+ JCheckBoxMenuItem _circular_type_cbmi;\r
// view as text menu:\r
- JMenuItem _view_as_NH_item;\r
- JMenuItem _view_as_XML_item;\r
- JMenuItem _view_as_nexus_item;\r
- JMenuItem _display_basic_information_item;\r
+ JMenuItem _view_as_NH_item;\r
+ JMenuItem _view_as_XML_item;\r
+ JMenuItem _view_as_nexus_item;\r
+ JMenuItem _display_basic_information_item;\r
// help menu:\r
- JMenuItem _about_item;\r
- JMenuItem _help_item;\r
- JMenuItem _website_item;\r
- JMenuItem _phyloxml_website_item;\r
- JMenuItem _phyloxml_ref_item;\r
- JMenuItem _aptx_ref_item;\r
+ JMenuItem _about_item;\r
+ JMenuItem _help_item;\r
+ JMenuItem _website_item;\r
+ JMenuItem _phyloxml_website_item;\r
+ JMenuItem _phyloxml_ref_item;\r
+ JMenuItem _aptx_ref_item;\r
//\r
- JFileChooser _writetopdf_filechooser;\r
+ JFileChooser _writetopdf_filechooser;\r
File _current_dir;\r
- \r
+ JFileChooser _save_filechooser;\r
+ JFileChooser _writetographics_filechooser;\r
// process menu:\r
- JMenu _process_menu;\r
+ JMenu _process_menu;\r
// Handy pointers to child components:\r
- MainPanel _mainpanel;\r
- Container _contentpane;\r
- final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>(); ;\r
- Configuration _configuration;\r
- Options _options;\r
- private Phylogeny _species_tree;\r
- InferenceManager _inference_manager;\r
- final ProcessPool _process_pool;\r
- private String _previous_node_annotation_ref;\r
+ MainPanel _mainpanel;\r
+ Container _contentpane;\r
+ final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();\r
+ Configuration _configuration;\r
+ Options _options;\r
+ private Phylogeny _species_tree;\r
+ InferenceManager _inference_manager;\r
+ final ProcessPool _process_pool;\r
+ private String _previous_node_annotation_ref;\r
\r
MainFrame() {\r
_process_pool = ProcessPool.createInstance();\r
_writetopdf_filechooser = new JFileChooser();\r
+ _save_filechooser = new JFileChooser();\r
+ _save_filechooser.setCurrentDirectory( new File( "." ) );\r
+ _save_filechooser.setMultiSelectionEnabled( false );\r
+ _save_filechooser.setFileFilter( MainFrame.xmlfilter );\r
+ _save_filechooser.addChoosableFileFilter( nhfilter );\r
+ _save_filechooser.addChoosableFileFilter( nexusfilter );\r
+ _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );\r
+ _writetographics_filechooser = new JFileChooser();\r
+ _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );\r
}\r
\r
/**\r
}\r
else if ( o == _phyloxml_ref_item ) {\r
try {\r
- AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
- }\r
- catch ( final IOException e1 ) {\r
- ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
- }\r
- }\r
- else if ( o == _write_to_pdf_item ) {\r
- writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
- }\r
- else {\r
- if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
- for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
- if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
- readPhylogeniesFromWebservice( i );\r
- }\r
- }\r
- }\r
- }\r
- _contentpane.repaint();\r
- }\r
-\r
- \r
- void setCurrentDir( final File current_dir ) {\r
- _current_dir = current_dir;\r
- } \r
- \r
- void writeToPdf( final Phylogeny t ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return;\r
- }\r
- String initial_filename = "";\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + ".pdf";\r
- _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
- File file = _writetopdf_filechooser.getSelectedFile();\r
- setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
- file = new File( file.toString() + ".pdf" );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "WARNING",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
+ AptxUtil.openWebsite( Constants.PHYLOXML_REFERENCE_URL, is_applet, applet );\r
+ }\r
+ catch ( final IOException e1 ) {\r
+ ForesterUtil.printErrorMessage( Constants.PRG_NAME, e1.toString() );\r
}\r
- printPhylogenyToPdf( file.toString() );\r
}\r
- }\r
-\r
- \r
- void printPhylogenyToPdf( final String file_name ) {\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getCurrentTreePanel()\r
- .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().repaint();\r
- }\r
- String pdf_written_to = "";\r
- boolean error = false;\r
- try {\r
- if ( getOptions().isPrintUsingActualSize() ) {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
- getCurrentTreePanel(),\r
- getCurrentTreePanel().getWidth(),\r
- getCurrentTreePanel().getHeight() );\r
- }\r
- else {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
- .getPrintSizeX(), getOptions().getPrintSizeY() );\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Wrote PDF to: " + pdf_written_to,\r
- "Information",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "There was an unknown problem when attempting to write to PDF file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getControlPanel().showWhole();\r
- }\r
- }\r
- \r
- ControlPanel getControlPanel() {\r
- return getMainPanel().getControlPanel();\r
- }\r
-\r
- \r
- File getCurrentDir() {\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( ForesterUtil.isWindows() ) {\r
- try {\r
- _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
- }\r
- catch ( final Exception e ) {\r
- _current_dir = null;\r
- }\r
- }\r
- }\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( System.getProperty( "user.home" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.home" ) );\r
- }\r
- else if ( System.getProperty( "user.dir" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.dir" ) );\r
- }\r
- }\r
- return _current_dir;\r
- }\r
- \r
- private void deleteSelectedNodes( final boolean delete ) {\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
- return;\r
+ else if ( o == _write_to_pdf_item ) {\r
+ writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
}\r
- final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
- for( final PhylogenyNode n : all_selected_nodes ) {\r
- if ( n.isExternal() ) {\r
- nodes.add( n );\r
- }\r
- }\r
+ else if ( o == _save_item ) {\r
+ writeToFile( _mainpanel.getCurrentPhylogeny() );\r
+ // If subtree currently displayed, save it, instead of complete\r
+ // tree.\r
}\r
- String function = "Retain";\r
- if ( delete ) {\r
- function = "Delete";\r
+ else if ( o == _write_to_png_item ) {\r
+ writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );\r
}\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
- "No external nodes selected to " + function.toLowerCase(),\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ else if ( o == _graphics_export_visible_only_cbmi ) {\r
+ updateOptions( getOptions() );\r
}\r
- final int todo = nodes.size();\r
- final int ext = phy.getNumberOfExternalNodes();\r
- int res = todo;\r
- if ( delete ) {\r
- res = ext - todo;\r
+ else if ( o == _antialias_print_cbmi ) {\r
+ updateOptions( getOptions() );\r
}\r
- if ( res < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Cannot delete all nodes",\r
- "Attempt to delete all nodes ",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ else if ( o == _print_black_and_white_cbmi ) {\r
+ updateOptions( getOptions() );\r
}\r
- final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
- + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
- + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- if ( !delete ) {\r
- final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !nodes.contains( n ) ) {\r
- to_delete.add( n );\r
+ else if ( o == _print_using_actual_size_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _graphics_export_using_actual_size_cbmi ) {\r
+ updateOptions( getOptions() );\r
+ }\r
+ else if ( o == _print_size_mi ) {\r
+ choosePrintSize();\r
+ }\r
+ else if ( o == _choose_pdf_width_mi ) {\r
+ choosePdfWidth();\r
+ }\r
+ else {\r
+ if ( _load_phylogeny_from_webservice_menu_items != null ) {\r
+ for( int i = 0; i < _load_phylogeny_from_webservice_menu_items.length; ++i ) {\r
+ if ( o == _load_phylogeny_from_webservice_menu_items[ i ] ) {\r
+ readPhylogeniesFromWebservice( i );\r
}\r
}\r
- for( final PhylogenyNode n : to_delete ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
- }\r
- else {\r
- for( final PhylogenyNode n : nodes ) {\r
- phy.deleteSubtree( n, true );\r
- }\r
}\r
- resetSearch();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().setEdited( true );\r
- repaint();\r
}\r
- }\r
-\r
- void resetSearch() {\r
- getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
- getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
- getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
- getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
- getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
- getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
- }\r
-\r
- public Configuration getConfiguration() {\r
- return _configuration;\r
- }\r
-\r
- /**\r
- * This method returns the current external node data which\r
- * has been selected by the user by clicking the "Return ..."\r
- * menu item. This method is expected to be called from Javascript or\r
- * something like it.\r
- *\r
- * @return current external node data as String\r
- */\r
- public String getCurrentExternalNodesDataBuffer() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
- }\r
-\r
- public int getCurrentExternalNodesDataBufferChangeCounter() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
- }\r
-\r
- public int getCurrentExternalNodesDataBufferLength() {\r
- return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
- }\r
-\r
- public InferenceManager getInferenceManager() {\r
- return _inference_manager;\r
- }\r
-\r
- public MainPanel getMainPanel() {\r
- return _mainpanel;\r
- }\r
-\r
- public Options getOptions() {\r
- return _options;\r
- }\r
-\r
- public ProcessPool getProcessPool() {\r
- return _process_pool;\r
- }\r
-\r
- public void showTextFrame( final String s, final String title ) {\r
- checkTextFrames();\r
- _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
- }\r
-\r
- public void showWhole() {\r
- _mainpanel.getControlPanel().showWhole();\r
- }\r
-\r
- public void updateProcessMenu() {\r
- // In general Swing is not thread safe.\r
- // See "Swing's Threading Policy".\r
- SwingUtilities.invokeLater( new Runnable() {\r
-\r
- @Override\r
- public void run() {\r
- doUpdateProcessMenu();\r
- }\r
- } );\r
+ _contentpane.repaint();\r
}\r
\r
void activateSaveAllIfNeeded() {\r
}\r
}\r
\r
-// void buildFileMenu() {\r
-// _file_jmenu = createMenu( "File", getConfiguration() );\r
-// _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
-// customizeJMenuItem( _exit_item );\r
-// _jmenubar.add( _file_jmenu );\r
-// }\r
- \r
+ private void annotateSequences() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ List<PhylogenyNode> nodes = null;\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
+ || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ }\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+ "No nodes selected for annotation",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final JTextField ref_field = new JTextField( 10 );\r
+ final JTextField desc_filed = new JTextField( 20 );\r
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
+ : getPreviousNodeAnnotationReference() );\r
+ final JPanel my_panel = new JPanel();\r
+ my_panel.add( new JLabel( "Reference " ) );\r
+ my_panel.add( ref_field );\r
+ my_panel.add( Box.createHorizontalStrut( 15 ) );\r
+ my_panel.add( new JLabel( "Description " ) );\r
+ my_panel.add( desc_filed );\r
+ final int result = JOptionPane.showConfirmDialog( null,\r
+ my_panel,\r
+ "Enter the sequence annotation(s) for the "\r
+ + nodes.size() + " selected nodes",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ String ref = ref_field.getText();\r
+ String desc = desc_filed.getText();\r
+ if ( !ForesterUtil.isEmpty( ref ) ) {\r
+ ref = ref.trim();\r
+ ref = ref.replaceAll( "\\s+", " " );\r
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
+ || ( ref.length() < 3 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Reference needs to be in the form of \"GO:1234567\"",\r
+ "Illegal Format for Annotation Reference",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ }\r
+ if ( ref != null ) {\r
+ setPreviousNodeAnnotationReference( ref );\r
+ }\r
+ if ( desc != null ) {\r
+ desc = desc.trim();\r
+ desc = desc.replaceAll( "\\s+", " " );\r
+ }\r
+ if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
+ for( final PhylogenyNode n : nodes ) {\r
+ ForesterUtil.ensurePresenceOfSequence( n );\r
+ final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
+ : new Annotation( ref );\r
+ if ( !ForesterUtil.isEmpty( desc ) ) {\r
+ ann.setDesc( desc );\r
+ }\r
+ n.getNodeData().getSequence().addAnnotation( ann );\r
+ }\r
+ }\r
+ getMainPanel().getControlPanel().showAnnotations();\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ // void buildFileMenu() {\r
+ // _file_jmenu = createMenu( "File", getConfiguration() );\r
+ // _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
+ // customizeJMenuItem( _exit_item );\r
+ // _jmenubar.add( _file_jmenu );\r
+ // }\r
void buildFileMenu() {\r
_file_jmenu = MainFrame.createMenu( "File", getConfiguration() );\r
- \r
- // _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
- // _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
- // _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
- // _save_all_item.setEnabled( false );\r
- // _file_jmenu.addSeparator();\r
+ _file_jmenu.add( _save_item = new JMenuItem( "Save Tree As..." ) );\r
+ // _file_jmenu.add( _save_all_item = new JMenuItem( "Save All Trees As..." ) );\r
+ // _save_all_item.setToolTipText( "Write all phylogenies to one file." );\r
+ // _save_all_item.setEnabled( false );\r
+ // _file_jmenu.addSeparator();\r
_file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );\r
-// if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
-// _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
-// }\r
-// _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
-// _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
-// if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
-// _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
-// }\r
-// if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
-// _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
-// }\r
- // _file_jmenu.addSeparator();\r
- // _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
+ // if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {\r
+ // _file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );\r
+ // }\r
+ _file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );\r
+ // _file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );\r
+ // if ( AptxUtil.canWriteFormat( "gif" ) ) {\r
+ // _file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );\r
+ // }\r
+ // if ( AptxUtil.canWriteFormat( "bmp" ) ) {\r
+ // _file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );\r
+ // }\r
+ // _file_jmenu.addSeparator();\r
+ // _file_jmenu.add( _print_item = new JMenuItem( "Print..." ) );\r
_file_jmenu.addSeparator();\r
-\r
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );\r
- \r
- customizeJMenuItem( _save_item );\r
-\r
-// customizeJMenuItem( _close_item );\r
- //customizeJMenuItem( _save_all_item );\r
+ customizeJMenuItem( _save_item );\r
+ // customizeJMenuItem( _close_item );\r
+ //customizeJMenuItem( _save_all_item );\r
customizeJMenuItem( _write_to_pdf_item );\r
-// customizeJMenuItem( _write_to_png_item );\r
-// customizeJMenuItem( _write_to_jpg_item );\r
-// customizeJMenuItem( _write_to_gif_item );\r
-// customizeJMenuItem( _write_to_tif_item );\r
-// customizeJMenuItem( _write_to_bmp_item );\r
-// customizeJMenuItem( _print_item );\r
+ customizeJMenuItem( _write_to_png_item );\r
+ // customizeJMenuItem( _write_to_jpg_item );\r
+ // customizeJMenuItem( _write_to_gif_item );\r
+ // customizeJMenuItem( _write_to_tif_item );\r
+ // customizeJMenuItem( _write_to_bmp_item );\r
+ // customizeJMenuItem( _print_item );\r
customizeJMenuItem( _exit_item );\r
_jmenubar.add( _file_jmenu );\r
}\r
_jmenubar.add( _view_jmenu );\r
}\r
\r
- void checkTextFrames() {\r
- if ( _textframes.size() > 5 ) {\r
- try {\r
- if ( _textframes.getFirst() != null ) {\r
- _textframes.getFirst().removeMe();\r
+ void checkTextFrames() {\r
+ if ( _textframes.size() > 5 ) {\r
+ try {\r
+ if ( _textframes.getFirst() != null ) {\r
+ _textframes.getFirst().removeMe();\r
+ }\r
+ else {\r
+ _textframes.removeFirst();\r
+ }\r
+ }\r
+ catch ( final NoSuchElementException e ) {\r
+ // Ignore.\r
+ }\r
+ }\r
+ }\r
+\r
+ private void chooseFont() {\r
+ final FontChooser fc = new FontChooser();\r
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
+ fc.showDialog( this, "Select the Base Font" );\r
+ getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
+ }\r
+\r
+ private void chooseMinimalConfidence() {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum for confidence values to be displayed.\n"\r
+ + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getMinConfidenceValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ getOptions().setMinConfidenceValue( m );\r
+ }\r
+ }\r
+ }\r
+\r
+ void choosePdfWidth() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the default line width for PDF export.\n"\r
+ + "[current value: "\r
+ + getOptions().getPrintLineWidth() + "]\n",\r
+ "Line Width for PDF Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintLineWidth() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ float f = 0.0f;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ f = Float.parseFloat( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( f > 0.0 ) ) {\r
+ getOptions().setPrintLineWidth( f );\r
+ }\r
+ }\r
+ }\r
+\r
+ void choosePrintSize() {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter values for width and height,\nseparated by a comma.\n"\r
+ + "[current values: "\r
+ + getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() + "]\n"\r
+ + "[A4: " + Constants.A4_SIZE_X + ", "\r
+ + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
+ + Constants.US_LETTER_SIZE_X + ", "\r
+ + Constants.US_LETTER_SIZE_Y + "]",\r
+ "Default Size for Graphics Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() );\r
+ if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
+ boolean success = true;\r
+ int x = 0;\r
+ int y = 0;\r
+ final String[] str_ary = s.split( "," );\r
+ if ( str_ary.length == 2 ) {\r
+ final String x_str = str_ary[ 0 ].trim();\r
+ final String y_str = str_ary[ 1 ].trim();\r
+ if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
+ try {\r
+ x = Integer.parseInt( x_str );\r
+ y = Integer.parseInt( y_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
}\r
else {\r
- _textframes.removeFirst();\r
+ success = false;\r
}\r
}\r
- catch ( final NoSuchElementException e ) {\r
- // Ignore.\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
+ getOptions().setPrintSizeX( x );\r
+ getOptions().setPrintSizeY( y );\r
}\r
}\r
}\r
}\r
}\r
\r
+ private void deleteSelectedNodes( final boolean delete ) {\r
+ final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
+ if ( ( phy == null ) || ( phy.getNumberOfExternalNodes() < 2 ) ) {\r
+ return;\r
+ }\r
+ final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();\r
+ if ( ( getCurrentTreePanel().getFoundNodes0() != null ) || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
+ final List<PhylogenyNode> all_selected_nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ for( final PhylogenyNode n : all_selected_nodes ) {\r
+ if ( n.isExternal() ) {\r
+ nodes.add( n );\r
+ }\r
+ }\r
+ }\r
+ String function = "Retain";\r
+ if ( delete ) {\r
+ function = "Delete";\r
+ }\r
+ if ( ( nodes == null ) || nodes.isEmpty() ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
+ "No external nodes selected to " + function.toLowerCase(),\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final int todo = nodes.size();\r
+ final int ext = phy.getNumberOfExternalNodes();\r
+ int res = todo;\r
+ if ( delete ) {\r
+ res = ext - todo;\r
+ }\r
+ if ( res < 1 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Cannot delete all nodes",\r
+ "Attempt to delete all nodes ",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
+ if ( result == JOptionPane.OK_OPTION ) {\r
+ if ( !delete ) {\r
+ final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !nodes.contains( n ) ) {\r
+ to_delete.add( n );\r
+ }\r
+ }\r
+ for( final PhylogenyNode n : to_delete ) {\r
+ phy.deleteSubtree( n, true );\r
+ }\r
+ }\r
+ else {\r
+ for( final PhylogenyNode n : nodes ) {\r
+ phy.deleteSubtree( n, true );\r
+ }\r
+ }\r
+ resetSearch();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().setEdited( true );\r
+ repaint();\r
+ }\r
+ }\r
+\r
void displayBasicInformation( final File treefile ) {\r
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {\r
String title = "Basic Information";\r
}\r
}\r
\r
+ private void doUpdateProcessMenu() {\r
+ if ( _process_pool.size() > 0 ) {\r
+ if ( _process_menu == null ) {\r
+ _process_menu = createMenu( "", getConfiguration() );\r
+ _process_menu.setForeground( Color.RED );\r
+ }\r
+ _process_menu.removeAll();\r
+ final String text = "processes running: " + _process_pool.size();\r
+ _process_menu.setText( text );\r
+ _jmenubar.add( _process_menu );\r
+ for( int i = 0; i < _process_pool.size(); ++i ) {\r
+ final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
+ _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
+ }\r
+ }\r
+ else {\r
+ if ( _process_menu != null ) {\r
+ _process_menu.removeAll();\r
+ _jmenubar.remove( _process_menu );\r
+ }\r
+ }\r
+ _jmenubar.validate();\r
+ _jmenubar.repaint();\r
+ repaint();\r
+ }\r
+\r
void exceptionOccuredDuringOpenFile( final Exception e ) {\r
try {\r
_mainpanel.getCurrentTreePanel().setArrowCursor();\r
}\r
}\r
\r
+ public Configuration getConfiguration() {\r
+ return _configuration;\r
+ }\r
+\r
+ ControlPanel getControlPanel() {\r
+ return getMainPanel().getControlPanel();\r
+ }\r
+\r
+ File getCurrentDir() {\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( ForesterUtil.isWindows() ) {\r
+ try {\r
+ _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ _current_dir = null;\r
+ }\r
+ }\r
+ }\r
+ if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
+ if ( System.getProperty( "user.home" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.home" ) );\r
+ }\r
+ else if ( System.getProperty( "user.dir" ) != null ) {\r
+ _current_dir = new File( System.getProperty( "user.dir" ) );\r
+ }\r
+ }\r
+ return _current_dir;\r
+ }\r
+\r
+ /**\r
+ * This method returns the current external node data which\r
+ * has been selected by the user by clicking the "Return ..."\r
+ * menu item. This method is expected to be called from Javascript or\r
+ * something like it.\r
+ *\r
+ * @return current external node data as String\r
+ */\r
+ public String getCurrentExternalNodesDataBuffer() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();\r
+ }\r
+\r
+ public int getCurrentExternalNodesDataBufferChangeCounter() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();\r
+ }\r
+\r
+ public int getCurrentExternalNodesDataBufferLength() {\r
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();\r
+ }\r
+\r
TreePanel getCurrentTreePanel() {\r
return getMainPanel().getCurrentTreePanel();\r
}\r
return _help_jmenu;\r
}\r
\r
+ public InferenceManager getInferenceManager() {\r
+ return _inference_manager;\r
+ }\r
+\r
JCheckBoxMenuItem getlabelDirectionCbmi() {\r
return _label_direction_cbmi;\r
}\r
\r
+ public MainPanel getMainPanel() {\r
+ return _mainpanel;\r
+ }\r
+\r
JMenuBar getMenuBarOfMainFrame() {\r
return _jmenubar;\r
}\r
\r
+ public Options getOptions() {\r
+ return _options;\r
+ }\r
+\r
+ private String getPreviousNodeAnnotationReference() {\r
+ return _previous_node_annotation_ref;\r
+ }\r
+\r
+ public ProcessPool getProcessPool() {\r
+ return _process_pool;\r
+ }\r
+\r
final Phylogeny getSpeciesTree() {\r
return _species_tree;\r
}\r
}\r
}\r
\r
+ void printPhylogenyToPdf( final String file_name ) {\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getCurrentTreePanel()\r
+ .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() );\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().repaint();\r
+ }\r
+ String pdf_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ if ( getOptions().isPrintUsingActualSize() ) {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
+ getCurrentTreePanel(),\r
+ getCurrentTreePanel().getWidth(),\r
+ getCurrentTreePanel().getHeight() );\r
+ }\r
+ else {\r
+ pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
+ .getPrintSizeX(), getOptions().getPrintSizeY() );\r
+ }\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Wrote PDF to: " + pdf_written_to,\r
+ "Information",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "There was an unknown problem when attempting to write to PDF file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ }\r
+ if ( !getOptions().isPrintUsingActualSize() ) {\r
+ getControlPanel().showWhole();\r
+ }\r
+ }\r
+\r
void readPhylogeniesFromWebservice( final int i ) {\r
final UrlTreeReader reader = new UrlTreeReader( this, i );\r
new Thread( reader ).start();\r
_textframes.clear();\r
}\r
\r
+ private void removeBranchColors() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
+ }\r
+ }\r
+\r
+ private void removeVisualStyles() {\r
+ if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
+ AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
+ }\r
+ }\r
+\r
+ void resetSearch() {\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes0( null );\r
+ getMainPanel().getCurrentTreePanel().setFoundNodes1( null );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel0( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel0().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField0().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton0().setVisible( false );\r
+ getMainPanel().getControlPanel().setSearchFoundCountsOnLabel1( 0 );\r
+ getMainPanel().getControlPanel().getSearchFoundCountsLabel1().setVisible( false );\r
+ getMainPanel().getControlPanel().getSearchTextField1().setText( "" );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setEnabled( false );\r
+ getMainPanel().getControlPanel().getSearchResetButton1().setVisible( false );\r
+ }\r
+\r
void setConfiguration( final Configuration configuration ) {\r
_configuration = configuration;\r
}\r
\r
+ void setCurrentDir( final File current_dir ) {\r
+ _current_dir = current_dir;\r
+ }\r
+\r
void setInferenceManager( final InferenceManager i ) {\r
_inference_manager = i;\r
}\r
_options = options;\r
}\r
\r
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
+ _previous_node_annotation_ref = previous_node_annotation_ref;\r
+ }\r
+\r
void setSelectedTypeInTypeMenu( final PHYLOGENY_GRAPHICS_TYPE type ) {\r
setTypeMenuToAllUnselected();\r
switch ( type ) {\r
_circular_type_cbmi.setSelected( false );\r
}\r
\r
+ public void showTextFrame( final String s, final String title ) {\r
+ checkTextFrames();\r
+ _textframes.addLast( TextFrame.instantiate( s, title, _textframes ) );\r
+ }\r
+\r
+ public void showWhole() {\r
+ _mainpanel.getControlPanel().showWhole();\r
+ }\r
+\r
void switchColors() {\r
final TreeColorSet colorset = _mainpanel.getTreeColorSet();\r
final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );\r
}\r
}\r
\r
+ public void updateProcessMenu() {\r
+ // In general Swing is not thread safe.\r
+ // See "Swing's Threading Policy".\r
+ SwingUtilities.invokeLater( new Runnable() {\r
+\r
+ @Override\r
+ public void run() {\r
+ doUpdateProcessMenu();\r
+ }\r
+ } );\r
+ }\r
+\r
void updateTypeCheckboxes( final Options options, final Object o ) {\r
setTypeMenuToAllUnselected();\r
( ( JCheckBoxMenuItem ) o ).setSelected( true );\r
}\r
}\r
\r
- private void annotateSequences() {\r
- if ( getCurrentTreePanel() != null ) {\r
- List<PhylogenyNode> nodes = null;\r
- if ( ( getCurrentTreePanel().getFoundNodes0() != null )\r
- || ( getCurrentTreePanel().getFoundNodes1() != null ) ) {\r
- nodes = getCurrentTreePanel().getFoundNodesAsListOfPhylogenyNodes();\r
+ boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {\r
+ try {\r
+ final PhylogenyWriter writer = new PhylogenyWriter();\r
+ writer.toPhyloXML( file, t, 0 );\r
+ }\r
+ catch ( final Exception e ) {\r
+ exception = true;\r
+ exceptionOccuredDuringSaveAs( e );\r
+ }\r
+ return exception;\r
+ }\r
+\r
+ void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
+ _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
+ _mainpanel.getCurrentTreePanel().getHeight() );\r
+ String file_written_to = "";\r
+ boolean error = false;\r
+ try {\r
+ file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
+ _mainpanel.getCurrentTreePanel().getWidth(),\r
+ _mainpanel.getCurrentTreePanel().getHeight(),\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getControlPanel(),\r
+ type,\r
+ getOptions() );\r
+ }\r
+ catch ( final IOException e ) {\r
+ error = true;\r
+ JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( !error ) {\r
+ if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Wrote image to: " + file_written_to,\r
+ "Graphics Export",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
- if ( ( nodes == null ) || nodes.isEmpty() ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select nodes, either via direct selection or via the \"Search\" function",\r
- "No nodes selected for annotation",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "There was an unknown problem when attempting to write to an image file: \""\r
+ + file_name + "\"",\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
- final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final JTextField ref_field = new JTextField( 10 );\r
- final JTextField desc_filed = new JTextField( 20 );\r
- ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""\r
- : getPreviousNodeAnnotationReference() );\r
- final JPanel my_panel = new JPanel();\r
- my_panel.add( new JLabel( "Reference " ) );\r
- my_panel.add( ref_field );\r
- my_panel.add( Box.createHorizontalStrut( 15 ) );\r
- my_panel.add( new JLabel( "Description " ) );\r
- my_panel.add( desc_filed );\r
- final int result = JOptionPane.showConfirmDialog( null,\r
- my_panel,\r
- "Enter the sequence annotation(s) for the "\r
- + nodes.size() + " selected nodes",\r
- JOptionPane.OK_CANCEL_OPTION );\r
- if ( result == JOptionPane.OK_OPTION ) {\r
- String ref = ref_field.getText();\r
- String desc = desc_filed.getText();\r
- if ( !ForesterUtil.isEmpty( ref ) ) {\r
- ref = ref.trim();\r
- ref = ref.replaceAll( "\\s+", " " );\r
- if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ( ref.length() - 2 ) )\r
- || ( ref.length() < 3 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Reference needs to be in the form of \"GO:1234567\"",\r
- "Illegal Format for Annotation Reference",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
+ }\r
+ _contentpane.repaint();\r
+ }\r
+\r
+ void writeToFile( final Phylogeny t ) {\r
+ if ( t == null ) {\r
+ return;\r
+ }\r
+ String initial_filename = null;\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ try {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
+ }\r
+ catch ( final IOException e ) {\r
+ initial_filename = null;\r
+ }\r
+ }\r
+ if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
+ _save_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ }\r
+ else {\r
+ _save_filechooser.setSelectedFile( new File( "" ) );\r
+ }\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _save_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _save_filechooser.showSaveDialog( _contentpane );\r
+ final File file = _save_filechooser.getSelectedFile();\r
+ setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
+ boolean exception = false;\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists.\nOverwrite?",\r
+ "Overwrite?",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
+ try {\r
+ ForesterUtil.copyFile( file, to );\r
}\r
- if ( ref != null ) {\r
- setPreviousNodeAnnotationReference( ref );\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to create backup copy " + to,\r
+ "Failed to Create Backup Copy",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
- if ( desc != null ) {\r
- desc = desc.trim();\r
- desc = desc.replaceAll( "\\s+", " " );\r
+ try {\r
+ file.delete();\r
}\r
- if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {\r
- for( final PhylogenyNode n : nodes ) {\r
- ForesterUtil.ensurePresenceOfSequence( n );\r
- final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
- : new Annotation( ref );\r
- if ( !ForesterUtil.isEmpty( desc ) ) {\r
- ann.setDesc( desc );\r
- }\r
- n.getNodeData().getSequence().addAnnotation( ann );\r
- }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Failed to Delete",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
- getMainPanel().getControlPanel().showAnnotations();\r
}\r
}\r
- }\r
- }\r
-\r
- private void chooseFont() {\r
- final FontChooser fc = new FontChooser();\r
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );\r
- fc.showDialog( this, "Select the Base Font" );\r
- getMainPanel().getTreeFontSet().setBaseFont( fc.getFont() );\r
- }\r
-\r
- private void chooseMinimalConfidence() {\r
- final String s = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "Please enter the minimum for confidence values to be displayed.\n"\r
- + "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getMinConfidenceValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
+ if ( _save_filechooser.getFileFilter() == MainFrame.nhfilter ) {\r
+ exception = writeAsNewHampshire( t, exception, file );\r
+ }\r
+ else if ( _save_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
+ exception = writeAsPhyloXml( t, exception, file );\r
}\r
+ else if ( _save_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
+ exception = writeAsNexus( t, exception, file );\r
+ }\r
+ // "*.*":\r
else {\r
- success = false;\r
+ final String file_name = file.getName().trim().toLowerCase();\r
+ if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".tree" ) ) {\r
+ exception = writeAsNewHampshire( t, exception, file );\r
+ }\r
+ else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
+ exception = writeAsNexus( t, exception, file );\r
+ }\r
+ // XML is default:\r
+ else {\r
+ exception = writeAsPhyloXml( t, exception, file );\r
+ }\r
}\r
- if ( success && ( m >= 0.0 ) ) {\r
- getOptions().setMinConfidenceValue( m );\r
+ if ( !exception ) {\r
+ getMainPanel().setTitleOfSelectedTab( file.getName() );\r
+ getMainPanel().getCurrentTreePanel().setTreeFile( file );\r
+ getMainPanel().getCurrentTreePanel().setEdited( false );\r
}\r
}\r
}\r
\r
- private void doUpdateProcessMenu() {\r
- if ( _process_pool.size() > 0 ) {\r
- if ( _process_menu == null ) {\r
- _process_menu = createMenu( "", getConfiguration() );\r
- _process_menu.setForeground( Color.RED );\r
+ void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return;\r
+ }\r
+ String initial_filename = "";\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+ }\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ }\r
+ initial_filename = initial_filename + "." + type;\r
+ _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _writetographics_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _writetographics_filechooser.showSaveDialog( _contentpane );\r
+ File file = _writetographics_filechooser.getSelectedFile();\r
+ setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
+ file = new File( file.toString() + "." + type );\r
}\r
- _process_menu.removeAll();\r
- final String text = "processes running: " + _process_pool.size();\r
- _process_menu.setText( text );\r
- _jmenubar.add( _process_menu );\r
- for( int i = 0; i < _process_pool.size(); ++i ) {\r
- final ProcessRunning p = _process_pool.getProcessByIndex( i );\r
- _process_menu.add( customizeJMenuItem( new JMenuItem( p.getName() + " [" + p.getStart() + "]" ) ) );\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "Warning",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
+ else {\r
+ try {\r
+ file.delete();\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Failed to delete: " + file,\r
+ "Error",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
}\r
+ writePhylogenyToGraphicsFile( file.toString(), type );\r
}\r
- else {\r
- if ( _process_menu != null ) {\r
- _process_menu.removeAll();\r
- _jmenubar.remove( _process_menu );\r
+ }\r
+\r
+ void writeToPdf( final Phylogeny t ) {\r
+ if ( ( t == null ) || t.isEmpty() ) {\r
+ return;\r
+ }\r
+ String initial_filename = "";\r
+ if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+ }\r
+ if ( initial_filename.indexOf( '.' ) > 0 ) {\r
+ initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
+ }\r
+ initial_filename = initial_filename + ".pdf";\r
+ _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = getCurrentDir();\r
+ if ( my_dir != null ) {\r
+ _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
+ File file = _writetopdf_filechooser.getSelectedFile();\r
+ setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
+ file = new File( file.toString() + ".pdf" );\r
+ }\r
+ if ( file.exists() ) {\r
+ final int i = JOptionPane.showConfirmDialog( this,\r
+ file + " already exists. Overwrite?",\r
+ "WARNING",\r
+ JOptionPane.OK_CANCEL_OPTION,\r
+ JOptionPane.WARNING_MESSAGE );\r
+ if ( i != JOptionPane.OK_OPTION ) {\r
+ return;\r
+ }\r
}\r
+ printPhylogenyToPdf( file.toString() );\r
}\r
- _jmenubar.validate();\r
- _jmenubar.repaint();\r
- repaint();\r
}\r
+}\r
\r
- private String getPreviousNodeAnnotationReference() {\r
- return _previous_node_annotation_ref;\r
- }\r
+class MsaFileFilter extends FileFilter {\r
\r
- private void removeBranchColors() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );\r
- }\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )\r
+ || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();\r
}\r
\r
- private void removeVisualStyles() {\r
- if ( getMainPanel().getCurrentPhylogeny() != null ) {\r
- AptxUtil.removeVisualStyles( getMainPanel().getCurrentPhylogeny() );\r
- }\r
+ @Override\r
+ public String getDescription() {\r
+ return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";\r
}\r
+}\r
\r
- private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {\r
- _previous_node_annotation_ref = previous_node_annotation_ref;\r
- }\r
+class NexusFilter extends FileFilter {\r
\r
- /**\r
- * Display the about box.\r
- */\r
- static void about() {\r
- final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );\r
- about.append( "Copyright (C) 2014 Christian M Zmasek\n" );\r
- about.append( "All Rights Reserved\n" );\r
- about.append( "License: GNU Lesser General Public License (LGPL)\n" );\r
- about.append( "Last modified: " + Constants.PRG_DATE + "\n" );\r
- about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );\r
- about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );\r
- about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );\r
- if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {\r
- about.append( "[your Java version: " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]\n" );\r
- }\r
- if ( !ForesterUtil.isEmpty( ForesterUtil.OS_NAME ) && !ForesterUtil.isEmpty( ForesterUtil.OS_ARCH )\r
- && !ForesterUtil.isEmpty( ForesterUtil.OS_VERSION ) ) {\r
- about.append( "[your OS: " + ForesterUtil.OS_NAME + " " + ForesterUtil.OS_ARCH + " "\r
- + ForesterUtil.OS_VERSION + "]\n" );\r
- }\r
- final Runtime rt = java.lang.Runtime.getRuntime();\r
- final long free_memory = rt.freeMemory() / 1000000;\r
- final long total_memory = rt.totalMemory() / 1000000;\r
- about.append( "[free memory: " + free_memory + "MB, total memory: " + total_memory + "MB]\n" );\r
- about.append( "[locale: " + Locale.getDefault() + "]\n" );\r
- about.append( "References:\n" );\r
- about.append( Constants.PHYLOXML_REFERENCE_SHORT + "\n" );\r
- about.append( "For more information & download:\n" );\r
- about.append( Constants.APTX_WEB_SITE + "\n" );\r
- about.append( "Documentation:\n" );\r
- about.append( Constants.APTX_DOC_SITE + "\n" );\r
- about.append( "Comments: " + Constants.AUTHOR_EMAIL );\r
- JOptionPane.showMessageDialog( null, about, Constants.PRG_NAME, JOptionPane.PLAIN_MESSAGE );\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )\r
+ || file_name.endsWith( ".tre" ) || f.isDirectory();\r
}\r
\r
- static void chooseNodeSize( final Options options, final Component parent ) {\r
- final String s = ( String ) JOptionPane.showInputDialog( parent,\r
- "Please enter the default size for node shapes.\n"\r
- + "[current value: "\r
- + options.getDefaultNodeShapeSize() + "]\n",\r
- "Node Shape Size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- options.getDefaultNodeShapeSize() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- final short size = ForesterUtil.roundToShort( m );\r
- if ( size >= 0.0 ) {\r
- options.setDefaultNodeShapeSize( size );\r
- }\r
- }\r
- }\r
+ @Override\r
+ public String getDescription() {\r
+ return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";\r
}\r
+} // NexusFilter\r
\r
- static String createCurrentFontDesc( final TreeFontSet tree_font_set ) {\r
- return tree_font_set.getLargeFont().getFamily() + " " + tree_font_set.getLargeFont().getSize();\r
- }\r
+class NHFilter extends FileFilter {\r
\r
- static JMenu createMenu( final String title, final Configuration conf ) {\r
- final JMenu jmenu = new JMenu( title );\r
- if ( !conf.isUseNativeUI() ) {\r
- jmenu.setFont( MainFrame.menu_font );\r
- jmenu.setBackground( conf.getGuiMenuBackgroundColor() );\r
- jmenu.setForeground( conf.getGuiMenuTextColor() );\r
- }\r
- return jmenu;\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
+ || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )\r
+ || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )\r
+ || f.isDirectory();\r
}\r
\r
- static JMenuItem customizeMenuItemAsLabel( final JMenuItem label, final Configuration configuration ) {\r
- label.setFont( MainFrame.menu_font.deriveFont( Font.BOLD ) );\r
- if ( !configuration.isUseNativeUI() ) {\r
- label.setBackground( configuration.getGuiMenuBackgroundColor() );\r
- label.setForeground( configuration.getGuiMenuTextColor() );\r
- label.setOpaque( true );\r
- }\r
- label.setSelected( false );\r
- label.setEnabled( false );\r
- return label;\r
+ @Override\r
+ public String getDescription() {\r
+ return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";\r
}\r
+} // NHFilter\r
\r
- static void cycleNodeFill( final Options op ) {\r
- switch ( op.getDefaultNodeFill() ) {\r
- case GRADIENT:\r
- op.setDefaultNodeFill( NodeFill.SOLID );\r
- break;\r
- case NONE:\r
- op.setDefaultNodeFill( NodeFill.GRADIENT );\r
- break;\r
- case SOLID:\r
- op.setDefaultNodeFill( NodeFill.NONE );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown fill: " + op.getDefaultNodeFill() );\r
- }\r
- }\r
+class NHXFilter extends FileFilter {\r
\r
- static void cycleNodeShape( final Options op ) {\r
- switch ( op.getDefaultNodeShape() ) {\r
- case CIRCLE:\r
- op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
- break;\r
- case RECTANGLE:\r
- op.setDefaultNodeShape( NodeShape.CIRCLE );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown shape: " + op.getDefaultNodeShape() );\r
- }\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".nhx" ) || f.isDirectory();\r
}\r
\r
- private static void cycleNodeDataReturn( final Options op, Configuration conf ) {\r
- switch ( op.getExtDescNodeDataToReturn() ) {\r
- case UNKNOWN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
- break;\r
- case DOMAINS_ALL:\r
- op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
- break;\r
- case DOMAINS_COLLAPSED_PER_PROTEIN:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
- break;\r
- case SEQ_ANNOTATIONS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
- break;\r
- case GO_TERM_IDS:\r
- op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
- break;\r
- case SEQUENCE_MOL_SEQ_FASTA:\r
- if ( conf != null && conf.getExtDescNodeDataToReturn() != null\r
- && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL\r
- && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN\r
- && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS\r
- && conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS\r
- && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA\r
- ) {\r
- op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
- }\r
- else {\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
- }\r
- break; \r
- default:\r
- op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
- }\r
+ @Override\r
+ public String getDescription() {\r
+ return "NHX files (*.nhx) [deprecated]";\r
}\r
+}\r
\r
- static void cycleOverview( final Options op, final TreePanel tree_panel ) {\r
- switch ( op.getOvPlacement() ) {\r
- case LOWER_LEFT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );\r
- break;\r
- case LOWER_RIGHT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_LEFT );\r
- break;\r
- case UPPER_LEFT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.UPPER_RIGHT );\r
- break;\r
- case UPPER_RIGHT:\r
- op.setOvPlacement( Options.OVERVIEW_PLACEMENT_TYPE.LOWER_RIGHT );\r
- break;\r
- default:\r
- throw new RuntimeException( "unknown placement: " + op.getOvPlacement() );\r
- }\r
- if ( tree_panel != null ) {\r
- tree_panel.updateOvSettings();\r
- }\r
- }\r
+class PdfFilter extends FileFilter {\r
\r
- static void setCycleNodeFillMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeFill() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeFill().toString().toLowerCase() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
- }\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();\r
}\r
\r
- static void setCycleNodeShapeMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getDefaultNodeShape() != null ) ) {\r
- mi.setText( "Cycle Node Shape Fill Type... (current: "\r
- + options.getDefaultNodeShape().toString().toLowerCase() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Shape Fill Type..." );\r
- }\r
+ @Override\r
+ public String getDescription() {\r
+ return "PDF files (*.pdf)";\r
}\r
+} // PdfFilter\r
\r
- static void setCycleDataReturnMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getExtDescNodeDataToReturn() != null ) ) {\r
- mi.setText( "Cycle Node Return Data... (current: "\r
- + options.getExtDescNodeDataToReturn().toString() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Node Return Data..." );\r
- }\r
- }\r
+class SequencesFileFilter extends FileFilter {\r
\r
- static void setOvPlacementColorChooseMenuItem( final JMenuItem mi, final Options options ) {\r
- if ( ( options != null ) && ( options.getOvPlacement() != null ) ) {\r
- mi.setText( "Cycle Overview Placement... (current: " + options.getOvPlacement() + ")" );\r
- }\r
- else {\r
- mi.setText( "Cycle Overview Placement..." );\r
- }\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )\r
+ || file_name.endsWith( ".seqs" ) || f.isDirectory();\r
}\r
\r
- static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
- if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
- mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
- + ")" );\r
- }\r
- else {\r
- mi.setText( "Select Color Scheme..." );\r
- }\r
+ @Override\r
+ public String getDescription() {\r
+ return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";\r
}\r
+}\r
\r
- static void setTextForFontChooserMenuItem( final JMenuItem mi, final String font_desc ) {\r
- mi.setText( "Select Default Font... (current: " + font_desc + ")" );\r
+class TolFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f\r
+ .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );\r
}\r
\r
- static void setTextMinSupportMenuItem( final JMenuItem mi, final Options options, final TreePanel current_tree_panel ) {\r
- if ( ( current_tree_panel == null ) || ( current_tree_panel.getPhylogeny() == null ) ) {\r
- mi.setEnabled( true );\r
- }\r
- else if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( current_tree_panel.getPhylogeny() ) ) {\r
- mi.setEnabled( true );\r
- }\r
- else {\r
- mi.setEnabled( false );\r
- }\r
- mi.setText( "Enter Min Confidence Value... (current: " + options.getMinConfidenceValue() + ")" );\r
+ @Override\r
+ public String getDescription() {\r
+ return "Tree of Life files (*.tol, *.tolxml)";\r
}\r
+} // TolFilter\r
\r
- static void setTextNodeSizeMenuItem( final JMenuItem mi, final Options options ) {\r
- mi.setText( "Enter Default Node Shape Size... (current: " + options.getDefaultNodeShapeSize() + ")" );\r
+class XMLFilter extends FileFilter {\r
+\r
+ @Override\r
+ public boolean accept( final File f ) {\r
+ final String file_name = f.getName().trim().toLowerCase();\r
+ return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )\r
+ || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();\r
}\r
\r
- static void updateScreenTextAntialias( final List<TreePanel> treepanels ) {\r
- for( final TreePanel tree_panel : treepanels ) {\r
- tree_panel.setTextAntialias();\r
- }\r
+ @Override\r
+ public String getDescription() {\r
+ return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";\r
}\r
-}\r
+} // XMLFilter\r
System.gc();
}
- private void readSpeciesTree( final Configuration configuration, final String species_tree_url_str )
- throws MalformedURLException, FileNotFoundException, IOException {
- final URL species_tree_url = new URL( species_tree_url_str );
- final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
- configuration
- .isValidatePhyloXmlAgainstSchema(),
- configuration
- .isReplaceUnderscoresInNhParsing(),
- false,
- TAXONOMY_EXTRACTION.NO,
- false );
- if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
- AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "successfully read species tree" );
- if ( species_trees[ 0 ].isEmpty() ) {
- ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is empty" );
- }
- else if ( !species_trees[ 0 ].isRooted() ) {
- ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" );
- }
- else {
- setSpeciesTree( species_trees[ 0 ] );
- AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" );
- }
- }
- else {
- ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
- + species_tree_url_str );
- }
- }
-
- @Override
- public MainPanel getMainPanel() {
- return _mainpanel;
- }
-
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
_analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel()
.getTreeFontSet() ) );
+ setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
+ setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
-
try {
getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
getMainPanel().getControlPanel().setVisibilityOfX();
_options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
_search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
_options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
+ //
+ _options_jmenu.addSeparator();
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
+ getConfiguration() ) );
+ _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
+ _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
+ _options_jmenu
+ .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) );
+ _options_jmenu
+ .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) );
+ _options_jmenu
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
+ _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
+ _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
+ //
+ customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
+ customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
+ customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
+ customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
+ customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
+ .isGraphicsExportUsingActualSize() );
+ customizeJMenuItem( _print_size_mi );
+ customizeJMenuItem( _choose_pdf_width_mi );
+ //
customizeJMenuItem( _choose_font_mi );
customizeJMenuItem( _switch_colors_mi );
customizeJMenuItem( _choose_minimal_confidence_mi );
JApplet getApplet() {
return _applet;
}
+
+ @Override
+ public MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
+ private void readSpeciesTree( final Configuration configuration, final String species_tree_url_str )
+ throws MalformedURLException, FileNotFoundException, IOException {
+ final URL species_tree_url = new URL( species_tree_url_str );
+ final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
+ configuration
+ .isValidatePhyloXmlAgainstSchema(),
+ configuration
+ .isReplaceUnderscoresInNhParsing(),
+ false,
+ TAXONOMY_EXTRACTION.NO,
+ false );
+ if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
+ AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "successfully read species tree" );
+ if ( species_trees[ 0 ].isEmpty() ) {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is empty" );
+ }
+ else if ( !species_trees[ 0 ].isRooted() ) {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "species tree is not rooted" );
+ }
+ else {
+ setSpeciesTree( species_trees[ 0 ] );
+ AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "species tree OK" );
+ }
+ }
+ else {
+ ForesterUtil.printErrorMessage( ArchaeopteryxA.NAME, "failed to read species tree from "
+ + species_tree_url_str );
+ }
+ }
}
import javax.swing.WindowConstants;\r
import javax.swing.event.ChangeEvent;\r
import javax.swing.event.ChangeListener;\r
-import javax.swing.filechooser.FileFilter;\r
import javax.swing.plaf.synth.SynthLookAndFeel;\r
\r
import org.forester.analysis.TaxonomyDataManager;\r
import org.forester.util.BasicTableParser;\r
import org.forester.util.DescriptiveStatistics;\r
import org.forester.util.ForesterUtil;\r
-import org.forester.util.WindowsUtils;\r
\r
public final class MainFrameApplication extends MainFrame {\r
\r
- static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
- static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
- private final static int FRAME_X_SIZE = 800;\r
- private final static int FRAME_Y_SIZE = 800;\r
+ public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
+ return new MainFrameApplication( phys, config );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
+ return new MainFrameApplication( phys, config, title );\r
+ }\r
+\r
+ public static MainFrame createInstance( final Phylogeny[] phys,\r
+ final Configuration config,\r
+ final String title,\r
+ final File current_dir ) {\r
+ return new MainFrameApplication( phys, config, title, current_dir );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
+ return new MainFrameApplication( phys, config_file_name, title );\r
+ }\r
+\r
+ static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
+ if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
+ JOptionPane\r
+ .showMessageDialog( null,\r
+ ForesterUtil\r
+ .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
+ 80 ),\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
+ private final static int FRAME_X_SIZE = 800;\r
+ private final static int FRAME_Y_SIZE = 800;\r
// Filters for the file-open dialog (classes defined in this file)\r
- private final static NHFilter nhfilter = new NHFilter();\r
- private final static NHXFilter nhxfilter = new NHXFilter();\r
- private final static XMLFilter xmlfilter = new XMLFilter();\r
- private final static TolFilter tolfilter = new TolFilter();\r
- private final static NexusFilter nexusfilter = new NexusFilter();\r
- private final static PdfFilter pdffilter = new PdfFilter();\r
- private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();\r
- private final static MsaFileFilter msafilter = new MsaFileFilter();\r
- private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();\r
- private final static DefaultFilter defaultfilter = new DefaultFilter();\r
- private static final long serialVersionUID = -799735726778865234L;\r
- private static final boolean PREPROCESS_TREES = false;\r
- private final JFileChooser _values_filechooser;\r
- private final JFileChooser _sequences_filechooser;\r
- private final JFileChooser _open_filechooser;\r
- private final JFileChooser _msa_filechooser;\r
- private final JFileChooser _seqs_pi_filechooser;\r
- private final JFileChooser _open_filechooser_for_species_tree;\r
- private final JFileChooser _save_filechooser;\r
- \r
- private final JFileChooser _writetographics_filechooser;\r
+ private static final long serialVersionUID = -799735726778865234L;\r
+ private static final boolean PREPROCESS_TREES = false;\r
+ private final JFileChooser _values_filechooser;\r
+ private final JFileChooser _sequences_filechooser;\r
+ private final JFileChooser _open_filechooser;\r
+ private final JFileChooser _msa_filechooser;\r
+ private final JFileChooser _seqs_pi_filechooser;\r
+ private final JFileChooser _open_filechooser_for_species_tree;\r
// Application-only print menu items\r
- \r
- private JMenuItem _collapse_below_threshold;\r
- private JMenuItem _collapse_below_branch_length;\r
- \r
- private ButtonGroup _radio_group_1;\r
- private ButtonGroup _radio_group_2;\r
+ private JMenuItem _collapse_below_threshold;\r
+ private JMenuItem _collapse_below_branch_length;\r
+ private ButtonGroup _radio_group_1;\r
+ private ButtonGroup _radio_group_2;\r
// Others:\r
- double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
- double _min_not_collapse_bl = 0.001;\r
+ double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
+ double _min_not_collapse_bl = 0.001;\r
// Phylogeny Inference menu\r
- private JMenu _inference_menu;\r
- private JMenuItem _inference_from_msa_item;\r
- private JMenuItem _inference_from_seqs_item;\r
+ private JMenu _inference_menu;\r
+ private JMenuItem _inference_from_msa_item;\r
+ private JMenuItem _inference_from_seqs_item;\r
// Phylogeny Inference\r
- private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;\r
- private Msa _msa = null;\r
- private File _msa_file = null;\r
- private List<MolecularSequence> _seqs = null;\r
- private File _seqs_file = null;\r
- JMenuItem _read_values_jmi;\r
- JMenuItem _read_seqs_jmi;\r
+ private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;\r
+ private Msa _msa = null;\r
+ private File _msa_file = null;\r
+ private List<MolecularSequence> _seqs = null;\r
+ private File _seqs_file = null;\r
+ JMenuItem _read_values_jmi;\r
+ JMenuItem _read_seqs_jmi;\r
\r
private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {\r
_configuration = config;\r
_open_filechooser = new JFileChooser();\r
_open_filechooser.setCurrentDirectory( new File( "." ) );\r
_open_filechooser.setMultiSelectionEnabled( false );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter );\r
_open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );\r
- _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );\r
+ _open_filechooser.setFileFilter( MainFrame.defaultfilter );\r
_open_filechooser_for_species_tree = new JFileChooser();\r
_open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );\r
_open_filechooser_for_species_tree.setMultiSelectionEnabled( false );\r
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );\r
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );\r
- _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );\r
+ _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter );\r
+ _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter );\r
+ _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter );\r
_save_filechooser = new JFileChooser();\r
_save_filechooser.setCurrentDirectory( new File( "." ) );\r
_save_filechooser.setMultiSelectionEnabled( false );\r
- _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );\r
- _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );\r
- _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );\r
+ _save_filechooser.setFileFilter( MainFrame.xmlfilter );\r
+ _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter );\r
+ _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );\r
_save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );\r
_writetopdf_filechooser = new JFileChooser();\r
- _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );\r
+ _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter );\r
_writetographics_filechooser = new JFileChooser();\r
- _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );\r
+ _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );\r
// Msa:\r
_msa_filechooser = new JFileChooser();\r
_msa_filechooser.setName( "Read Multiple Sequence Alignment File" );\r
_msa_filechooser.setCurrentDirectory( new File( "." ) );\r
_msa_filechooser.setMultiSelectionEnabled( false );\r
_msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );\r
- _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );\r
+ _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter );\r
// Seqs:\r
_seqs_pi_filechooser = new JFileChooser();\r
_seqs_pi_filechooser.setName( "Read Sequences File" );\r
_seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );\r
_seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
_seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );\r
- _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );\r
+ _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter );\r
// Expression\r
_values_filechooser = new JFileChooser();\r
_values_filechooser.setCurrentDirectory( new File( "." ) );\r
if ( o == _open_url_item ) {\r
readPhylogeniesFromURL();\r
}\r
- else if ( o == _save_item ) {\r
- writeToFile( _mainpanel.getCurrentPhylogeny() );\r
- // If subtree currently displayed, save it, instead of complete\r
- // tree.\r
- }\r
else if ( o == _new_item ) {\r
newTree();\r
}\r
else if ( o == _write_to_jpg_item ) {\r
writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );\r
}\r
- else if ( o == _write_to_png_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );\r
- }\r
else if ( o == _write_to_gif_item ) {\r
writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );\r
}\r
else if ( o == _extract_tax_code_from_node_names_jmi ) {\r
extractTaxDataFromNodeNames();\r
}\r
- else if ( o == _graphics_export_visible_only_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _antialias_print_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_black_and_white_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_using_actual_size_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _graphics_export_using_actual_size_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_size_mi ) {\r
- choosePrintSize();\r
- }\r
- else if ( o == _choose_pdf_width_mi ) {\r
- choosePdfWidth();\r
- }\r
else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
}\r
}\r
\r
- public void end() {\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- }\r
-\r
- @Override\r
- public MainPanel getMainPanel() {\r
- return _mainpanel;\r
- }\r
-\r
- public Msa getMsa() {\r
- return _msa;\r
- }\r
-\r
- public File getMsaFile() {\r
- return _msa_file;\r
- }\r
-\r
- public List<MolecularSequence> getSeqs() {\r
- return _seqs;\r
- }\r
-\r
- public File getSeqsFile() {\r
- return _seqs_file;\r
- }\r
-\r
- public void readMsaFromFile() {\r
- // Set an initial directory if none set yet\r
+ private void addExpressionValuesFromFile() {\r
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Need to load evolutionary tree first",\r
+ "Can Not Read Expression Values",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return;\r
+ }\r
final File my_dir = getCurrentDir();\r
- _msa_filechooser.setMultiSelectionEnabled( false );\r
- // Open file-open dialog and set current directory\r
if ( my_dir != null ) {\r
- _msa_filechooser.setCurrentDirectory( my_dir );\r
+ _values_filechooser.setCurrentDirectory( my_dir );\r
}\r
- final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the msa\r
- final File file = _msa_filechooser.getSelectedFile();\r
- setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setMsaFile( null );\r
- setMsa( null );\r
- Msa msa = null;\r
+ final int result = _values_filechooser.showOpenDialog( _contentpane );\r
+ final File file = _values_filechooser.getSelectedFile();\r
+ if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ BasicTable<String> t = null;\r
try {\r
- final InputStream is = new FileInputStream( file );\r
- if ( FastaParser.isLikelyFasta( file ) ) {\r
- msa = FastaParser.parseMsa( is );\r
+ t = BasicTableParser.parse( file, '\t' );\r
+ if ( t.getNumberOfColumns() < 2 ) {\r
+ t = BasicTableParser.parse( file, ',' );\r
}\r
- else {\r
- msa = GeneralMsaParser.parse( is );\r
+ if ( t.getNumberOfColumns() < 2 ) {\r
+ t = BasicTableParser.parse( file, ' ' );\r
}\r
}\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence alignment format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
catch ( final IOException e ) {\r
- setArrowCursor();\r
JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence alignment",\r
+ e.getMessage(),\r
+ "Could Not Read Expression Value Table",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
- catch ( final IllegalArgumentException e ) {\r
- setArrowCursor();\r
+ if ( t.getNumberOfColumns() < 2 ) {\r
JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
+ "Table contains " + t.getNumberOfColumns() + " column(s)",\r
+ "Problem with Expression Value Table",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
+ if ( t.getNumberOfRows() < 1 ) {\r
JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
+ "Table contains zero rows",\r
+ "Problem with Expression Value Table",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
- if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {\r
JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment is empty",\r
- "Illegal Multiple Sequence Alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ "Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
+ + phy.getNumberOfExternalNodes() + " external nodes",\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
- if ( msa.getNumberOfSequences() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 3 sequences",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
+ int not_found = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ final String node_name = node.getName();\r
+ if ( !ForesterUtil.isEmpty( node_name ) ) {\r
+ int row = -1;\r
+ try {\r
+ row = t.findRow( node_name );\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ e.getMessage(),\r
+ "Error Mapping Node Identifiers to Expression Value Identifiers",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( row < 0 ) {\r
+ if ( node.isExternal() ) {\r
+ not_found++;\r
+ }\r
+ continue;\r
+ }\r
+ final List<Double> l = new ArrayList<Double>();\r
+ for( int col = 1; col < t.getNumberOfColumns(); ++col ) {\r
+ double d = -100;\r
+ try {\r
+ d = Double.parseDouble( t.getValueAsString( col, row ) );\r
+ }\r
+ catch ( final NumberFormatException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Could not parse \"" + t.getValueAsString( col, row )\r
+ + "\" into a decimal value",\r
+ "Issue with Expression Value Table",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ stats.addValue( d );\r
+ l.add( d );\r
+ }\r
+ if ( !l.isEmpty() ) {\r
+ if ( node.getNodeData().getProperties() != null ) {\r
+ node.getNodeData().getProperties()\r
+ .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
+ }\r
+ node.getNodeData().setVector( l );\r
+ }\r
+ }\r
}\r
- if ( msa.getLength() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 2 residues",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ if ( not_found > 0 ) {\r
+ JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
+ + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
}\r
- System.gc();\r
- setMsaFile( _msa_filechooser.getSelectedFile() );\r
- setMsa( msa );\r
+ getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
}\r
}\r
\r
- public void readSeqsFromFileforPI() {\r
- // Set an initial directory if none set yet\r
+ private void addSequencesFromFile() {\r
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Need to load evolutionary tree first",\r
+ "Can Not Read Sequences",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return;\r
+ }\r
final File my_dir = getCurrentDir();\r
- _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
- // Open file-open dialog and set current directory\r
if ( my_dir != null ) {\r
- _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
+ _sequences_filechooser.setCurrentDirectory( my_dir );\r
}\r
- final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the seqs\r
- final File file = _seqs_pi_filechooser.getSelectedFile();\r
- setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
+ final int result = _sequences_filechooser.showOpenDialog( _contentpane );\r
+ final File file = _sequences_filechooser.getSelectedFile();\r
+ List<MolecularSequence> seqs = null;\r
if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setSeqsFile( null );\r
- setSeqs( null );\r
- List<MolecularSequence> seqs = null;\r
try {\r
if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
seqs = FastaParser.parse( new FileInputStream( file ) );\r
- for( final MolecularSequence seq : seqs ) {\r
- System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
- }\r
}\r
else {\r
- //TODO error\r
+ JOptionPane.showMessageDialog( this,\r
+ "Format does not appear to be Fasta",\r
+ "Multiple sequence file format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
}\r
catch ( final MsaFormatException e ) {\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
- catch ( final IllegalArgumentException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
catch ( final Exception e ) {\r
setArrowCursor();\r
e.printStackTrace();\r
if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
JOptionPane.showMessageDialog( this,\r
"Multiple sequence file is empty",\r
- "Illegal multiple sequence file",\r
+ "Empty multiple sequence file",\r
JOptionPane.ERROR_MESSAGE );\r
+ setArrowCursor();\r
return;\r
}\r
- if ( seqs.size() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file needs to contain at least 3 sequences",\r
- "Illegal multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ }\r
+ if ( seqs != null ) {\r
+ for( final MolecularSequence seq : seqs ) {\r
+ System.out.println( seq.getIdentifier() );\r
+ }\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ int total_counter = 0;\r
+ int attached_counter = 0;\r
+ for( final MolecularSequence seq : seqs ) {\r
+ ++total_counter;\r
+ final String seq_name = seq.getIdentifier();\r
+ if ( !ForesterUtil.isEmpty( seq_name ) ) {\r
+ List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodesViaSequenceSymbol( seq_name );\r
+ }\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodesViaGeneName( seq_name );\r
+ }\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodes( seq_name );\r
+ }\r
+ if ( nodes.size() > 1 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Sequence name \"" + seq_name + "\" is not unique",\r
+ "Sequence name not unique",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ setArrowCursor();\r
+ return;\r
+ }\r
+ final String[] a = seq_name.split( "\\s" );\r
+ if ( nodes.isEmpty() && ( a.length > 1 ) ) {\r
+ final String seq_name_split = a[ 0 ];\r
+ nodes = phy.getNodesViaSequenceName( seq_name_split );\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodesViaSequenceSymbol( seq_name_split );\r
+ }\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodes( seq_name_split );\r
+ }\r
+ if ( nodes.size() > 1 ) {\r
+ JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
+ + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
+ setArrowCursor();\r
+ return;\r
+ }\r
+ }\r
+ if ( nodes.size() == 1 ) {\r
+ ++attached_counter;\r
+ final PhylogenyNode n = nodes.get( 0 );\r
+ if ( !n.getNodeData().isHasSequence() ) {\r
+ n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );\r
+ }\r
+ n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );\r
+ if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {\r
+ n.getNodeData().getSequence().setName( seq_name );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if ( attached_counter > 0 ) {\r
+ int ext_nodes = 0;\r
+ int ext_nodes_with_seq = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ ++ext_nodes;\r
+ final PhylogenyNode n = iter.next();\r
+ if ( n.getNodeData().isHasSequence()\r
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {\r
+ ++ext_nodes_with_seq;\r
+ }\r
+ }\r
+ final String s;\r
+ if ( ext_nodes == ext_nodes_with_seq ) {\r
+ s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";\r
+ }\r
+ else {\r
+ s = ext_nodes_with_seq + " out of " + ext_nodes\r
+ + " external nodes now have a molecular sequence attached to them.";\r
+ }\r
+ if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Attached all " + total_counter + " sequences to tree nodes.\n" + s,\r
+ "All sequences attached",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
+ + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
+ + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
+ + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
}\r
- // if ( msa.getLength() < 2 ) {\r
- // JOptionPane.showMessageDialog( this,\r
- // "Multiple sequence alignment needs to contain at least 2 residues",\r
- // "Illegal multiple sequence file",\r
- // JOptionPane.ERROR_MESSAGE );\r
- // return;\r
- // }\r
- System.gc();\r
- setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
- setSeqs( seqs );\r
}\r
}\r
\r
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
.createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
- setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
- setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
+ MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
+ MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
- \r
MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );\r
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
try {\r
customizeJMenuItem( _cycle_node_shape_mi );\r
customizeJMenuItem( _cycle_node_fill_mi );\r
customizeJMenuItem( _choose_node_size_mi );\r
- customizeJMenuItem( _cycle_data_return);\r
- \r
+ customizeJMenuItem( _cycle_data_return );\r
customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
exit();\r
}\r
\r
- void executeLineageInference() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Phylogeny is not rooted.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ private void closeCurrentPane() {\r
+ if ( getMainPanel().getCurrentTreePanel() != null ) {\r
+ if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
+ final int r = JOptionPane.showConfirmDialog( this,\r
+ "Close tab despite potentially unsaved changes?",\r
+ "Close Tab?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ getMainPanel().closeCurrentPane();\r
+ activateSaveAllIfNeeded();\r
}\r
- final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getCurrentPhylogeny()\r
- .copy() );\r
- new Thread( inferrer ).start();\r
- }\r
-\r
- void exit() {\r
- removeAllTextFrames();\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.\r
}\r
\r
- void readPhylogeniesFromURL() {\r
- URL url = null;\r
- Phylogeny[] phys = null;\r
- final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";\r
- final String url_string = JOptionPane.showInputDialog( this,\r
- message,\r
- "Use URL/webservice to obtain a phylogeny",\r
- JOptionPane.QUESTION_MESSAGE );\r
- boolean nhx_or_nexus = false;\r
- if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {\r
- try {\r
- url = new URL( url_string );\r
- PhylogenyParser parser = null;\r
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {\r
- parser = new TolParser();\r
- }\r
- else {\r
- parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
- }\r
- if ( parser instanceof NexusPhylogeniesParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- else if ( parser instanceof NHXParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setWaitCursor();\r
- }\r
- else {\r
- _mainpanel.setWaitCursor();\r
+ private void collapse( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
+ double min_support = Double.MAX_VALUE;\r
+ boolean conf_present = false;\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ final List<Confidence> c = n.getBranchData().getConfidences();\r
+ if ( ( c != null ) && ( c.size() > 0 ) ) {\r
+ conf_present = true;\r
+ double max = 0;\r
+ for( final Confidence confidence : c ) {\r
+ if ( confidence.getValue() > max ) {\r
+ max = confidence.getValue();\r
+ }\r
+ }\r
+ if ( max < getMinNotCollapseConfidenceValue() ) {\r
+ to_be_removed.add( n );\r
+ }\r
+ if ( max < min_support ) {\r
+ min_support = max;\r
+ }\r
}\r
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
- phys = factory.create( url.openStream(), parser );\r
}\r
- catch ( final MalformedURLException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),\r
- "Malformed URL",\r
- JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( conf_present ) {\r
+ for( final PhylogenyNode node : to_be_removed ) {\r
+ PhylogenyMethods.removeNode( node, phy );\r
}\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not read from " + url + "\n"\r
- + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Failed to read URL",\r
- JOptionPane.ERROR_MESSAGE );\r
+ if ( to_be_removed.size() > 0 ) {\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
+ getCurrentTreePanel().calculateLongestExtNodeInfo();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().setEdited( true );\r
+ getCurrentTreePanel().repaint();\r
+ repaint();\r
}\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Unexpected Exception",\r
- JOptionPane.ERROR_MESSAGE );\r
+ if ( to_be_removed.size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
+ + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
}\r
- finally {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- else {\r
- _mainpanel.setArrowCursor();\r
- }\r
- }\r
- if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
- if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
- for( final Phylogeny phy : phys ) {\r
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
- }\r
- }\r
- AptxUtil.addPhylogeniesToTabs( phys,\r
- new File( url.getFile() ).getName(),\r
- new File( url.getFile() ).toString(),\r
- getConfiguration(),\r
- getMainPanel() );\r
- _mainpanel.getControlPanel().showWhole();\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
+ + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
- }\r
-\r
- void setMsa( final Msa msa ) {\r
- _msa = msa;\r
- }\r
-\r
- void setMsaFile( final File msa_file ) {\r
- _msa_file = msa_file;\r
- }\r
-\r
- void setSeqs( final List<MolecularSequence> seqs ) {\r
- _seqs = seqs;\r
- }\r
-\r
- void setSeqsFile( final File seqs_file ) {\r
- _seqs_file = seqs_file;\r
- }\r
-\r
- void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight() );\r
- String file_written_to = "";\r
- boolean error = false;\r
- try {\r
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
- _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getControlPanel(),\r
- type,\r
- getOptions() );\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Wrote image to: " + file_written_to,\r
- "Graphics Export",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "There was an unknown problem when attempting to write to an image file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- _contentpane.repaint();\r
- }\r
-\r
- private void addExpressionValuesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
+ else {\r
JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Expression Values",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _values_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _values_filechooser.showOpenDialog( _contentpane );\r
- final File file = _values_filechooser.getSelectedFile();\r
- if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- BasicTable<String> t = null;\r
- try {\r
- t = BasicTableParser.parse( file, '\t' );\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ',' );\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ' ' );\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getMessage(),\r
- "Could Not Read Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfColumns() + " column(s)",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfRows() < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains zero rows",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
- + phy.getNumberOfExternalNodes() + " external nodes",\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
- int not_found = 0;\r
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
- final PhylogenyNode node = iter.next();\r
- final String node_name = node.getName();\r
- if ( !ForesterUtil.isEmpty( node_name ) ) {\r
- int row = -1;\r
- try {\r
- row = t.findRow( node_name );\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- e.getMessage(),\r
- "Error Mapping Node Identifiers to Expression Value Identifiers",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( row < 0 ) {\r
- if ( node.isExternal() ) {\r
- not_found++;\r
- }\r
- continue;\r
- }\r
- final List<Double> l = new ArrayList<Double>();\r
- for( int col = 1; col < t.getNumberOfColumns(); ++col ) {\r
- double d = -100;\r
- try {\r
- d = Double.parseDouble( t.getValueAsString( col, row ) );\r
- }\r
- catch ( final NumberFormatException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not parse \"" + t.getValueAsString( col, row )\r
- + "\" into a decimal value",\r
- "Issue with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- stats.addValue( d );\r
- l.add( d );\r
- }\r
- if ( !l.isEmpty() ) {\r
- if ( node.getNodeData().getProperties() != null ) {\r
- node.getNodeData().getProperties()\r
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
- }\r
- node.getNodeData().setVector( l );\r
- }\r
- }\r
- }\r
- if ( not_found > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
- }\r
- getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
+ "No branch collapsed because no confidence values present",\r
+ "No confidence values present",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
\r
- private void addSequencesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Sequences",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _sequences_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _sequences_filechooser.showOpenDialog( _contentpane );\r
- final File file = _sequences_filechooser.getSelectedFile();\r
- List<MolecularSequence> seqs = null;\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- try {\r
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
- seqs = FastaParser.parse( new FileInputStream( file ) );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Format does not appear to be Fasta",\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file is empty",\r
- "Empty multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- }\r
- if ( seqs != null ) {\r
- for( final MolecularSequence seq : seqs ) {\r
- System.out.println( seq.getIdentifier() );\r
- }\r
+ private void collapseBelowBranchLengthThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- int total_counter = 0;\r
- int attached_counter = 0;\r
- for( final MolecularSequence seq : seqs ) {\r
- ++total_counter;\r
- final String seq_name = seq.getIdentifier();\r
- if ( !ForesterUtil.isEmpty( seq_name ) ) {\r
- List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaSequenceSymbol( seq_name );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaGeneName( seq_name );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodes( seq_name );\r
- }\r
- if ( nodes.size() > 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Sequence name \"" + seq_name + "\" is not unique",\r
- "Sequence name not unique",\r
- JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- final String[] a = seq_name.split( "\\s" );\r
- if ( nodes.isEmpty() && ( a.length > 1 ) ) {\r
- final String seq_name_split = a[ 0 ];\r
- nodes = phy.getNodesViaSequenceName( seq_name_split );\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaSequenceSymbol( seq_name_split );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodes( seq_name_split );\r
- }\r
- if ( nodes.size() > 1 ) {\r
- JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- }\r
- if ( nodes.size() == 1 ) {\r
- ++attached_counter;\r
- final PhylogenyNode n = nodes.get( 0 );\r
- if ( !n.getNodeData().isHasSequence() ) {\r
- n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );\r
- }\r
- n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );\r
- if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {\r
- n.getNodeData().getSequence().setName( seq_name );\r
- }\r
- }\r
- }\r
- }\r
- if ( attached_counter > 0 ) {\r
- int ext_nodes = 0;\r
- int ext_nodes_with_seq = 0;\r
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
- ++ext_nodes;\r
- final PhylogenyNode n = iter.next();\r
- if ( n.getNodeData().isHasSequence()\r
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {\r
- ++ext_nodes_with_seq;\r
- }\r
- }\r
- final String s;\r
- if ( ext_nodes == ext_nodes_with_seq ) {\r
- s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";\r
- }\r
- else {\r
- s = ext_nodes_with_seq + " out of " + ext_nodes\r
- + " external nodes now have a molecular sequence attached to them.";\r
- }\r
- if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Attached all " + total_counter + " sequences to tree nodes.\n" + s,\r
- "All sequences attached",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
- + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- }\r
-\r
- private void choosePdfWidth() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the default line width for PDF export.\n"\r
- + "[current value: "\r
- + getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- float f = 0.0f;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- f = Float.parseFloat( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( f > 0.0 ) ) {\r
- getOptions().setPrintLineWidth( f );\r
- }\r
- }\r
- }\r
-\r
- private void choosePrintSize() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter values for width and height,\nseparated by a comma.\n"\r
- + "[current values: "\r
- + getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() + "]\n"\r
- + "[A4: " + Constants.A4_SIZE_X + ", "\r
- + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
- + Constants.US_LETTER_SIZE_X + ", "\r
- + Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
- if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
- boolean success = true;\r
- int x = 0;\r
- int y = 0;\r
- final String[] str_ary = s.split( "," );\r
- if ( str_ary.length == 2 ) {\r
- final String x_str = str_ary[ 0 ].trim();\r
- final String y_str = str_ary[ 1 ].trim();\r
- if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
- try {\r
- x = Integer.parseInt( x_str );\r
- y = Integer.parseInt( y_str );\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum branch length value\n",\r
+ "Minimal Branch Length Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseBlValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
}\r
- catch ( final Exception ex ) {\r
+ else {\r
success = false;\r
}\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseBlValue( m );\r
+ collapseBl( phy );\r
+ }\r
}\r
- else {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
- getOptions().setPrintSizeX( x );\r
- getOptions().setPrintSizeY( y );\r
}\r
}\r
}\r
\r
- private void closeCurrentPane() {\r
- if ( getMainPanel().getCurrentTreePanel() != null ) {\r
- if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Close tab despite potentially unsaved changes?",\r
- "Close Tab?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
+ private void collapseBelowThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the minimum confidence value\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseConfidenceValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseConfidenceValue( m );\r
+ collapse( phy );\r
+ }\r
}\r
}\r
- getMainPanel().closeCurrentPane();\r
- activateSaveAllIfNeeded();\r
}\r
}\r
\r
}\r
}\r
\r
- private void collapse( final Phylogeny phy ) {\r
- final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
- final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
- double min_support = Double.MAX_VALUE;\r
- boolean conf_present = false;\r
- while ( it.hasNext() ) {\r
- final PhylogenyNode n = it.next();\r
- if ( !n.isExternal() && !n.isRoot() ) {\r
- final List<Confidence> c = n.getBranchData().getConfidences();\r
- if ( ( c != null ) && ( c.size() > 0 ) ) {\r
- conf_present = true;\r
- double max = 0;\r
- for( final Confidence confidence : c ) {\r
- if ( confidence.getValue() > max ) {\r
- max = confidence.getValue();\r
- }\r
- }\r
- if ( max < getMinNotCollapseConfidenceValue() ) {\r
- to_be_removed.add( n );\r
- }\r
- if ( max < min_support ) {\r
- min_support = max;\r
- }\r
- }\r
- }\r
- }\r
- if ( conf_present ) {\r
- for( final PhylogenyNode node : to_be_removed ) {\r
- PhylogenyMethods.removeNode( node, phy );\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- phy.externalNodesHaveChanged();\r
- phy.clearHashIdToNodeMap();\r
- phy.recalculateNumberOfExternalDescendants( true );\r
- getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
- getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
- getCurrentTreePanel().calculateLongestExtNodeInfo();\r
- getCurrentTreePanel().setNodeInPreorderToNull();\r
- getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().setEdited( true );\r
- getCurrentTreePanel().repaint();\r
- repaint();\r
- }\r
- if ( to_be_removed.size() > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
- + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "No branch collapsed because no confidence values present",\r
- "No confidence values present",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- }\r
-\r
- private void collapseBelowThreshold() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the minimum confidence value\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getMinNotCollapseConfidenceValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- setMinNotCollapseConfidenceValue( m );\r
- collapse( phy );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- private void collapseBelowBranchLengthThreshold() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final String s = ( String ) JOptionPane\r
- .showInputDialog( this,\r
- "Please enter the minimum branch length value\n",\r
- "Minimal Branch Length Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getMinNotCollapseBlValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- setMinNotCollapseBlValue( m );\r
- collapseBl( phy );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
private PhyloXmlParser createPhyloXmlParser() {\r
PhyloXmlParser xml_parser = null;\r
if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {\r
return xml_parser;\r
}\r
\r
+ public void end() {\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ void executeLineageInference() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Phylogeny is not rooted.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getCurrentPhylogeny()\r
+ .copy() );\r
+ new Thread( inferrer ).start();\r
+ }\r
+\r
private void executePhyleneticInference( final boolean from_unaligned_seqs ) {\r
final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,\r
getPhylogeneticInferenceOptions(),\r
}\r
}\r
\r
+ void exit() {\r
+ removeAllTextFrames();\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.\r
+ }\r
+\r
private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {\r
final StringBuilder sb = new StringBuilder();\r
final StringBuilder sb_failed = new StringBuilder();\r
}\r
}\r
\r
- \r
- \r
+ @Override\r
+ public MainPanel getMainPanel() {\r
+ return _mainpanel;\r
+ }\r
+\r
+ private double getMinNotCollapseBlValue() {\r
+ return _min_not_collapse_bl;\r
+ }\r
\r
private double getMinNotCollapseConfidenceValue() {\r
return _min_not_collapse;\r
}\r
\r
- private double getMinNotCollapseBlValue() {\r
- return _min_not_collapse_bl;\r
+ public Msa getMsa() {\r
+ return _msa;\r
+ }\r
+\r
+ public File getMsaFile() {\r
+ return _msa_file;\r
}\r
\r
private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {\r
return _phylogenetic_inference_options;\r
}\r
\r
+ public List<MolecularSequence> getSeqs() {\r
+ return _seqs;\r
+ }\r
+\r
+ public File getSeqsFile() {\r
+ return _seqs_file;\r
+ }\r
+\r
private boolean isUnsavedDataPresent() {\r
final List<TreePanel> tps = getMainPanel().getTreePanels();\r
for( final TreePanel tp : tps ) {\r
}\r
}\r
\r
+ private void preProcessTreesUponReading( final Phylogeny[] phys ) {\r
+ for( final Phylogeny phy : phys ) {\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( n.isExternal() ) {\r
+ if ( n.getNodeData().isHasSequence() ) {\r
+ final Sequence s = n.getNodeData().getSequence();\r
+ if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {\r
+ if ( ( s.getAccession() != null )\r
+ && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {\r
+ s.setGeneName( s.getAccession().getValue() );\r
+ }\r
+ else if ( !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ s.setGeneName( n.getName() );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
private void print() {\r
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )\r
|| getCurrentTreePanel().getPhylogeny().isEmpty() ) {\r
}\r
}\r
\r
- \r
+ public void readMsaFromFile() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _msa_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _msa_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the msa\r
+ final File file = _msa_filechooser.getSelectedFile();\r
+ setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setMsaFile( null );\r
+ setMsa( null );\r
+ Msa msa = null;\r
+ try {\r
+ final InputStream is = new FileInputStream( file );\r
+ if ( FastaParser.isLikelyFasta( file ) ) {\r
+ msa = FastaParser.parseMsa( is );\r
+ }\r
+ else {\r
+ msa = GeneralMsaParser.parse( is );\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence alignment format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment is empty",\r
+ "Illegal Multiple Sequence Alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getNumberOfSequences() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getLength() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 2 residues",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ System.gc();\r
+ setMsaFile( _msa_filechooser.getSelectedFile() );\r
+ setMsa( msa );\r
+ }\r
+ }\r
\r
private void readPhylogeniesFromFile() {\r
boolean exception = false;\r
else {\r
_mainpanel.setWaitCursor();\r
}\r
- if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )\r
- || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {\r
+ if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter )\r
+ || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) {\r
try {\r
final NHXParser nhx = new NHXParser();\r
setSpecialOptionsForNhxParser( nhx );\r
exceptionOccuredDuringOpenFile( e );\r
}\r
}\r
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
+ else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
warnIfNotPhyloXmlValidation( getConfiguration() );\r
try {\r
final PhyloXmlParser xml_parser = createPhyloXmlParser();\r
exceptionOccuredDuringOpenFile( e );\r
}\r
}\r
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {\r
+ else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) {\r
try {\r
phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
}\r
exceptionOccuredDuringOpenFile( e );\r
}\r
}\r
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {\r
+ else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
try {\r
final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();\r
setSpecialOptionsForNexParser( nex );\r
System.gc();\r
}\r
\r
- private void preProcessTreesUponReading( final Phylogeny[] phys ) {\r
- for( final Phylogeny phy : phys ) {\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {\r
- final PhylogenyNode n = it.next();\r
- if ( n.isExternal() ) {\r
- if ( n.getNodeData().isHasSequence() ) {\r
- final Sequence s = n.getNodeData().getSequence();\r
- if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {\r
- if ( ( s.getAccession() != null )\r
- && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {\r
- s.setGeneName( s.getAccession().getValue() );\r
- }\r
- else if ( !ForesterUtil.isEmpty( n.getName() ) ) {\r
- s.setGeneName( n.getName() );\r
- }\r
- }\r
- }\r
+ void readPhylogeniesFromURL() {\r
+ URL url = null;\r
+ Phylogeny[] phys = null;\r
+ final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";\r
+ final String url_string = JOptionPane.showInputDialog( this,\r
+ message,\r
+ "Use URL/webservice to obtain a phylogeny",\r
+ JOptionPane.QUESTION_MESSAGE );\r
+ boolean nhx_or_nexus = false;\r
+ if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {\r
+ try {\r
+ url = new URL( url_string );\r
+ PhylogenyParser parser = null;\r
+ if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {\r
+ parser = new TolParser();\r
+ }\r
+ else {\r
+ parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
+ .isValidatePhyloXmlAgainstSchema() );\r
+ }\r
+ if ( parser instanceof NexusPhylogeniesParser ) {\r
+ nhx_or_nexus = true;\r
+ }\r
+ else if ( parser instanceof NHXParser ) {\r
+ nhx_or_nexus = true;\r
+ }\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().setWaitCursor();\r
+ }\r
+ else {\r
+ _mainpanel.setWaitCursor();\r
+ }\r
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
+ phys = factory.create( url.openStream(), parser );\r
+ }\r
+ catch ( final MalformedURLException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),\r
+ "Malformed URL",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ catch ( final IOException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Could not read from " + url + "\n"\r
+ + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Failed to read URL",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Unexpected Exception",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ finally {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ else {\r
+ _mainpanel.setArrowCursor();\r
+ }\r
+ }\r
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
+ if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
+ for( final Phylogeny phy : phys ) {\r
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
+ }\r
+ }\r
+ AptxUtil.addPhylogeniesToTabs( phys,\r
+ new File( url.getFile() ).getName(),\r
+ new File( url.getFile() ).toString(),\r
+ getConfiguration(),\r
+ getMainPanel() );\r
+ _mainpanel.getControlPanel().showWhole();\r
+ }\r
+ }\r
+ activateSaveAllIfNeeded();\r
+ System.gc();\r
+ }\r
+\r
+ public void readSeqsFromFileforPI() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the seqs\r
+ final File file = _seqs_pi_filechooser.getSelectedFile();\r
+ setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setSeqsFile( null );\r
+ setSeqs( null );\r
+ List<MolecularSequence> seqs = null;\r
+ try {\r
+ if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
+ seqs = FastaParser.parse( new FileInputStream( file ) );\r
+ for( final MolecularSequence seq : seqs ) {\r
+ System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
}\r
}\r
+ else {\r
+ //TODO error\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence file format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file is empty",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( seqs.size() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
+ // if ( msa.getLength() < 2 ) {\r
+ // JOptionPane.showMessageDialog( this,\r
+ // "Multiple sequence alignment needs to contain at least 2 residues",\r
+ // "Illegal multiple sequence file",\r
+ // JOptionPane.ERROR_MESSAGE );\r
+ // return;\r
+ // }\r
+ System.gc();\r
+ setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
+ setSeqs( seqs );\r
}\r
}\r
\r
final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
+ if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {\r
try {\r
final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
.createPhyloXmlParserXsdValidating(), file );\r
exceptionOccuredDuringOpenFile( e );\r
}\r
}\r
- else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {\r
+ else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {\r
try {\r
final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
t = trees[ 0 ];\r
}\r
}\r
\r
- \r
+ private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
+ _min_not_collapse_bl = min_not_collapse_bl;\r
+ }\r
\r
private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
_min_not_collapse = min_not_collapse;\r
}\r
\r
- private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
- _min_not_collapse_bl = min_not_collapse_bl;\r
+ void setMsa( final Msa msa ) {\r
+ _msa = msa;\r
+ }\r
+\r
+ void setMsaFile( final File msa_file ) {\r
+ _msa_file = msa_file;\r
}\r
\r
private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
_phylogenetic_inference_options = phylogenetic_inference_options;\r
}\r
\r
+ void setSeqs( final List<MolecularSequence> seqs ) {\r
+ _seqs = seqs;\r
+ }\r
+\r
+ void setSeqsFile( final File seqs_file ) {\r
+ _seqs_file = seqs_file;\r
+ }\r
+\r
private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
}\r
}\r
}\r
-\r
- private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
- }\r
- return exception;\r
- }\r
-\r
- private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
- }\r
- return exception;\r
- }\r
-\r
- private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toPhyloXML( file, t, 0 );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
- }\r
- return exception;\r
- }\r
-\r
- private void writeToFile( final Phylogeny t ) {\r
- if ( t == null ) {\r
- return;\r
- }\r
- String initial_filename = null;\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- try {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
- }\r
- catch ( final IOException e ) {\r
- initial_filename = null;\r
- }\r
- }\r
- if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
- _save_filechooser.setSelectedFile( new File( initial_filename ) );\r
- }\r
- else {\r
- _save_filechooser.setSelectedFile( new File( "" ) );\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _save_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _save_filechooser.showSaveDialog( _contentpane );\r
- final File file = _save_filechooser.getSelectedFile();\r
- setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
- boolean exception = false;\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists.\nOverwrite?",\r
- "Overwrite?",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.QUESTION_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- else {\r
- final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
- try {\r
- ForesterUtil.copyFile( file, to );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to create backup copy " + to,\r
- "Failed to Create Backup Copy",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Failed to Delete",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // "*.*":\r
- else {\r
- final String file_name = file.getName().trim().toLowerCase();\r
- if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tree" ) ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // XML is default:\r
- else {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
- }\r
- if ( !exception ) {\r
- getMainPanel().setTitleOfSelectedTab( file.getName() );\r
- getMainPanel().getCurrentTreePanel().setTreeFile( file );\r
- getMainPanel().getCurrentTreePanel().setEdited( false );\r
- }\r
- }\r
- }\r
-\r
- private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return;\r
- }\r
- String initial_filename = "";\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + "." + type;\r
- _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _writetographics_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _writetographics_filechooser.showSaveDialog( _contentpane );\r
- File file = _writetographics_filechooser.getSelectedFile();\r
- setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
- file = new File( file.toString() + "." + type );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- writePhylogenyToGraphicsFile( file.toString(), type );\r
- }\r
- }\r
-\r
- \r
- public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
- return new MainFrameApplication( phys, config );\r
- }\r
-\r
- public static MainFrame createInstance( final Phylogeny[] phys,\r
- final Configuration config,\r
- final String title,\r
- final File current_dir ) {\r
- return new MainFrameApplication( phys, config, title, current_dir );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
- return new MainFrameApplication( phys, config, title );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
- return new MainFrameApplication( phys, config_file_name, title );\r
- }\r
-\r
- static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
- + o.getPrintSizeY() + ")" );\r
- }\r
-\r
- static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
- }\r
-\r
- static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
- if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
- JOptionPane\r
- .showMessageDialog( null,\r
- ForesterUtil\r
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
- 80 ),\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
} // MainFrameApplication.\r
-\r
-class DefaultFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )\r
- || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )\r
- || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )\r
- || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )\r
- || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )\r
- || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )\r
- || file_name.endsWith( ".con" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";\r
- }\r
-}\r
-\r
-class GraphicsFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )\r
- || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";\r
- }\r
-}\r
-\r
-class MsaFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )\r
- || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";\r
- }\r
-}\r
-\r
-class NexusFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )\r
- || file_name.endsWith( ".tre" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";\r
- }\r
-} // NexusFilter\r
-\r
-class NHFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )\r
- || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )\r
- || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";\r
- }\r
-} // NHFilter\r
-\r
-class NHXFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nhx" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "NHX files (*.nhx) [deprecated]";\r
- }\r
-}\r
-\r
-class PdfFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "PDF files (*.pdf)";\r
- }\r
-} // PdfFilter\r
-\r
-class SequencesFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )\r
- || file_name.endsWith( ".seqs" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";\r
- }\r
-}\r
-\r
-class TolFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f\r
- .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Tree of Life files (*.tol, *.tolxml)";\r
- }\r
-} // TolFilter\r
-\r
-class XMLFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )\r
- || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";\r
- }\r
-} // XMLFilter\r
git://source.jalview.org / jalview.git / commitdiff