From: cmzmasek@gmail.com Date: Wed, 11 Mar 2015 02:27:09 +0000 (+0000) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=236967e4df09b7a3fd6659a8131aa97ef9906a28;p=jalview.git in progress --- diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 14bcc07..f06965b 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -98,7 +98,7 @@ public final class AptxUtil { } } private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment() - .getAvailableFontFamilyNames(); + .getAvailableFontFamilyNames(); static { Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED ); } @@ -290,7 +290,7 @@ public final class AptxUtil { final boolean internal_numbers_are_confidences, final TAXONOMY_EXTRACTION taxonomy_extraction, final boolean midpoint_reroot ) - throws FileNotFoundException, IOException { + throws FileNotFoundException, IOException { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final PhylogenyParser parser; boolean nhx_or_nexus = false; @@ -338,7 +338,7 @@ public final class AptxUtil { final public static void showErrorMessage( final Component parent, final String error_msg ) { printAppletMessage( Constants.PRG_NAME, error_msg ); JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION - + "] Error", JOptionPane.ERROR_MESSAGE ); + + "] Error", JOptionPane.ERROR_MESSAGE ); } public static void writePhylogenyToGraphicsFile( final File intree, @@ -363,7 +363,7 @@ public final class AptxUtil { phys[ 0 ] = phy; final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config ); AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel() - .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() ); + .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() ); mf.end(); } @@ -417,8 +417,8 @@ public final class AptxUtil { } final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException, - SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException, - InvocationTargetException, InterruptedException { + SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException, + InvocationTargetException, InterruptedException { final String os = System.getProperty( "os.name" ); final Runtime runtime = Runtime.getRuntime(); if ( os.toLowerCase().startsWith( "win" ) ) { @@ -453,8 +453,8 @@ public final class AptxUtil { final MainPanel main_panel ) { if ( phys.length > Constants.MAX_TREES_TO_LOAD ) { JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length - + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME - + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE ); + + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME + + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE ); } int i = 1; for( final Phylogeny phy : phys ) { @@ -825,8 +825,8 @@ public final class AptxUtil { JOptionPane.showMessageDialog( null, "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" + "\n\nError: " + e.getLocalizedMessage(), - "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]", - JOptionPane.ERROR_MESSAGE ); + "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]", + JOptionPane.ERROR_MESSAGE ); System.exit( -1 ); } @@ -855,10 +855,10 @@ public final class AptxUtil { sb.append( s + "\n" ); } JOptionPane - .showMessageDialog( null, - "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: " - + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n" - + sb, + .showMessageDialog( null, + "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: " + + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n" + + sb, "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE ); System.exit( -1 ); @@ -876,8 +876,8 @@ public final class AptxUtil { "An unexpected exception has occured. \nPlease contact: " + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage() + "\n" + sb, - "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]", - JOptionPane.ERROR_MESSAGE ); + "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]", + JOptionPane.ERROR_MESSAGE ); } final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos, diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java index e1a8a47..f88a8f0 100644 --- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java +++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java @@ -88,7 +88,7 @@ public final class Archaeopteryx { } boolean nhx_or_nexus = false; final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( f, conf - .isValidatePhyloXmlAgainstSchema() ); + .isValidatePhyloXmlAgainstSchema() ); if ( p instanceof NHXParser ) { nhx_or_nexus = true; final NHXParser nhx = ( NHXParser ) p; diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java index 87ba7b7..c78bde4 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java @@ -138,9 +138,9 @@ public class ArchaeopteryxA extends JApplet { _mainframe_applet = new MainFrameApplet( this, configuration, getSpeciesTreeUrlStr() ); final URL tree_url = new URL( getTreeUrlStr() ); final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( tree_url, configuration - .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration - .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration - .isMidpointReroot() ); + .isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration + .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration + .isMidpointReroot() ); if ( phys == null ) { ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are null" ); } @@ -183,12 +183,12 @@ public class ArchaeopteryxA extends JApplet { final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE ); if ( default_relation != null ) { getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationTypeBox() - .setSelectedItem( default_relation ); + .setSelectedItem( default_relation ); } final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE ); if ( default_sequence != null ) { getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox() - .setSelectedItem( default_sequence ); + .setSelectedItem( default_sequence ); } /* GUILHEM_END */ } diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 4321360..229b787 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -478,31 +478,31 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { setCurrentDir( new_dir ); } } // TODO - // TODO - // TODO - // TODO - // TODO - // else if ( o == _graphics_export_visible_only_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _antialias_print_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _print_black_and_white_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _print_using_actual_size_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _graphics_export_using_actual_size_cbmi ) { - // updateOptions( getOptions() ); - // } - // else if ( o == _print_size_mi ) { - // choosePrintSize(); - // } - // else if ( o == _choose_pdf_width_mi ) { - // choosePdfWidth(); - // } + // TODO + // TODO + // TODO + // TODO + // else if ( o == _graphics_export_visible_only_cbmi ) { + // updateOptions( getOptions() ); + // } + // else if ( o == _antialias_print_cbmi ) { + // updateOptions( getOptions() ); + // } + // else if ( o == _print_black_and_white_cbmi ) { + // updateOptions( getOptions() ); + // } + // else if ( o == _print_using_actual_size_cbmi ) { + // updateOptions( getOptions() ); + // } + // else if ( o == _graphics_export_using_actual_size_cbmi ) { + // updateOptions( getOptions() ); + // } + // else if ( o == _print_size_mi ) { + // choosePrintSize(); + // } + // else if ( o == _choose_pdf_width_mi ) { + // choosePdfWidth(); + // } repaint(); } @@ -646,7 +646,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { ForesterUtil.printErrorMessage( NAME, "error: " + e ); e.printStackTrace(); JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str - + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE ); + + "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE ); } if ( phys_url == null ) { ForesterUtil.printErrorMessage( NAME, "failed to get tree URL from " @@ -710,7 +710,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } catch ( final IOException e ) { ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str - + "]" ); + + "]" ); JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from [" + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE ); } @@ -758,11 +758,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { public void componentResized( final ComponentEvent e ) { if ( getMainPanel().getCurrentTreePanel() != null ) { getMainPanel().getCurrentTreePanel().calcParametersForPainting( getMainPanel() - .getCurrentTreePanel() - .getWidth(), + .getCurrentTreePanel() + .getWidth(), getMainPanel() - .getCurrentTreePanel() - .getHeight() ); + .getCurrentTreePanel() + .getHeight() ); } } } ); @@ -784,7 +784,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { AptxUtil.printAppletMessage( NAME, "not using tabbed display" ); if ( getSpeciesTree() != null ) { AptxUtil.printAppletMessage( NAME, - "Warning: gsdi (gene duplication inference) only available tabbed display" ); + "Warning: gsdi (gene duplication inference) only available tabbed display" ); } AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() ); } @@ -845,11 +845,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .showInputDialog( this, "Please the minimum for confidence values to be displayed.\n" + "[current value: " + getOptions().getMinConfidenceValue() + "]\n", - "Minimal Confidence Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getMinConfidenceValue() ); + "Minimal Confidence Value", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getMinConfidenceValue() ); if ( !ForesterUtil.isEmpty( s ) ) { boolean success = true; double m = 0.0; @@ -1024,9 +1024,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); MainFrame - .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); + .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame - .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); + .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); @@ -1042,10 +1042,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), getConfiguration() ) ); _options_jmenu - .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); + .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu - .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) ); + .add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.NON_LINED_UP_CLADOGRAMS_LABEL ) ); _radio_group_1 = new ButtonGroup(); _radio_group_1.add( _ext_node_dependent_cladogram_rbmi ); _radio_group_1.add( _uniform_cladograms_rbmi ); @@ -1053,11 +1053,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); _options_jmenu - .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu - .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); _options_jmenu - .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); + .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); @@ -1066,9 +1066,9 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu - .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); _options_jmenu - .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); + .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); @@ -1086,12 +1086,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), getConfiguration() ) ); _options_jmenu - .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); + .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) ); _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); _options_jmenu - .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) ); + .add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( MainFrame.INVERSE_SEARCH_RESULT_LABEL ) ); customizeJMenuItem( _choose_font_mi ); customizeJMenuItem( _choose_minimal_confidence_mi ); customizeJMenuItem( _switch_colors_mi ); @@ -1105,11 +1105,11 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() ); customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() ); customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() - .isShowDefaultNodeShapesExternal() ); + .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() - .isShowDefaultNodeShapesInternal() ); + .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() - .isShowDefaultNodeShapesForMarkedNodes() ); + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -1141,7 +1141,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _tools_menu.addSeparator(); _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); _remove_visual_styles_item - .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); customizeJMenuItem( _remove_visual_styles_item ); _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); @@ -1182,7 +1182,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { void buildViewMenu() { _view_jmenu = MainFrame.createMenu( "View", getConfiguration() ); _view_jmenu - .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) ); + .add( _display_basic_information_item = new JMenuItem( MainFrame.SHOW_BASIC_TREE_INFORMATION_LABEL ) ); _view_jmenu.addSeparator(); _view_jmenu.add( _view_as_XML_item = new JMenuItem( "as phyloXML" ) ); _view_jmenu.add( _view_as_NH_item = new JMenuItem( "as Newick" ) ); @@ -1301,8 +1301,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.WARNING_MESSAGE ); + "GSDI successfully completed", + JOptionPane.WARNING_MESSAGE ); } else { JOptionPane.showMessageDialog( this, @@ -1314,8 +1314,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.INFORMATION_MESSAGE ); + "GSDI successfully completed", + JOptionPane.INFORMATION_MESSAGE ); } } @@ -1374,8 +1374,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.WARNING_MESSAGE ); + "GSDIR successfully completed", + JOptionPane.WARNING_MESSAGE ); } else { JOptionPane.showMessageDialog( this, @@ -1385,8 +1385,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.INFORMATION_MESSAGE ); + "GSDIR successfully completed", + JOptionPane.INFORMATION_MESSAGE ); } } @@ -1501,10 +1501,10 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { if ( getCurrentTreePanel() != null ) { if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { JOptionPane - .showMessageDialog( this, - "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", - "Operation can not be exectuted on a sub-tree", - JOptionPane.WARNING_MESSAGE ); + .showMessageDialog( this, + "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", + "Operation can not be exectuted on a sub-tree", + JOptionPane.WARNING_MESSAGE ); return true; } } @@ -1633,20 +1633,20 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { void updateOptions( final Options options ) { options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() ); options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) - && _background_gradient_cbmi.isSelected() ); + && _background_gradient_cbmi.isSelected() ); options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) - && _show_annotation_ref_source.isSelected() ); + && _show_annotation_ref_source.isSelected() ); options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) - && _abbreviate_scientific_names.isSelected() ); + && _abbreviate_scientific_names.isSelected() ); options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) - && _color_labels_same_as_parent_branch.isSelected() ); + && _color_labels_same_as_parent_branch.isSelected() ); options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) - && _show_default_node_shapes_internal_cbmi.isSelected() ); + && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) - && _show_default_node_shapes_external_cbmi.isSelected() ); + && _show_default_node_shapes_external_cbmi.isSelected() ); options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) - && _show_default_node_shapes_for_marked_cbmi.isSelected() ); + && _show_default_node_shapes_for_marked_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } @@ -1657,7 +1657,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); } options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null ) - && _search_case_senstive_cbmi.isSelected() ); + && _search_case_senstive_cbmi.isSelected() ); if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) { options.setShowScale( _show_scale_cbmi.isSelected() ); } @@ -1671,12 +1671,12 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() ); options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null ) - && _show_confidence_stddev_cbmi.isSelected() ); + && _show_confidence_stddev_cbmi.isSelected() ); options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) - && _search_whole_words_only_cbmi.isSelected() ); + && _search_whole_words_only_cbmi.isSelected() ); options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() ); options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) - && _inverse_search_result_cbmi.isSelected() ); + && _inverse_search_result_cbmi.isSelected() ); if ( ( _rectangular_type_cbmi != null ) && _rectangular_type_cbmi.isSelected() ) { options.setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); } @@ -1724,8 +1724,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toNexus( getOptions() - .getNhConversionSupportValueStyle() ), - title ); + .getNhConversionSupportValueStyle() ), + title ); } } @@ -1736,8 +1736,8 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( getMainPanel().getCurrentPhylogeny().toNewHampshire( getOptions() - .getNhConversionSupportValueStyle() ), - title ); + .getNhConversionSupportValueStyle() ), + title ); } } diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 8ec94ab..27e616a 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -67,32 +67,32 @@ public final class Configuration { FALSE, TRUE, UNKNOWN } final static String clickto_options[][] = { - { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" }, - { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" }, - { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" }, - { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" }, - { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, - { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" }, - { "List Node Data", "display" }, { "Select Node(s)", "display" } }; + { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, + { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" }, + { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" }, + { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" }, + { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" }, + { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, + { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" }, + { "List Node Data", "display" }, { "Select Node(s)", "display" } }; private final static String DEFAULT_SPECIES_COLORS[][] = { - { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" }, - { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" }, - { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" }, - { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" }, - { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" }, - { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" }, - { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" }, - { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" }, - { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" }, - { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" }, - { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" }, - { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" }, - { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" }, - { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" }, - { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" }, - { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" }, - { "PORGI", "0x918E00" } }; + { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" }, + { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" }, + { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" }, + { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" }, + { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" }, + { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" }, + { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" }, + { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" }, + { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" }, + { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" }, + { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" }, + { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" }, + { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" }, + { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" }, + { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" }, + { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" }, + { "PORGI", "0x918E00" } }; final static int display_node_data = 0; final static int collapse_uncollapse = 1; final static int reroot = 2; @@ -118,20 +118,20 @@ public final class Configuration { // Click-to options // ------------------ final static String display_options[][] = { - { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, - { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" }, - { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, - { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" }, - { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" }, - { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, - { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" }, - { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, - { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, - { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" }, - { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, - { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, - { "Properties", "display", "no" }, { "Gene Name", "display", "yes" }, - { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } }; + { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, + { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" }, + { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, + { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" }, + { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" }, + { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, + { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" }, + { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, + { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, + { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" }, + { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, + { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, + { "Properties", "display", "no" }, { "Gene Name", "display", "yes" }, + { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } }; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -644,8 +644,8 @@ public final class Configuration { if ( name.equals( "edit_info" ) ) { index = Configuration.display_node_data; ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [edit_info] is deprecated, use [display node data] instead" ); + .printWarningMessage( Constants.PRG_NAME, + "configuration key [edit_info] is deprecated, use [display node data] instead" ); } else if ( name.equals( "display_node_data" ) ) { index = Configuration.display_node_data; @@ -670,7 +670,7 @@ public final class Configuration { } else if ( name.equals( "display_sequences" ) ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); + .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); return DEPRECATED; } else if ( name.equals( "open_seq_web" ) ) { @@ -708,7 +708,7 @@ public final class Configuration { } else if ( name.equals( "display_node_popup" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [display_node_popup] is deprecated" ); + "configuration key [display_node_popup] is deprecated" ); return DEPRECATED; } else if ( name.equals( "custom_option" ) ) { @@ -879,7 +879,7 @@ public final class Configuration { default_clickto = getClickToIndex( clickto_name ); if ( default_clickto == -1 ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name - + "] for [default_click_to]" ); + + "] for [default_click_to]" ); default_clickto = 0; } else if ( default_clickto == DEPRECATED ) { @@ -899,7 +899,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str - + "]" ); + + "]" ); _ui = UI.UNKNOWN; } } @@ -938,7 +938,7 @@ public final class Configuration { else { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [phylogeny_graphics_type]" ); + + "] for [phylogeny_graphics_type]" ); } } else if ( key.equals( "min_confidence_value" ) ) { @@ -992,7 +992,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "value for [pdf_export_line_width] cannot be zero or negative" ); + "value for [pdf_export_line_width] cannot be zero or negative" ); } } else if ( key.equals( "window_initial_size_x" ) ) { @@ -1017,8 +1017,8 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "value for [default_number_of_bootstrap_resamples] cannot be negative" ); + .printWarningMessage( Constants.PRG_NAME, + "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } else if ( key.equals( "mafft_local" ) ) { @@ -1073,13 +1073,13 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [cladogram_type]" ); + + "] for [cladogram_type]" ); } } else if ( key.equals( "non_lined_up_cladogram" ) ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" ); + .printWarningMessage( Constants.PRG_NAME, + "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" ); } else if ( key.equals( "hide_controls_and_menus" ) ) { _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() ); @@ -1112,7 +1112,7 @@ public final class Configuration { else { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [overview_placement_type]" ); + + "] for [overview_placement_type]" ); } } else if ( key.equals( "node_label_direction" ) ) { @@ -1126,7 +1126,7 @@ public final class Configuration { else { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [node_label_direction]" ); + + "] for [node_label_direction]" ); } } else if ( key.equals( "branch_length_value_digits" ) ) { @@ -1136,7 +1136,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [branch_length_value_digits]" ); + + "] for [branch_length_value_digits]" ); } } else if ( key.equals( "confidence_value_digits" ) ) { @@ -1146,7 +1146,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [confidence_value_digits]" ); + + "] for [confidence_value_digits]" ); } } else if ( key.equals( "allow_editing" ) ) { @@ -1159,8 +1159,8 @@ public final class Configuration { final boolean r = parseBoolean( ( String ) st.nextElement() ); if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "attempt to extract taxonomies and replace underscores at the same time" ); + .printWarningMessage( Constants.PRG_NAME, + "attempt to extract taxonomies and replace underscores at the same time" ); } else { setReplaceUnderscoresInNhParsing( r ); @@ -1182,15 +1182,15 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "unknown value for \"taxonomy_extraction_in_nh_parsing\": " - + s - + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" ); + .printWarningMessage( Constants.PRG_NAME, + "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + + s + + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" ); } if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "attempt to extract taxonomies and replace underscores at the same time" ); + .printWarningMessage( Constants.PRG_NAME, + "attempt to extract taxonomies and replace underscores at the same time" ); } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { @@ -1246,7 +1246,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str - + "] for [default_node_fill]" ); + + "] for [default_node_fill]" ); } } else if ( key.equals( "default_node_shape" ) ) { @@ -1259,7 +1259,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str - + "] for [default_node_shape]" ); + + "] for [default_node_shape]" ); } } else if ( key.equals( "midpoint_reroot" ) ) { @@ -1308,7 +1308,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s - + "] for [ext_descendents_data_to_return]" ); + + "] for [ext_descendents_data_to_return]" ); } } else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) { @@ -1330,7 +1330,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s - + "] for [ext_descendents_data_to_return_on]" ); + + "] for [ext_descendents_data_to_return_on]" ); } } else if ( key.equals( "vector_data_min_color" ) ) { @@ -1399,8 +1399,8 @@ public final class Configuration { else if ( key.equals( "color_branches" ) ) { key_index = Configuration.use_style; ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); + .printWarningMessage( Constants.PRG_NAME, + "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); } else if ( key.equals( "width_branches" ) ) { key_index = Configuration.width_branches; @@ -1496,18 +1496,18 @@ public final class Configuration { } else if ( key.equals( "annotation_color" ) ) { getAnnotationColors() - .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); + .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( "function_color" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [function_color] is deprecated" ); + "configuration key [function_color] is deprecated" ); } else if ( key.equals( DISPLAY_COLOR_KEY ) ) { putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key - + "] in: " + config_filename ); + + "] in: " + config_filename ); } } } diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 22dc4a3..cd43a92 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -46,7 +46,7 @@ public final class Constants { final static String PRG_DATE = "150306"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica", - "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; + "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; final static boolean VERBOSE_DEFAULT = false; final static int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 100; final static String AUTHOR_EMAIL = "phyloxml@gmail.com"; diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 1bc7d4b..4cc4960 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -527,7 +527,7 @@ final class ControlPanel extends JPanel implements ActionListener { cellHasFocus ); if ( ( value != null ) && ( value instanceof SequenceRelation.SEQUENCE_RELATION_TYPE ) ) { ( ( DefaultListCellRenderer ) component ).setText( SequenceRelation - .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) ); + .getPrintableNameByType( ( SequenceRelation.SEQUENCE_RELATION_TYPE ) value ) ); } return component; } @@ -610,7 +610,7 @@ final class ControlPanel extends JPanel implements ActionListener { isShowDomainArchitectures(), tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) - : 0 ) ); + : 0 ) ); } else { nodes.addAll( PhylogenyMethods.searchData( query, @@ -620,7 +620,7 @@ final class ControlPanel extends JPanel implements ActionListener { getOptions().isSearchWithRegex(), isShowDomainArchitectures(), tp != null ? Math.pow( 10, tp - .getDomainStructureEvalueThresholdExp() ) : 0 ) ); + .getDomainStructureEvalueThresholdExp() ) : 0 ) ); } } if ( getOptions().isInverseSearchResult() ) { @@ -672,7 +672,7 @@ final class ControlPanel extends JPanel implements ActionListener { isShowDomainArchitectures(), tp != null ? Math.pow( 10, tp.getDomainStructureEvalueThresholdExp() ) - : 0 ) ); + : 0 ) ); } else { nodes.addAll( PhylogenyMethods.searchData( query, @@ -682,7 +682,7 @@ final class ControlPanel extends JPanel implements ActionListener { getOptions().isSearchWithRegex(), isShowDomainArchitectures(), tp != null ? Math.pow( 10, tp - .getDomainStructureEvalueThresholdExp() ) : 0 ) ); + .getDomainStructureEvalueThresholdExp() ) : 0 ) ); } } if ( getOptions().isInverseSearchResult() ) { @@ -834,7 +834,7 @@ final class ControlPanel extends JPanel implements ActionListener { _get_ext_desc_data = cb_index; if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) { addClickToOption( Configuration.get_ext_desc_data, getConfiguration() - .getLabelForGetExtDescendentsData() ); + .getLabelForGetExtDescendentsData() ); } else { addClickToOption( Configuration.get_ext_desc_data, @@ -1205,7 +1205,7 @@ final class ControlPanel extends JPanel implements ActionListener { case Configuration.color_according_to_annotation: _color_according_to_annotation = new JCheckBox( title ); _color_according_to_annotation - .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" ); + .setToolTipText( "To colorize sequence annotation labels as a function of sequence annotation" ); addJCheckBox( _color_according_to_annotation, ch_panel ); add( ch_panel ); break; @@ -1262,7 +1262,7 @@ final class ControlPanel extends JPanel implements ActionListener { case Configuration.use_style: _use_visual_styles_cb = new JCheckBox( title ); getUseVisualStylesCb() - .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" ); + .setToolTipText( "To use visual styles (node colors, fonts) and branch colors, if present" ); addJCheckBox( getUseVisualStylesCb(), ch_panel ); add( ch_panel ); break; @@ -1791,13 +1791,13 @@ final class ControlPanel extends JPanel implements ActionListener { getNodeDescPopupCb().setSelected( state ); } break; - /* GUILHEM_BEG */ + /* GUILHEM_BEG */ case Configuration.show_relation_confidence: if ( _seq_relation_confidence_switch != null ) { _seq_relation_confidence_switch.setSelected( state ); } break; - /* GUILHEM_END */ + /* GUILHEM_END */ default: throw new AssertionError( "unknown checkbox: " + which ); } @@ -2326,7 +2326,7 @@ final class ControlPanel extends JPanel implements ActionListener { } else { getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getMainPanel().getCurrentTreePanel() - .getPhylogenyGraphicsType() ); + .getPhylogenyGraphicsType() ); } getMainPanel().getCurrentTreePanel().updateSubSuperTreeButton(); getMainPanel().getControlPanel().search0(); @@ -2384,7 +2384,7 @@ final class ControlPanel extends JPanel implements ActionListener { treepanel.resetPreferredSize(); getMainPanel().getCurrentScrollPane().getViewport().validate(); sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - - ( sb.getVisibleAmount() / 2.0 ) ) ); + - ( sb.getVisibleAmount() / 2.0 ) ) ); } else { final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue(); @@ -2409,7 +2409,7 @@ final class ControlPanel extends JPanel implements ActionListener { treepanel.resetPreferredSize(); getMainPanel().getCurrentScrollPane().getViewport().validate(); sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - - ( sb.getVisibleAmount() / 2.0 ) ) ); + - ( sb.getVisibleAmount() / 2.0 ) ) ); treepanel.resetPreferredSize(); treepanel.updateOvSizes(); } @@ -2434,7 +2434,7 @@ final class ControlPanel extends JPanel implements ActionListener { treepanel.resetPreferredSize(); getMainPanel().getCurrentScrollPane().getViewport().validate(); sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - - ( sb.getVisibleAmount() / 2.0 ) ) ); + - ( sb.getVisibleAmount() / 2.0 ) ) ); } else { final int x = sb.getMaximum() - sb.getMinimum() - sb.getVisibleAmount() - sb.getValue(); @@ -2463,7 +2463,7 @@ final class ControlPanel extends JPanel implements ActionListener { treepanel.resetPreferredSize(); getMainPanel().getCurrentScrollPane().getViewport().validate(); sb.setValue( ForesterUtil.roundToInt( ( ( sb.getMaximum() - sb.getMinimum() ) / x ) - - ( sb.getVisibleAmount() / 2.0 ) ) ); + - ( sb.getVisibleAmount() / 2.0 ) ) ); treepanel.resetPreferredSize(); treepanel.updateOvSizes(); } diff --git a/forester/java/src/org/forester/archaeopteryx/FontChooser.java b/forester/java/src/org/forester/archaeopteryx/FontChooser.java index f8b2f17..966a461 100644 --- a/forester/java/src/org/forester/archaeopteryx/FontChooser.java +++ b/forester/java/src/org/forester/archaeopteryx/FontChooser.java @@ -41,7 +41,7 @@ public class FontChooser extends JDialog implements ActionListener, ListSelectio public static final long serialVersionUID = 62256323L; private static final String[] STYLE = { REGULAR, BOLD, ITALIC, BOLD_ITALIC }; private static final String[] SIZE = { "3", "4", "6", "8", "10", "12", "14", "16", "18", "20", "22", - "24", "26", "28", "36", "72" }; + "24", "26", "28", "36", "72" }; private static final int OK_OPTION = 1; private static final int CANCEL_OPTION = 2; private Font _font; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 80a5ac7..d91758d 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -801,10 +801,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { } if ( ( nodes == null ) || nodes.isEmpty() ) { JOptionPane - .showMessageDialog( this, - "Need to select nodes, either via direct selection or via the \"Search\" function", - "No nodes selected for annotation", - JOptionPane.ERROR_MESSAGE ); + .showMessageDialog( this, + "Need to select nodes, either via direct selection or via the \"Search\" function", + "No nodes selected for annotation", + JOptionPane.ERROR_MESSAGE ); return; } final Phylogeny phy = getMainPanel().getCurrentPhylogeny(); @@ -823,7 +823,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { my_panel, "Enter the sequence annotation(s) for the " + nodes.size() + " selected nodes", - JOptionPane.OK_CANCEL_OPTION ); + JOptionPane.OK_CANCEL_OPTION ); if ( result == JOptionPane.OK_OPTION ) { String ref = ref_field.getText(); String desc = desc_filed.getText(); @@ -850,7 +850,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { for( final PhylogenyNode n : nodes ) { ForesterUtil.ensurePresenceOfSequence( n ); final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation() - : new Annotation( ref ); + : new Annotation( ref ); if ( !ForesterUtil.isEmpty( desc ) ) { ann.setDesc( desc ); } @@ -875,11 +875,11 @@ public abstract class MainFrame extends JFrame implements ActionListener { .showInputDialog( this, "Please enter the minimum for confidence values to be displayed.\n" + "[current value: " + getOptions().getMinConfidenceValue() + "]\n", - "Minimal Confidence Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getMinConfidenceValue() ); + "Minimal Confidence Value", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getMinConfidenceValue() ); if ( !ForesterUtil.isEmpty( s ) ) { boolean success = true; double m = 0.0; @@ -921,10 +921,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { } if ( ( nodes == null ) || nodes.isEmpty() ) { JOptionPane - .showMessageDialog( this, - "Need to select external nodes, either via direct selection or via the \"Search\" function", - "No external nodes selected to " + function.toLowerCase(), - JOptionPane.ERROR_MESSAGE ); + .showMessageDialog( this, + "Need to select external nodes, either via direct selection or via the \"Search\" function", + "No external nodes selected to " + function.toLowerCase(), + JOptionPane.ERROR_MESSAGE ); return; } final int todo = nodes.size(); @@ -941,8 +941,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { return; } final int result = JOptionPane.showConfirmDialog( null, function + " " + todo - + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res - + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION ); + + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res + + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION ); if ( result == JOptionPane.OK_OPTION ) { if ( !delete ) { final List to_delete = new ArrayList(); @@ -1212,11 +1212,11 @@ public abstract class MainFrame extends JFrame implements ActionListener { "Please enter the default line width for PDF export.\n" + "[current value: " + getOptions().getPrintLineWidth() + "]\n", - "Line Width for PDF Export", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getPrintLineWidth() ); + "Line Width for PDF Export", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getPrintLineWidth() ); if ( !ForesterUtil.isEmpty( s ) ) { boolean success = true; float f = 0.0f; @@ -1248,12 +1248,12 @@ public abstract class MainFrame extends JFrame implements ActionListener { + Constants.A4_SIZE_Y + "]\n" + "[US Letter: " + Constants.US_LETTER_SIZE_X + ", " + Constants.US_LETTER_SIZE_Y + "]", - "Default Size for Graphics Export", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getPrintSizeX() + ", " - + getOptions().getPrintSizeY() ); + "Default Size for Graphics Export", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getOptions().getPrintSizeX() + ", " + + getOptions().getPrintSizeY() ); if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) { boolean success = true; int x = 0; @@ -1432,8 +1432,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.WARNING_MESSAGE ); + "GSDI successfully completed", + JOptionPane.WARNING_MESSAGE ); } else { JOptionPane.showMessageDialog( this, @@ -1445,8 +1445,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDI successfully completed", - JOptionPane.INFORMATION_MESSAGE ); + "GSDI successfully completed", + JOptionPane.INFORMATION_MESSAGE ); } } @@ -1505,8 +1505,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.WARNING_MESSAGE ); + "GSDIR successfully completed", + JOptionPane.WARNING_MESSAGE ); } else { JOptionPane.showMessageDialog( this, @@ -1516,8 +1516,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n" + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n" + "Number of polytomies in species tree used: " + poly + "\n", - "GSDIR successfully completed", - JOptionPane.INFORMATION_MESSAGE ); + "GSDIR successfully completed", + JOptionPane.INFORMATION_MESSAGE ); } } @@ -1651,10 +1651,10 @@ public abstract class MainFrame extends JFrame implements ActionListener { if ( getCurrentTreePanel() != null ) { if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) { JOptionPane - .showMessageDialog( this, - "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", - "Operation can not be exectuted on a sub-tree", - JOptionPane.WARNING_MESSAGE ); + .showMessageDialog( this, + "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.", + "Operation can not be exectuted on a sub-tree", + JOptionPane.WARNING_MESSAGE ); return true; } } @@ -1805,20 +1805,20 @@ public abstract class MainFrame extends JFrame implements ActionListener { void updateOptions( final Options options ) { options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() ); options.setBackgroundColorGradient( ( _background_gradient_cbmi != null ) - && _background_gradient_cbmi.isSelected() ); + && _background_gradient_cbmi.isSelected() ); options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() ); options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null ) - && _show_annotation_ref_source.isSelected() ); + && _show_annotation_ref_source.isSelected() ); options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null ) - && _abbreviate_scientific_names.isSelected() ); + && _abbreviate_scientific_names.isSelected() ); options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null ) - && _color_labels_same_as_parent_branch.isSelected() ); + && _color_labels_same_as_parent_branch.isSelected() ); options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null ) - && _show_default_node_shapes_internal_cbmi.isSelected() ); + && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) - && _show_default_node_shapes_external_cbmi.isSelected() ); + && _show_default_node_shapes_external_cbmi.isSelected() ); options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null ) - && _show_default_node_shapes_for_marked_cbmi.isSelected() ); + && _show_default_node_shapes_for_marked_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } @@ -1829,7 +1829,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); } options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null ) - && _search_case_senstive_cbmi.isSelected() ); + && _search_case_senstive_cbmi.isSelected() ); if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) { options.setShowScale( _show_scale_cbmi.isSelected() ); } @@ -1843,14 +1843,14 @@ public abstract class MainFrame extends JFrame implements ActionListener { } options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() ); options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null ) - && _show_confidence_stddev_cbmi.isSelected() ); + && _show_confidence_stddev_cbmi.isSelected() ); if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) { options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() ); } options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null ) - && ( _print_using_actual_size_cbmi.isSelected() ) ); + && ( _print_using_actual_size_cbmi.isSelected() ) ); options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null ) - && ( _graphics_export_using_actual_size_cbmi.isSelected() ) ); + && ( _graphics_export_using_actual_size_cbmi.isSelected() ) ); options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() ); if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null ) && _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) { @@ -1864,9 +1864,9 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE ); } options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null ) - && _print_black_and_white_cbmi.isSelected() ); + && _print_black_and_white_cbmi.isSelected() ); options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null ) - && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); + && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() ); if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) { options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); } @@ -1880,14 +1880,14 @@ public abstract class MainFrame extends JFrame implements ActionListener { options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null ) - && _replace_underscores_cbmi.isSelected() ); + && _replace_underscores_cbmi.isSelected() ); options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null ) - && _allow_errors_in_distance_to_parent_cbmi.isSelected() ); + && _allow_errors_in_distance_to_parent_cbmi.isSelected() ); options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null ) - && _search_whole_words_only_cbmi.isSelected() ); + && _search_whole_words_only_cbmi.isSelected() ); options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() ); options.setInverseSearchResult( ( _inverse_search_result_cbmi != null ) - && _inverse_search_result_cbmi.isSelected() ); + && _inverse_search_result_cbmi.isSelected() ); if ( _graphics_export_visible_only_cbmi != null ) { options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() ); if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) { @@ -1953,8 +1953,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions() - .getNhConversionSupportValueStyle() ), - title ); + .getNhConversionSupportValueStyle() ), + title ); } } @@ -2043,11 +2043,11 @@ public abstract class MainFrame extends JFrame implements ActionListener { "Please enter the default size for node shapes.\n" + "[current value: " + options.getDefaultNodeShapeSize() + "]\n", - "Node Shape Size", - JOptionPane.QUESTION_MESSAGE, - null, - null, - options.getDefaultNodeShapeSize() ); + "Node Shape Size", + JOptionPane.QUESTION_MESSAGE, + null, + null, + options.getDefaultNodeShapeSize() ); if ( !ForesterUtil.isEmpty( s ) ) { boolean success = true; double m = 0.0; @@ -2227,8 +2227,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { JOptionPane.showMessageDialog( comp, "There was an unknown problem when attempting to write to PDF file: \"" + file_name + "\"", - "Error", - JOptionPane.ERROR_MESSAGE ); + "Error", + JOptionPane.ERROR_MESSAGE ); } } if ( !opts.isPrintUsingActualSize() ) { @@ -2277,7 +2277,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) { if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) { mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName() - + ")" ); + + ")" ); } else { mi.setText( "Select Color Scheme..." ); @@ -2389,8 +2389,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { JOptionPane.showMessageDialog( comp, "There was an unknown problem when attempting to write to an image file: \"" + file_name + "\"", - "Error", - JOptionPane.ERROR_MESSAGE ); + "Error", + JOptionPane.ERROR_MESSAGE ); } } contentpane.repaint(); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index 6374275..2547acf 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -99,7 +99,7 @@ public final class MainFrameApplet extends MainFrame { _contentpane.setLayout( new BorderLayout() ); _contentpane.add( _mainpanel, BorderLayout.CENTER ); setSize( getConfiguration().getFrameXSize() > 40 ? getConfiguration().getFrameXSize() : DEFAULT_FRAME_X_SIZE, - getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE ); + getConfiguration().getFrameYSize() > 40 ? getConfiguration().getFrameYSize() : DEFAULT_FRAME_Y_SIZE ); addWindowListener( new WindowAdapter() { @Override @@ -113,9 +113,9 @@ public final class MainFrameApplet extends MainFrame { public void componentResized( final ComponentEvent e ) { if ( _mainpanel.getCurrentTreePanel() != null ) { _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() - .getWidth(), + .getWidth(), _mainpanel.getCurrentTreePanel() - .getHeight() ); + .getHeight() ); } } } ); @@ -136,9 +136,9 @@ public final class MainFrameApplet extends MainFrame { final URL species_tree_url = new URL( species_tree_url_str ); final Phylogeny[] species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url, configuration - .isValidatePhyloXmlAgainstSchema(), + .isValidatePhyloXmlAgainstSchema(), configuration - .isReplaceUnderscoresInNhParsing(), + .isReplaceUnderscoresInNhParsing(), false, TAXONOMY_EXTRACTION.NO, false ); @@ -183,9 +183,9 @@ public final class MainFrameApplet extends MainFrame { MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); MainFrame - .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); + .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, createCurrentFontDesc( getMainPanel() - .getTreeFontSet() ) ); + .getTreeFontSet() ) ); setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); @@ -203,7 +203,7 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.DISPLAY_SUBHEADER ), getConfiguration() ) ); _options_jmenu - .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); + .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) ); _radio_group_1 = new ButtonGroup(); @@ -213,11 +213,11 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_SCALE_LABEL ) ); _options_jmenu - .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu - .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_EXT ) ); _options_jmenu - .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); + .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); @@ -226,9 +226,9 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( MainFrame.SHOW_ANN_REF_SOURCE_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( MainFrame.SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu - .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); + .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); _options_jmenu - .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); + .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( MainFrame.LABEL_DIRECTION_LABEL ) ); @@ -246,7 +246,7 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu.add( MainFrame.customizeMenuItemAsLabel( new JMenuItem( MainFrame.SEARCH_SUBHEADER ), getConfiguration() ) ); _options_jmenu - .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); + .add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_CASE_SENSITIVE_LABEL ) ); _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_TERMS_ONLY_LABEL ) ); _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) ); _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP ); @@ -258,11 +258,11 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); _options_jmenu - .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) ); + .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) ); _options_jmenu - .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) ); + .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) ); _options_jmenu - .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); + .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); // @@ -271,7 +271,7 @@ public final class MainFrameApplet extends MainFrame { customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() ); customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() ); customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions() - .isGraphicsExportUsingActualSize() ); + .isGraphicsExportUsingActualSize() ); customizeJMenuItem( _print_size_mi ); customizeJMenuItem( _choose_pdf_width_mi ); // @@ -280,11 +280,11 @@ public final class MainFrameApplet extends MainFrame { customizeJMenuItem( _choose_minimal_confidence_mi ); customizeJMenuItem( _overview_placment_mi ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() - .isShowDefaultNodeShapesInternal() ); + .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() - .isShowDefaultNodeShapesExternal() ); + .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() - .isShowDefaultNodeShapesForMarkedNodes() ); + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -324,7 +324,7 @@ public final class MainFrameApplet extends MainFrame { _tools_menu.addSeparator(); _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); _remove_visual_styles_item - .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." ); customizeJMenuItem( _remove_visual_styles_item ); _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 6b2c76c..853b1d5 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -362,9 +362,9 @@ public final class MainFrameApplication extends MainFrame { public void componentResized( final ComponentEvent e ) { if ( _mainpanel.getCurrentTreePanel() != null ) { _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() - .getWidth(), + .getWidth(), _mainpanel.getCurrentTreePanel() - .getHeight() ); + .getHeight() ); } } } ); @@ -756,8 +756,8 @@ public final class MainFrameApplication extends MainFrame { JOptionPane.showMessageDialog( this, "Table contains " + t.getNumberOfRows() + " rows, but tree contains " + phy.getNumberOfExternalNodes() + " external nodes", - "Warning", - JOptionPane.WARNING_MESSAGE ); + "Warning", + JOptionPane.WARNING_MESSAGE ); } final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); int not_found = 0; @@ -771,10 +771,10 @@ public final class MainFrameApplication extends MainFrame { } catch ( final IllegalArgumentException e ) { JOptionPane - .showMessageDialog( this, - e.getMessage(), - "Error Mapping Node Identifiers to Expression Value Identifiers", - JOptionPane.ERROR_MESSAGE ); + .showMessageDialog( this, + e.getMessage(), + "Error Mapping Node Identifiers to Expression Value Identifiers", + JOptionPane.ERROR_MESSAGE ); return; } if ( row < 0 ) { @@ -792,7 +792,7 @@ public final class MainFrameApplication extends MainFrame { catch ( final NumberFormatException e ) { JOptionPane.showMessageDialog( this, "Could not parse \"" + t.getValueAsString( col, row ) - + "\" into a decimal value", + + "\" into a decimal value", "Issue with Expression Value Table", JOptionPane.ERROR_MESSAGE ); return; @@ -803,7 +803,7 @@ public final class MainFrameApplication extends MainFrame { if ( !l.isEmpty() ) { if ( node.getNodeData().getProperties() != null ) { node.getNodeData().getProperties() - .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); + .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); } node.getNodeData().setVector( l ); } @@ -811,7 +811,7 @@ public final class MainFrameApplication extends MainFrame { } if ( not_found > 0 ) { JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found - + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE ); + + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE ); } getCurrentTreePanel().setStatisticsForExpressionValues( stats ); } @@ -920,7 +920,7 @@ public final class MainFrameApplication extends MainFrame { } if ( nodes.size() > 1 ) { JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split - + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE ); + + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE ); setArrowCursor(); return; } @@ -965,13 +965,13 @@ public final class MainFrameApplication extends MainFrame { } else { JOptionPane.showMessageDialog( this, "Attached " + attached_counter - + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter - + " sequences attached", JOptionPane.WARNING_MESSAGE ); + + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter + + " sequences attached", JOptionPane.WARNING_MESSAGE ); } } else { JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter - + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE ); + + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE ); } } } @@ -1038,8 +1038,8 @@ public final class MainFrameApplication extends MainFrame { } if ( to_be_removed.size() > 0 ) { JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() - + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed " - + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); + + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed " + + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); } else { JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is " @@ -1165,8 +1165,8 @@ public final class MainFrameApplication extends MainFrame { } if ( to_be_removed.size() > 0 ) { JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() - + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed " - + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); + + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed " + + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); } else { JOptionPane.showMessageDialog( this, @@ -1212,7 +1212,7 @@ public final class MainFrameApplication extends MainFrame { if ( getMsa() != null ) { final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(), getPhylogeneticInferenceOptions() - .copy(), this ); + .copy(), this ); new Thread( inferrer ).start(); } else { @@ -1226,7 +1226,7 @@ public final class MainFrameApplication extends MainFrame { if ( getSeqs() != null ) { final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(), getPhylogeneticInferenceOptions() - .copy(), this ); + .copy(), this ); new Thread( inferrer ).start(); } else { @@ -1284,17 +1284,17 @@ public final class MainFrameApplication extends MainFrame { } JOptionPane.showMessageDialog( this, "Extracted taxonomic data from " + all + counter - + " named external nodes:\n" + sb.toString() + failed, + + " named external nodes:\n" + sb.toString() + failed, "Taxonomic Data Extraction Completed", counter_failed > 0 ? JOptionPane.WARNING_MESSAGE : JOptionPane.INFORMATION_MESSAGE ); } else { JOptionPane - .showMessageDialog( this, - "Could not extract any taxonomic data.\nMaybe node names are empty\n" - + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n" - + "or nodes already have taxonomic data?\n", + .showMessageDialog( this, + "Could not extract any taxonomic data.\nMaybe node names are empty\n" + + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n" + + "or nodes already have taxonomic data?\n", "No Taxonomic Data Extracted", JOptionPane.ERROR_MESSAGE ); } @@ -1332,7 +1332,7 @@ public final class MainFrameApplication extends MainFrame { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); if ( ( phy != null ) && !phy.isEmpty() ) { PhylogenyMethods - .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false ); + .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false ); } } } @@ -1362,7 +1362,7 @@ public final class MainFrameApplication extends MainFrame { if ( getMainPanel().getMainFrame() == null ) { // Must be "E" applet version. ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); } else { getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); @@ -1509,7 +1509,7 @@ public final class MainFrameApplication extends MainFrame { try { final PhylogenyParser parser = ParserUtils .createParserDependingOnFileType( file, getConfiguration() - .isValidatePhyloXmlAgainstSchema() ); + .isValidatePhyloXmlAgainstSchema() ); if ( parser instanceof NexusPhylogeniesParser ) { final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser; setSpecialOptionsForNexParser( nex ); @@ -1560,10 +1560,10 @@ public final class MainFrameApplication extends MainFrame { _mainpanel.getControlPanel().showWhole(); if ( nhx_or_nexus && one_desc ) { JOptionPane - .showMessageDialog( this, - "One or more trees contain (a) node(s) with one descendant, " - + ForesterUtil.LINE_SEPARATOR - + "possibly indicating illegal parentheses within node names.", + .showMessageDialog( this, + "One or more trees contain (a) node(s) with one descendant, " + + ForesterUtil.LINE_SEPARATOR + + "possibly indicating illegal parentheses within node names.", "Warning: Possible Error in New Hampshire Formatted Data", JOptionPane.WARNING_MESSAGE ); } @@ -1589,7 +1589,7 @@ public final class MainFrameApplication extends MainFrame { if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) { try { final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser - .createPhyloXmlParserXsdValidating(), file ); + .createPhyloXmlParserXsdValidating(), file ); t = trees[ 0 ]; } catch ( final Exception e ) { @@ -1611,7 +1611,7 @@ public final class MainFrameApplication extends MainFrame { else { try { final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser - .createPhyloXmlParserXsdValidating(), file ); + .createPhyloXmlParserXsdValidating(), file ); t = trees[ 0 ]; } catch ( final Exception e ) { @@ -1635,10 +1635,10 @@ public final class MainFrameApplication extends MainFrame { exception = true; t = null; JOptionPane - .showMessageDialog( this, - "Species tree contains external node(s) without taxonomy information", - "Species tree not loaded", - JOptionPane.ERROR_MESSAGE ); + .showMessageDialog( this, + "Species tree contains external node(s) without taxonomy information", + "Species tree not loaded", + JOptionPane.ERROR_MESSAGE ); break; } else { @@ -1649,8 +1649,8 @@ public final class MainFrameApplication extends MainFrame { "Taxonomy [" + node.getNodeData().getTaxonomy().asSimpleText() + "] is not unique in species tree", - "Species tree not loaded", - JOptionPane.ERROR_MESSAGE ); + "Species tree not loaded", + JOptionPane.ERROR_MESSAGE ); break; } else { @@ -1727,7 +1727,7 @@ public final class MainFrameApplication extends MainFrame { _file_jmenu.addSeparator(); final WebservicesManager webservices_manager = WebservicesManager.getInstance(); _load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager - .getAvailablePhylogeniesWebserviceClients().size() ]; + .getAvailablePhylogeniesWebserviceClients().size() ]; for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) { final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i ); _load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() ); @@ -1766,7 +1766,7 @@ public final class MainFrameApplication extends MainFrame { _file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) ); customizeJMenuItem( _open_item ); _open_item - .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) ); + .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) ); customizeJMenuItem( _open_url_item ); for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) { customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] ); @@ -1797,9 +1797,9 @@ public final class MainFrameApplication extends MainFrame { MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() ); MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() ); MainFrame - .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); + .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame - .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); + .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); @@ -1817,7 +1817,7 @@ public final class MainFrameApplication extends MainFrame { } ); _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) ); _options_jmenu - .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); + .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) ); _options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) ); _radio_group_1 = new ButtonGroup(); @@ -1827,11 +1827,11 @@ public final class MainFrameApplication extends MainFrame { _options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) ); _options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) ); _options_jmenu - .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); _options_jmenu - .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); _options_jmenu - .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); + .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) ); _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) ); if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) { _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) ); @@ -1869,33 +1869,33 @@ public final class MainFrameApplication extends MainFrame { _options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) ); _options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) ); _options_jmenu - .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) ); + .add( _print_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PDF export and Printing" ) ); _options_jmenu - .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) ); + .add( _graphics_export_using_actual_size_cbmi = new JCheckBoxMenuItem( "Use Current Image Size for PNG, JPG, and GIF export" ) ); _options_jmenu - .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); + .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) ); _options_jmenu.add( _print_size_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) ); _options_jmenu.addSeparator(); _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) ); _options_jmenu - .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) ); + .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) ); _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) ); _options_jmenu - .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) ); + .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) ); _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) ); _options_jmenu - .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) ); + .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) ); _options_jmenu - .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) ); + .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) ); _options_jmenu - .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) ); + .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) ); _extract_taxonomy_pfam_strict_rbmi - .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" ); + .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" ); _extract_taxonomy_pfam_relaxed_rbmi - .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" ); + .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" ); _extract_taxonomy_agressive_rbmi - .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" ); + .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" ); _radio_group_2 = new ButtonGroup(); _radio_group_2.add( _extract_taxonomy_no_rbmi ); _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi ); @@ -1903,11 +1903,11 @@ public final class MainFrameApplication extends MainFrame { _radio_group_2.add( _extract_taxonomy_agressive_rbmi ); _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) ); _options_jmenu - .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) ); + .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) ); _use_brackets_for_conf_in_nh_export_cbmi - .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" ); + .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" ); _options_jmenu - .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) ); + .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) ); customizeJMenuItem( _choose_font_mi ); customizeJMenuItem( _choose_minimal_confidence_mi ); customizeJMenuItem( _switch_colors_mi ); @@ -1915,11 +1915,11 @@ public final class MainFrameApplication extends MainFrame { customizeJMenuItem( _choose_pdf_width_mi ); customizeJMenuItem( _overview_placment_mi ); customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() - .isShowDefaultNodeShapesExternal() ); + .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() - .isShowDefaultNodeShapesInternal() ); + .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions() - .isShowDefaultNodeShapesForMarkedNodes() ); + .isShowDefaultNodeShapesForMarkedNodes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -1945,7 +1945,7 @@ public final class MainFrameApplication extends MainFrame { customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() ); customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() ); customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions() - .isInternalNumberAreConfidenceForNhParsing() ); + .isInternalNumberAreConfidenceForNhParsing() ); customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi, getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO ); customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi, @@ -1956,19 +1956,19 @@ public final class MainFrameApplication extends MainFrame { getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE ); customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() ); customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions() - .isReplaceUnderscoresInNhParsing() ); + .isReplaceUnderscoresInNhParsing() ); customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() ); customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() ); customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() ); customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() ); customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() ); customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions() - .isGraphicsExportUsingActualSize() ); + .isGraphicsExportUsingActualSize() ); customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() ); customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions() - .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); + .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS ); customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions() - .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); + .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ); customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() ); customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() ); _jmenubar.add( _options_jmenu ); @@ -1984,11 +1984,11 @@ public final class MainFrameApplication extends MainFrame { _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) ); customizeJMenuItem( _inference_from_seqs_item ); _inference_from_seqs_item - .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" ); + .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" ); } else { _inference_menu - .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) ); + .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) ); customizeJMenuItem( _inference_from_seqs_item ); _inference_from_seqs_item.setEnabled( false ); } @@ -2007,7 +2007,7 @@ public final class MainFrameApplication extends MainFrame { _tools_menu.addSeparator(); _tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) ); _remove_visual_styles_item - .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" ); + .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" ); customizeJMenuItem( _remove_visual_styles_item ); _tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) ); _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" ); @@ -2030,25 +2030,25 @@ public final class MainFrameApplication extends MainFrame { customizeJMenuItem( _collapse_species_specific_subtrees ); _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" ); _tools_menu - .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) ); + .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) ); customizeJMenuItem( _collapse_below_threshold ); _collapse_below_threshold - .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" ); + .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" ); // _tools_menu - .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) ); + .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) ); customizeJMenuItem( _collapse_below_branch_length ); _collapse_below_branch_length - .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" ); + .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" ); // _tools_menu.addSeparator(); _tools_menu - .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) ); + .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) ); customizeJMenuItem( _extract_tax_code_from_node_names_jmi ); _extract_tax_code_from_node_names_jmi - .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" ); + .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" ); _tools_menu - .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) ); + .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) ); customizeJMenuItem( _move_node_names_to_tax_sn_jmi ); _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" ); _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) ); @@ -2059,15 +2059,15 @@ public final class MainFrameApplication extends MainFrame { customizeJMenuItem( _obtain_seq_information_jmi ); _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" ); _tools_menu - .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) ); + .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) ); customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi ); _obtain_detailed_taxonomic_information_jmi - .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" ); + .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" ); _tools_menu - .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) ); + .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) ); customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi ); _obtain_detailed_taxonomic_information_deleting_jmi - .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" ); + .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" ); _tools_menu.addSeparator(); _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) ); customizeJMenuItem( _read_values_jmi ); @@ -2076,7 +2076,7 @@ public final class MainFrameApplication extends MainFrame { _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) ); customizeJMenuItem( _read_seqs_jmi ); _read_seqs_jmi - .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" ); + .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" ); _jmenubar.add( _tools_menu ); } @@ -2108,7 +2108,7 @@ public final class MainFrameApplication extends MainFrame { final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this, _mainpanel.getCurrentTreePanel(), _mainpanel.getCurrentPhylogeny() - .copy() ); + .copy() ); new Thread( inferrer ).start(); } @@ -2139,7 +2139,7 @@ public final class MainFrameApplication extends MainFrame { } else { parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration() - .isValidatePhyloXmlAgainstSchema() ); + .isValidatePhyloXmlAgainstSchema() ); } if ( parser instanceof NexusPhylogeniesParser ) { nhx_or_nexus = true; @@ -2166,8 +2166,8 @@ public final class MainFrameApplication extends MainFrame { JOptionPane.showMessageDialog( this, "Could not read from " + url + "\n" + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), - "Failed to read URL", - JOptionPane.ERROR_MESSAGE ); + "Failed to read URL", + JOptionPane.ERROR_MESSAGE ); } catch ( final Exception e ) { JOptionPane.showMessageDialog( this, @@ -2239,12 +2239,12 @@ public final class MainFrameApplication extends MainFrame { static void warnIfNotPhyloXmlValidation( final Configuration c ) { if ( !c.isValidatePhyloXmlAgainstSchema() ) { JOptionPane - .showMessageDialog( null, - ForesterUtil - .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]", - 80 ), - "Warning", - JOptionPane.WARNING_MESSAGE ); + .showMessageDialog( null, + ForesterUtil + .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]", + 80 ), + "Warning", + JOptionPane.WARNING_MESSAGE ); } } } // MainFrameApplication. diff --git a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java index 31189dd..0917131 100644 --- a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java @@ -355,12 +355,12 @@ class NodeEditPanel extends JPanel { NodePanel.EVENTS_DUPLICATIONS, String.valueOf( events.getNumberOfDuplications() >= 0 ? events.getNumberOfDuplications() : 0 ), - PHYLOXML_TAG.EVENTS_DUPLICATIONS ); + PHYLOXML_TAG.EVENTS_DUPLICATIONS ); addSubelementEditable( category, NodePanel.EVENTS_SPECIATIONS, String.valueOf( events.getNumberOfSpeciations() >= 0 ? events.getNumberOfSpeciations() : 0 ), - PHYLOXML_TAG.EVENTS_SPECIATIONS ); + PHYLOXML_TAG.EVENTS_SPECIATIONS ); addSubelementEditable( category, NodePanel.EVENTS_GENE_LOSSES, String.valueOf( events.getNumberOfGeneLosses() >= 0 ? events.getNumberOfGeneLosses() : 0 ), @@ -418,7 +418,7 @@ class NodeEditPanel extends JPanel { for( final Uri uri : seq.getUris() ) { if ( uri != null ) { addSubelementEditable( category, NodePanel.SEQ_URI + " [" + uri_counter + "]", uri.getValue() - .toString(), PHYLOXML_TAG.SEQ_URI, uri_counter++ ); + .toString(), PHYLOXML_TAG.SEQ_URI, uri_counter++ ); } } } @@ -545,7 +545,7 @@ class NodeEditPanel extends JPanel { for( final Uri uri : tax.getUris() ) { if ( uri != null ) { addSubelementEditable( category, NodePanel.TAXONOMY_URI + " [" + uri_counter + "]", uri.getValue() - .toString(), PHYLOXML_TAG.TAXONOMY_URI, uri_counter++ ); + .toString(), PHYLOXML_TAG.TAXONOMY_URI, uri_counter++ ); } } } diff --git a/forester/java/src/org/forester/archaeopteryx/NodePanel.java b/forester/java/src/org/forester/archaeopteryx/NodePanel.java index 0511476..e39b580 100644 --- a/forester/java/src/org/forester/archaeopteryx/NodePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/NodePanel.java @@ -351,7 +351,7 @@ class NodePanel extends JPanel implements TreeSelectionListener { for( final String key : properties_map.keySet() ) { final Property prop = properties_map.get( key ); category.add( new DefaultMutableTreeNode( prop.getRef() + "=" + prop.getValue() + " " + prop.getUnit() - + " [" + prop.getAppliesTo().toString() + "]" ) ); + + " [" + prop.getAppliesTo().toString() + "]" ) ); } } diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 6d55014..dede12e 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -570,16 +570,16 @@ final public class Options { instance.setBackgroundColorGradient( configuration.isBackgroundColorGradient() ); if ( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() >= 0 ) { instance.setNumberOfDigitsAfterCommaForBranchLength( configuration - .getNumberOfDigitsAfterCommaForBranchLengthValues() ); + .getNumberOfDigitsAfterCommaForBranchLengthValues() ); } if ( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() >= 0 ) { instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration - .getNumberOfDigitsAfterCommaForConfidenceValues() ); + .getNumberOfDigitsAfterCommaForConfidenceValues() ); } instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() ); instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() ); instance.setInternalNumberAreConfidenceForNhParsing( configuration - .isInternalNumberAreConfidenceForNhParsing() ); + .isInternalNumberAreConfidenceForNhParsing() ); instance.setEditable( configuration.isEditable() ); instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() ); instance.setShowDomainLabels( configuration.isShowDomainLabels() ); @@ -599,7 +599,7 @@ final public class Options { } if ( !ForesterUtil.isEmpty( configuration.getBaseFontFamilyName() ) ) { instance.setBaseFont( new Font( configuration.getBaseFontFamilyName(), Font.PLAIN, instance - .getBaseFont().getSize() ) ); + .getBaseFont().getSize() ) ); } if ( configuration.getPhylogenyGraphicsType() != null ) { instance.setPhylogenyGraphicsType( configuration.getPhylogenyGraphicsType() ); diff --git a/forester/java/src/org/forester/archaeopteryx/PdfExporter.java b/forester/java/src/org/forester/archaeopteryx/PdfExporter.java index 21f20d3..9a422d3 100644 --- a/forester/java/src/org/forester/archaeopteryx/PdfExporter.java +++ b/forester/java/src/org/forester/archaeopteryx/PdfExporter.java @@ -45,11 +45,11 @@ import com.itextpdf.text.pdf.PdfContentByte; import com.itextpdf.text.pdf.PdfWriter; /* - * + * * This uses iText. - * + * * See: http://www.lowagie.com/iText/ - * + * * Current version: iText-2.1.7 */ final class PdfExporter { diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java index c83d135..177eba8 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java +++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java @@ -54,233 +54,233 @@ public final class TreeColorSet { public static final String SPECIATION = "Speciation"; public static final String TAXONOMY = "Taxonomy"; static final String[] COLOR_FIELDS = { BACKGROUND, BACKGROUND_GRADIENT_BOTTOM, SEQUENCE, - TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B, - MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAIN_LABEL, DOMAIN_BASE, - BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW }; + TAXONOMY, CONFIDENCE, BRANCH_LENGTH, BRANCH, NODE_BOX, COLLAPSED, MATCHING_NODES_A, MATCHING_NODES_B, + MATCHING_NODES_A_AND_B, DUPLICATION, SPECIATION, DUPLICATION_OR_SPECATION, DOMAIN_LABEL, DOMAIN_BASE, + BINARY_DOMAIN_COMBINATIONS, ANNOTATION, OVERVIEW }; static final String[] SCHEME_NAMES = { "Default", "Black", "Black & White", "Silver", "Green", - "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" }; + "White & Blue", "Cyan", "Orange", "Blue", "Blue & White", "Neon" }; private int _color_scheme; private final Color[][] _color_schemes = { { new Color( 0, 0, 0 ), // background_color - new Color( 0, 100, 100 ), // background_color_gradient_bottom - new Color( 230, 230, 230 ), // sequence __ Default (same as Black) - new Color( 180, 180, 180 ), // taxonomy - new Color( 180, 180, 180 ), // support - new Color( 140, 140, 140 ), // branch_length_color - new Color( 255, 255, 255 ), // branch_color - new Color( 255, 255, 255 ), // box_color - new Color( 255, 255, 255 ), // collapesed_fill_color - new Color( 0, 255, 0 ), // found_color 0 - new Color( 255, 0, 0 ), // found_color 1 - new Color( 255, 255, 0 ), // found_color 1 + 2 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base - new Color( 65, 105, 255 ), // binary_domain_combinations_color - new Color( 173, 255, 47 ) // annotation - , new Color( 130, 130, 130 ) // overview - }, { new Color( 0, 0, 0 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 230, 230, 230 ), // sequence __ Black - new Color( 180, 180, 180 ), // taxonomy - new Color( 180, 180, 180 ), // support - new Color( 140, 140, 140 ), // branch_length_color - new Color( 255, 255, 255 ), // branch_color - new Color( 255, 255, 255 ), // box_color - new Color( 255, 255, 255 ), // collapesed_fill_color - new Color( 0, 255, 0 ), // found_color 0 - new Color( 255, 0, 0 ), // found_color 1 - new Color( 255, 255, 0 ), // found_color 1 + 2 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base - new Color( 65, 105, 255 ), // binary_domain_combinations_color - new Color( 173, 255, 47 ) // annotation - , new Color( 130, 130, 130 ) // ov - }, { new Color( 255, 255, 255 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 0, 0, 0 ), // sequence __ Black & White - new Color( 0, 0, 0 ), // taxonomy - new Color( 0, 0, 0 ), // support - new Color( 0, 0, 0 ), // branch_length_color - new Color( 0, 0, 0 ), // branch_color - new Color( 0, 0, 0 ), // box_color - new Color( 0, 0, 0 ), // collapesed_fill_color - new Color( 255, 0, 0 ), // found_color 0 - new Color( 0, 255, 0 ), // found_color 1 - new Color( 0, 0, 255 ), // found_color 1 + 2 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 0, 0, 0 ), // domain_label - new Color( 100, 100, 100 ), // domains_base - new Color( 0, 0, 0 ), // binary_domain_combinations_color - new Color( 0, 0, 0 ) // annotation - , new Color( 220, 220, 220 ) // ov - }, { new Color( 0, 0, 0 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 220, 220, 220 ), // sequence __ Silver - new Color( 180, 180, 180 ), // taxonomy - new Color( 140, 140, 140 ), // support - new Color( 140, 140, 140 ), // branch_length_color - new Color( 240, 240, 240 ), // branch_color - new Color( 140, 140, 140 ), // box_color - new Color( 240, 240, 240 ), // collapesed_fill_color - new Color( 255, 0, 0 ), // found_color 0 - new Color( 0, 255, 0 ), // found_color 1 - new Color( 255, 255, 0 ), // found_color 1 + 2 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base - new Color( 180, 180, 180 ), // binary_domain_combinations_color - new Color( 140, 140, 140 ) // annotation - , new Color( 40, 40, 40 ) // ov - }, { new Color( 0, 10, 0 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 0, 255, 0 ), // sequence __ the Matrix - new Color( 30, 200, 30 ), // taxonomy - new Color( 0, 155, 0 ), // support - new Color( 0, 100, 0 ), // branch_length_color - new Color( 0, 155, 0 ), // branch_color - new Color( 0, 255, 0 ), // box_color - new Color( 0, 155, 0 ), // collapesed_fill_color - new Color( 255, 0, 0 ), // found_color 0 - new Color( 0, 255, 0 ), // found_color 1 - new Color( 255, 255, 0 ), // found_color 1 + 2 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base - new Color( 0, 235, 0 ), // binary_domain_combinations_color - new Color( 0, 235, 0 ) // annotation - , new Color( 40, 40, 40 ) // ov - }, { new Color( 255, 255, 255 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 0, 0, 0 ), //sequence __ White & Blue - new Color( 40, 40, 40 ), // taxonomy - new Color( 0, 125, 0 ), // support - new Color( 70, 70, 0 ), // branch_length_color - new Color( 0, 20, 200 ), // branch_color - new Color( 0, 20, 200 ), // box_color - new Color( 0, 20, 200 ), // collapesed_fill_color - new Color( 0, 255, 0 ), // found_color 0 - new Color( 255, 0, 0 ), // found_color 1 - new Color( 0, 0, 255 ), // found_color 0 + 1 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 0, 0, 0 ), // domain_label - new Color( 50, 50, 50 ), // domains_base - new Color( 65, 105, 225 ), // binary_domain_combinations_color - new Color( 173, 255, 47 ) // annotation - , new Color( 220, 220, 220 ) // ov - }, { new Color( 0, 0, 0 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 255, 255, 255 ), // sequence __ Cyan - new Color( 200, 200, 200 ), // taxonomy - new Color( 255, 255, 255 ), // support - new Color( 200, 200, 200 ), // branch_length_color - new Color( 0, 255, 255 ), // branch_color - new Color( 0, 255, 255 ), // box_color - new Color( 0, 255, 255 ), // collapesed_fill_color - new Color( 0, 255, 0 ), // found_color 0 - new Color( 0, 0, 255 ), // found_color 1 - new Color( 0, 255, 255 ), // found_color 0 + 1 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 230, 230, 230 ), // domain_label - new Color( 100, 100, 100 ), // domains_base - new Color( 65, 105, 225 ), // binary_domain_combinations_color - new Color( 173, 255, 47 ) // annotation - , new Color( 0, 120, 120 ) // ov - }, { new Color( 0, 0, 0 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 255, 200, 0 ), // sequence __ Clockwork - new Color( 255, 200, 0 ), // taxonomy - new Color( 255, 200, 0 ), // support - new Color( 255, 200, 0 ), // branch_length_color - new Color( 255, 200, 0 ), // branch_color - new Color( 255, 200, 0 ), // box_color - new Color( 255, 200, 0 ), // collapesed_fill_color - new Color( 255, 255, 0 ), // found_color 0 - new Color( 0, 255, 255 ), // found_color 1 - new Color( 255, 255, 255 ), // found_color 0 + 1 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 255, 200, 0 ), // domain_label - new Color( 255, 200, 0 ), // domains_base - new Color( 150, 150, 150 ), // binary_domain_combinations_color - new Color( 150, 150, 150 ) // annotation - , new Color( 150, 150, 150 ) // ov - }, { new Color( 0, 0, 100 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 255, 255, 255 ), // sequence __ Blue - new Color( 255, 255, 255 ), // taxonomy - new Color( 255, 0, 0 ), // support - new Color( 255, 0, 0 ), // branch_length_color - new Color( 255, 0, 0 ), // branch_color - new Color( 255, 0, 0 ), // box_color - new Color( 255, 0, 0 ), // collapesed_fill_color - new Color( 0, 255, 0 ), // found_color - new Color( 255, 0, 0 ), // found_color 1 - new Color( 255, 255, 0 ), // found_color 1 + 2 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 255, 255, 255 ), // domain_label - new Color( 100, 100, 100 ), // domains_base - new Color( 255, 255, 255 ), // binary_domain_combinations_color - new Color( 255, 255, 255 ) // annotation - , new Color( 77, 77, 255 ) // ov - }, { new Color( 0, 0, 0 ), // background_color - new Color( 0, 255, 255 ), // background_color_gradient_bottom - new Color( 255, 255, 255 ), // sequence __ blue & white - new Color( 255, 255, 255 ), // taxonomy - new Color( 255, 255, 255 ), // support - new Color( 0, 191, 255 ), // branch_length_color - new Color( 0, 191, 255 ), // branch_color - new Color( 0, 191, 255 ), // box_color - new Color( 0, 191, 255 ), // collapesed_fill_color - new Color( 255, 0, 0 ), // found_color 0 - new Color( 0, 255, 0 ), // found_color 1 - new Color( 255, 255, 0 ), // found_color 0 + 1 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 255, 255, 255 ), // domain_label - new Color( 150, 150, 150 ), // domains_base - new Color( 255, 255, 255 ), // binary_domain_combinations_color - new Color( 255, 255, 255 ) // annotation - , new Color( 170, 187, 204 ) // ov - }, { new Color( 0, 0, 0 ), // background_color - new Color( 255, 255, 0 ), // background_color_gradient_bottom - new Color( 127, 255, 0 ), // sequence __ Neon - new Color( 255, 110, 199 ), // taxonomy - new Color( 234, 173, 234 ), // support - new Color( 77, 77, 255 ), // branch_length_color - new Color( 234, 173, 234 ), // branch_color - new Color( 77, 77, 255 ), // box_color - new Color( 234, 173, 234 ), // collapsed_fill_color - new Color( 243, 243, 21 ), // found_color 0 - new Color( 255, 20, 147 ), // found_color 1 - new Color( 255, 255, 255 ), // found_color 1 + 2 - new Color( 255, 0, 0 ), // duplication_box_color - new Color( 0, 255, 0 ), // speciation_box_color - new Color( 255, 255, 0 ), // duplication_speciation_color - new Color( 127, 255, 0 ), // domain_label - new Color( 234, 173, 234 ), // domains_base - new Color( 27, 255, 0 ), // binary_domain_combinations_color - new Color( 27, 255, 0 ) // annotation - , new Color( 77, 77, 255 ) // ov - } }; + new Color( 0, 100, 100 ), // background_color_gradient_bottom + new Color( 230, 230, 230 ), // sequence __ Default (same as Black) + new Color( 180, 180, 180 ), // taxonomy + new Color( 180, 180, 180 ), // support + new Color( 140, 140, 140 ), // branch_length_color + new Color( 255, 255, 255 ), // branch_color + new Color( 255, 255, 255 ), // box_color + new Color( 255, 255, 255 ), // collapesed_fill_color + new Color( 0, 255, 0 ), // found_color 0 + new Color( 255, 0, 0 ), // found_color 1 + new Color( 255, 255, 0 ), // found_color 1 + 2 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base + new Color( 65, 105, 255 ), // binary_domain_combinations_color + new Color( 173, 255, 47 ) // annotation + , new Color( 130, 130, 130 ) // overview + }, { new Color( 0, 0, 0 ), // background_color + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 230, 230, 230 ), // sequence __ Black + new Color( 180, 180, 180 ), // taxonomy + new Color( 180, 180, 180 ), // support + new Color( 140, 140, 140 ), // branch_length_color + new Color( 255, 255, 255 ), // branch_color + new Color( 255, 255, 255 ), // box_color + new Color( 255, 255, 255 ), // collapesed_fill_color + new Color( 0, 255, 0 ), // found_color 0 + new Color( 255, 0, 0 ), // found_color 1 + new Color( 255, 255, 0 ), // found_color 1 + 2 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base + new Color( 65, 105, 255 ), // binary_domain_combinations_color + new Color( 173, 255, 47 ) // annotation + , new Color( 130, 130, 130 ) // ov + }, { new Color( 255, 255, 255 ), // background_color + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 0, 0, 0 ), // sequence __ Black & White + new Color( 0, 0, 0 ), // taxonomy + new Color( 0, 0, 0 ), // support + new Color( 0, 0, 0 ), // branch_length_color + new Color( 0, 0, 0 ), // branch_color + new Color( 0, 0, 0 ), // box_color + new Color( 0, 0, 0 ), // collapesed_fill_color + new Color( 255, 0, 0 ), // found_color 0 + new Color( 0, 255, 0 ), // found_color 1 + new Color( 0, 0, 255 ), // found_color 1 + 2 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 0, 0, 0 ), // domain_label + new Color( 100, 100, 100 ), // domains_base + new Color( 0, 0, 0 ), // binary_domain_combinations_color + new Color( 0, 0, 0 ) // annotation + , new Color( 220, 220, 220 ) // ov + }, { new Color( 0, 0, 0 ), // background_color + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 220, 220, 220 ), // sequence __ Silver + new Color( 180, 180, 180 ), // taxonomy + new Color( 140, 140, 140 ), // support + new Color( 140, 140, 140 ), // branch_length_color + new Color( 240, 240, 240 ), // branch_color + new Color( 140, 140, 140 ), // box_color + new Color( 240, 240, 240 ), // collapesed_fill_color + new Color( 255, 0, 0 ), // found_color 0 + new Color( 0, 255, 0 ), // found_color 1 + new Color( 255, 255, 0 ), // found_color 1 + 2 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base + new Color( 180, 180, 180 ), // binary_domain_combinations_color + new Color( 140, 140, 140 ) // annotation + , new Color( 40, 40, 40 ) // ov + }, { new Color( 0, 10, 0 ), // background_color + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 0, 255, 0 ), // sequence __ the Matrix + new Color( 30, 200, 30 ), // taxonomy + new Color( 0, 155, 0 ), // support + new Color( 0, 100, 0 ), // branch_length_color + new Color( 0, 155, 0 ), // branch_color + new Color( 0, 255, 0 ), // box_color + new Color( 0, 155, 0 ), // collapesed_fill_color + new Color( 255, 0, 0 ), // found_color 0 + new Color( 0, 255, 0 ), // found_color 1 + new Color( 255, 255, 0 ), // found_color 1 + 2 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base + new Color( 0, 235, 0 ), // binary_domain_combinations_color + new Color( 0, 235, 0 ) // annotation + , new Color( 40, 40, 40 ) // ov + }, { new Color( 255, 255, 255 ), // background_color + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 0, 0, 0 ), //sequence __ White & Blue + new Color( 40, 40, 40 ), // taxonomy + new Color( 0, 125, 0 ), // support + new Color( 70, 70, 0 ), // branch_length_color + new Color( 0, 20, 200 ), // branch_color + new Color( 0, 20, 200 ), // box_color + new Color( 0, 20, 200 ), // collapesed_fill_color + new Color( 0, 255, 0 ), // found_color 0 + new Color( 255, 0, 0 ), // found_color 1 + new Color( 0, 0, 255 ), // found_color 0 + 1 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 0, 0, 0 ), // domain_label + new Color( 50, 50, 50 ), // domains_base + new Color( 65, 105, 225 ), // binary_domain_combinations_color + new Color( 173, 255, 47 ) // annotation + , new Color( 220, 220, 220 ) // ov + }, { new Color( 0, 0, 0 ), // background_color + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 255, 255, 255 ), // sequence __ Cyan + new Color( 200, 200, 200 ), // taxonomy + new Color( 255, 255, 255 ), // support + new Color( 200, 200, 200 ), // branch_length_color + new Color( 0, 255, 255 ), // branch_color + new Color( 0, 255, 255 ), // box_color + new Color( 0, 255, 255 ), // collapesed_fill_color + new Color( 0, 255, 0 ), // found_color 0 + new Color( 0, 0, 255 ), // found_color 1 + new Color( 0, 255, 255 ), // found_color 0 + 1 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 230, 230, 230 ), // domain_label + new Color( 100, 100, 100 ), // domains_base + new Color( 65, 105, 225 ), // binary_domain_combinations_color + new Color( 173, 255, 47 ) // annotation + , new Color( 0, 120, 120 ) // ov + }, { new Color( 0, 0, 0 ), // background_color + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 255, 200, 0 ), // sequence __ Clockwork + new Color( 255, 200, 0 ), // taxonomy + new Color( 255, 200, 0 ), // support + new Color( 255, 200, 0 ), // branch_length_color + new Color( 255, 200, 0 ), // branch_color + new Color( 255, 200, 0 ), // box_color + new Color( 255, 200, 0 ), // collapesed_fill_color + new Color( 255, 255, 0 ), // found_color 0 + new Color( 0, 255, 255 ), // found_color 1 + new Color( 255, 255, 255 ), // found_color 0 + 1 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 255, 200, 0 ), // domain_label + new Color( 255, 200, 0 ), // domains_base + new Color( 150, 150, 150 ), // binary_domain_combinations_color + new Color( 150, 150, 150 ) // annotation + , new Color( 150, 150, 150 ) // ov + }, { new Color( 0, 0, 100 ), // background_color + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 255, 255, 255 ), // sequence __ Blue + new Color( 255, 255, 255 ), // taxonomy + new Color( 255, 0, 0 ), // support + new Color( 255, 0, 0 ), // branch_length_color + new Color( 255, 0, 0 ), // branch_color + new Color( 255, 0, 0 ), // box_color + new Color( 255, 0, 0 ), // collapesed_fill_color + new Color( 0, 255, 0 ), // found_color + new Color( 255, 0, 0 ), // found_color 1 + new Color( 255, 255, 0 ), // found_color 1 + 2 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 255, 255, 255 ), // domain_label + new Color( 100, 100, 100 ), // domains_base + new Color( 255, 255, 255 ), // binary_domain_combinations_color + new Color( 255, 255, 255 ) // annotation + , new Color( 77, 77, 255 ) // ov + }, { new Color( 0, 0, 0 ), // background_color + new Color( 0, 255, 255 ), // background_color_gradient_bottom + new Color( 255, 255, 255 ), // sequence __ blue & white + new Color( 255, 255, 255 ), // taxonomy + new Color( 255, 255, 255 ), // support + new Color( 0, 191, 255 ), // branch_length_color + new Color( 0, 191, 255 ), // branch_color + new Color( 0, 191, 255 ), // box_color + new Color( 0, 191, 255 ), // collapesed_fill_color + new Color( 255, 0, 0 ), // found_color 0 + new Color( 0, 255, 0 ), // found_color 1 + new Color( 255, 255, 0 ), // found_color 0 + 1 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 255, 255, 255 ), // domain_label + new Color( 150, 150, 150 ), // domains_base + new Color( 255, 255, 255 ), // binary_domain_combinations_color + new Color( 255, 255, 255 ) // annotation + , new Color( 170, 187, 204 ) // ov + }, { new Color( 0, 0, 0 ), // background_color + new Color( 255, 255, 0 ), // background_color_gradient_bottom + new Color( 127, 255, 0 ), // sequence __ Neon + new Color( 255, 110, 199 ), // taxonomy + new Color( 234, 173, 234 ), // support + new Color( 77, 77, 255 ), // branch_length_color + new Color( 234, 173, 234 ), // branch_color + new Color( 77, 77, 255 ), // box_color + new Color( 234, 173, 234 ), // collapsed_fill_color + new Color( 243, 243, 21 ), // found_color 0 + new Color( 255, 20, 147 ), // found_color 1 + new Color( 255, 255, 255 ), // found_color 1 + 2 + new Color( 255, 0, 0 ), // duplication_box_color + new Color( 0, 255, 0 ), // speciation_box_color + new Color( 255, 255, 0 ), // duplication_speciation_color + new Color( 127, 255, 0 ), // domain_label + new Color( 234, 173, 234 ), // domains_base + new Color( 27, 255, 0 ), // binary_domain_combinations_color + new Color( 27, 255, 0 ) // annotation + , new Color( 77, 77, 255 ) // ov + } }; private Color annotation_color; private Color background_color; private Color background_color_gradient_bottom; diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index c6c8a67..cf4bb2e 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -361,7 +361,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee calculateScaleDistance(); FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() ); FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration - .getNumberOfDigitsAfterCommaForBranchLengthValues() ); + .getNumberOfDigitsAfterCommaForBranchLengthValues() ); } @Override @@ -1448,7 +1448,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return ( ( x >= ( getOvVirtualRectangle().x - 1 ) ) && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) ) && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y - + getOvVirtualRectangle().height + 1 ) ) ); + + getOvVirtualRectangle().height + 1 ) ) ); } final private boolean inOvVirtualRectangle( final MouseEvent e ) { @@ -1475,8 +1475,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node - .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node - .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) { + .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node + .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) { return true; } else { @@ -1511,14 +1511,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) ) || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node - .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) ); + .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) ); } final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) { return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) ) || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) ) || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect() - .getMaxX() + 20 ) ) ); + .getMaxX() + 20 ) ) ); } final private boolean isNonLinedUpCladogram() { @@ -1936,7 +1936,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), isApplet() ? obtainApplet() : null, - "_aptx_seq" ); + "_aptx_seq" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -1964,7 +1964,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), isApplet() ? obtainApplet() : null, - "_aptx_seq" ); + "_aptx_seq" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -2047,7 +2047,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), isApplet() ? obtainApplet() : null, - "_aptx_tax" ); + "_aptx_tax" ); } catch ( final IOException e ) { AptxUtil.showErrorMessage( this, e.toString() ); @@ -2077,20 +2077,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !node.isRoot() ) { if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); + .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); } else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); + .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); } else { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); + .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); } } else { TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord() - - getTreeFontSet().getSmallMaxDescent(), g ); + - getTreeFontSet().getSmallMaxDescent(), g ); } } @@ -2112,7 +2112,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final float dx = x2 - x1; final float dy = y2 - y1; _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1 - + ( dy * 0.8f ), x2, y2 ); + + ( dy * 0.8f ), x2, y2 ); ( g ).draw( _cubic_curve ); } else { @@ -2151,7 +2151,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final float dx = x2 - x1; final float dy = y2 - y1; _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1 - + ( dy * 0.8f ), x2, y2 ); + + ( dy * 0.8f ), x2, y2 ); g.draw( _cubic_curve ); } else { @@ -2414,13 +2414,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee not_first = true; } sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); if ( getOptions().isShowConfidenceStddev() ) { if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { sb.append( "(" ); sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence - .getStandardDeviation(), getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + .getStandardDeviation(), getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); sb.append( ")" ); } } @@ -2446,10 +2446,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final String conf_str = sb.toString(); TreePanel.drawString( conf_str, parent_x - + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall() - .stringWidth( conf_str ) ) / 2 ), - ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1, - g ); + + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall() + .stringWidth( conf_str ) ) / 2 ), + ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1, + g ); } } @@ -2466,24 +2466,24 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.setColor( Color.BLUE ); } TreePanel - .drawString( gained, - parent_x - + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ), - ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ), - g ); + .drawString( gained, + parent_x + + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ), + ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ), + g ); g.setColor( getTreeColorSet().getLostCharactersColor() ); TreePanel - .drawString( lost, - parent_x - + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ), - ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ), - g ); + .drawString( lost, + parent_x + + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ), + ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ), + g ); } } private void paintMolecularSequences( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf ) { final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence() - .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() ); + .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() ); if ( rs != null ) { final int default_height = 8; final float y = getYdistance(); @@ -2535,16 +2535,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() ) || ( getOptions().isShowDefaultNodeShapesForMarkedNodes() && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData() - .getNodeVisualData().isEmpty() ) ) - || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node - .getNodeData().getNodeVisualData().getNodeColor() != null ) - || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE ) - || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node - .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) ) - || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent() - .isDuplication() - || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent() - .isSpeciationOrDuplication() ) ) ) { + .getNodeVisualData().isEmpty() ) ) + || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node + .getNodeData().getNodeVisualData().getNodeColor() != null ) + || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE ) + || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node + .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) ) + || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent() + .isDuplication() + || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent() + .isSpeciationOrDuplication() ) ) ) { NodeVisualData vis = null; if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) { @@ -2704,7 +2704,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getControlPanel().isWriteBranchLengthValues() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) - && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { + && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { paintBranchLength( g, node, to_pdf, to_graphics_file ); } if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) { @@ -2772,12 +2772,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation .getRef1().isEqual( _query_sequence ) ) && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox() - .getSelectedItem() ); + .getSelectedItem() ); if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query final double linePosX = node.getXcoord() + 2 + half_box_size; final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue() - + ")"; + + ")"; if ( sConfidence != null ) { float confidenceX = pos_x; if ( sb_str.length() > 0 ) { @@ -2786,7 +2786,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc ) - .getBounds().getWidth(); + .getBounds().getWidth(); TreePanel.drawString( sConfidence, confidenceX, pos_y, g ); x += CONFIDENCE_LEFT_MARGIN + confidenceWidth; } @@ -2800,7 +2800,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee nodeTextBoundsWidth += 2; } g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x - + nodeTextBoundsWidth, 3 + ( int ) pos_y ); + + nodeTextBoundsWidth, 3 + ( int ) pos_y ); break; } } @@ -2831,7 +2831,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() ); TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord() - + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g ); + + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g ); _sb.setLength( 0 ); _sb.append( ann_str ); if ( _sb.length() > 0 ) { @@ -2856,22 +2856,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( getControlPanel().isShowBinaryCharacters() ) { TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer() - .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord() - + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g ); + .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord() + + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g ); paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters() - .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters() - .getLostCharactersAsStringBuffer().toString() ); + .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters() + .getLostCharactersAsStringBuffer().toString() ); } else { TreePanel - .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), - node.getXcoord() + x + 4 + half_box_size, - node.getYcoord() - + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), - g ); + .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), + node.getXcoord() + x + 4 + half_box_size, + node.getYcoord() + + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), + g ); paintGainedAndLostCharacters( g, node, "+" + node.getNodeData().getBinaryCharacters().getGainedCount(), "-" - + node.getNodeData().getBinaryCharacters().getLostCount() ); + + node.getNodeData().getBinaryCharacters().getLostCount() ); } } } @@ -3028,7 +3028,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { g.setColor( getColorForFoundNode( node ) ); drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary() - - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); + - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); } float new_x = 0; if ( !node.isExternal() && !node.isCollapse() ) { @@ -3090,7 +3090,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && !node.isRoot() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) - && node.getBranchData().isHasConfidences() ) { + && node.getBranchData().isHasConfidences() ) { paintConfidenceValues( g, node, to_pdf, to_graphics_file ); } // Draw a line to root: @@ -3165,7 +3165,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && !is_in_found_nodes && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont() - .getHeight() ) ) ) ) ) { + .getHeight() ) ) ) ) ) { return; } final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); @@ -3206,7 +3206,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getOptions().isRightLineUpDomains() ) { rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text + ( ( _longest_domain - rds.getTotalLength() ) * rds - .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf ); + .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf ); } else { rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ), @@ -3223,12 +3223,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { if ( getOptions().isRightLineUpDomains() ) { rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) - 20 ) - + ( ( _longest_domain - rds.getTotalLength() ) * rds - .getRenderingFactorWidth() ), - node.getYcoord() - ( h / 2.0f ), - g, - this, - to_pdf ); + + ( ( _longest_domain - rds.getTotalLength() ) * rds + .getRenderingFactorWidth() ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); } else { rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text, @@ -3307,9 +3307,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final private void paintPhylogenyLite( final Graphics2D g ) { _phylogeny - .getRoot() - .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle() - .getWidth() ) ) ) ); + .getRoot() + .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle() + .getWidth() ) ) ) ); _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) ); final Stroke s = g.getStroke(); g.setStroke( STROKE_05 ); @@ -3409,7 +3409,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null, false, false ) ) - .getBounds(); + .getBounds(); g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 ); g.setColor( getTreeColorSet().getBackgroundColor() ); } @@ -3888,7 +3888,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee ann_str = ann.toString(); } sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence() - .getMolecularSequence(), 60 ) ); + .getMolecularSequence(), 60 ) ); data.add( sb.toString() ); } break; @@ -3981,7 +3981,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { if ( sb.length() < 1 ) { TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData() - + ")", "Descendants of selected node do not contain selected data" ); + + ")", "Descendants of selected node do not contain selected data" ); clearCurrentExternalNodesDataBuffer(); } else { @@ -4023,10 +4023,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee try { if ( ( node.getName().length() > 0 ) || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData() - .getTaxonomy() ) ) - || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData() - .getSequence() ) ) || ( node.getNodeData().isHasDate() ) - || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) { + .getTaxonomy() ) ) + || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData() + .getSequence() ) ) || ( node.getNodeData().isHasDate() ) + || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) { _popup_buffer.setLength( 0 ); short lines = 0; if ( node.getName().length() > 0 ) { @@ -4190,14 +4190,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _popup_buffer.append( "] " ); } _popup_buffer - .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), - getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { _popup_buffer.append( " (sd=" ); _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence - .getStandardDeviation(), getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + .getStandardDeviation(), getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); _popup_buffer.append( ")" ); } } @@ -4218,7 +4218,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( _popup_buffer.length() > 0 ) { if ( !getConfiguration().isUseNativeUI() ) { _rollover_popup - .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) ); + .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) ); _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() ); if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) { _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() ); @@ -4241,7 +4241,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _rollover_popup, e.getLocationOnScreen().x + 10, e.getLocationOnScreen().y - - ( lines * 20 ) ); + - ( lines * 20 ) ); _node_desc_popup.show(); } } @@ -4327,7 +4327,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getMainPanel().getMainFrame() == null ) { // Must be "E" applet version. ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); + .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); } else { getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); @@ -4437,7 +4437,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE ) - * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO ); + * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO ); if ( max_length < 40 ) { max_length = 40; } @@ -4473,7 +4473,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) { sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters() - .getGainedCharactersAsStringBuffer().toString() ); + .getGainedCharactersAsStringBuffer().toString() ); } if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) && ( node.getNodeData().getVector().size() > 0 ) ) { @@ -4630,7 +4630,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } catch ( final NumberFormatException e ) { JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str - + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE ); + + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE ); return; } int i = -1; @@ -4640,7 +4640,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee catch ( final NumberFormatException e ) { JOptionPane.showMessageDialog( this, "Could not parse \"" + index_str - + "\" into index for vector data", + + "\" into index for vector data", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE ); return; @@ -4956,11 +4956,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { if ( SPECIAL_DOMAIN_COLORING ) { rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() - .getDomainArchitecture(), node.getName() ); + .getDomainArchitecture(), node.getName() ); } else { rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() - .getDomainArchitecture() ); + .getDomainArchitecture() ); } node.getNodeData().getSequence().setDomainArchitecture( rds ); } @@ -4993,14 +4993,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) ) && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) ) && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y - + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) ); + + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) ); } final boolean inOvRectangle( final MouseEvent e ) { return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) ) && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) ) && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY() - + getOvRectangle().getHeight() + 1 ) ) ); + + getOvRectangle().getHeight() + 1 ) ) ); } final boolean isApplet() { @@ -5105,7 +5105,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee y = max_y; } getMainPanel().getCurrentScrollPane().getViewport() - .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); + .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); setInOvRect( true ); repaint(); } @@ -5353,7 +5353,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) { g.setColor( getColorForFoundNode( c ) ); drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, c.getYSecondary() - - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); + - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); } } @@ -5443,7 +5443,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { if ( !to_graphics_file ) { g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y - + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) ); + + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) ); g.fill( r ); } else { @@ -5477,7 +5477,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } // Position starting Y of tree _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() ) - + ( TreePanel.MOVE / 2.0f ) ); + + ( TreePanel.MOVE / 2.0f ) ); final int dynamic_hiding_factor = calcDynamicHidingFactor(); if ( getControlPanel().isDynamicallyHideData() ) { if ( dynamic_hiding_factor > 1 ) { @@ -5613,7 +5613,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee y_pos + radius_ov, ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle() .getWidth() ) ) ), - g ); + g ); g.setTransform( _at ); paintOvRectangle( g ); } @@ -5695,20 +5695,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil - .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() ); + .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() ); } else { if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil.roundToInt( getXdistance() - * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); + * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); } else { x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil.roundToInt( getXdistance() - * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); + * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); } } setPreferredSize( new Dimension( x, y ) ); diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java index b58894d..a6017d9 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java @@ -150,7 +150,7 @@ public class TreePanelUtil { if ( cp.isShowSeqSymbols() && node.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) { TreePanelUtil - .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb ); + .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb ); } if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) { @@ -161,22 +161,22 @@ public class TreePanelUtil { && ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) { TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession() - .toString(), sb ); + .toString(), sb ); } if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy() - .getTaxonomyCode(), sb ); + .getTaxonomyCode(), sb ); } if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) { TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy() - .getScientificName(), sb ); + .getScientificName(), sb ); } if ( cp.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) { TreePanelUtil - .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb ); + .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb ); } // if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() ) // && node.getNodeData().isHasSequence() @@ -211,7 +211,7 @@ public class TreePanelUtil { TreePanelUtil.collapseSubtree( n, true ); if ( !n.getNodeData().isHasTaxonomy() ) { n.getNodeData().setTaxonomy( ( Taxonomy ) n.getAllExternalDescendants().get( 0 ).getNodeData() - .getTaxonomy().copy() ); + .getTaxonomy().copy() ); } inferred = true; } @@ -283,7 +283,7 @@ public class TreePanelUtil { final List descs = PhylogenyMethods.getAllDescendants( n ); for( final PhylogenyNode desc : descs ) { desc.getBranchData() - .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) ); + .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) ); } } } @@ -298,11 +298,11 @@ public class TreePanelUtil { if ( n.getNodeData().isHasTaxonomy() && ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil - .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) { + .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) { if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) { final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData() - .getTaxonomy() ) ); + .getTaxonomy() ) ); TreePanelUtil.colorizeSubtree( n, c ); ++colorizations; if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { @@ -320,7 +320,7 @@ public class TreePanelUtil { for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) { if ( true_lineage_to_color_map.containsKey( lin ) ) { TreePanelUtil - .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) ); + .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) ); ++colorizations; success = true; break; diff --git a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java index 36c6265..f5babe7 100644 --- a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java +++ b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java @@ -29,7 +29,6 @@ import java.io.File; import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; -import java.util.Date; import javax.swing.JOptionPane; @@ -65,7 +64,6 @@ public class UrlTreeReader implements Runnable { } synchronized void readPhylogeniesFromWebservice() { - final long start_time = new Date().getTime(); URL url = null; Phylogeny[] trees = null; final WebservicesManager webservices_manager = WebservicesManager.getInstance(); @@ -132,7 +130,7 @@ public class UrlTreeReader implements Runnable { case PFAM: parser = new NHXParser(); ( ( NHXParser ) parser ) - .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); + .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); ( ( NHXParser ) parser ).setReplaceUnderscores( false ); ( ( NHXParser ) parser ).setGuessRootedness( true ); break; @@ -245,23 +243,23 @@ public class UrlTreeReader implements Runnable { } _main_frame.getMainPanel().getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) ); AptxUtil.lookAtSomeTreePropertiesForAptxControlSettings( phylogeny, _main_frame.getMainPanel() - .getControlPanel(), _main_frame.getConfiguration() ); + .getControlPanel(), _main_frame.getConfiguration() ); _main_frame.getMainPanel().getControlPanel().showWhole(); } } } else if ( !exception ) { JOptionPane.showMessageDialog( null, ForesterUtil.wordWrap( "Failed to read in tree(s) from [" + url - + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE ); + + "]", 80 ), "Error", JOptionPane.ERROR_MESSAGE ); } _main_frame.getContentPane().repaint(); if ( ( trees != null ) && ( trees.length > 0 ) ) { try { JOptionPane.showMessageDialog( null, ForesterUtil.wordWrap( "Successfully read in " + trees.length - + " tree(s) from [" + url + "]", 80 ), - "Success", - JOptionPane.INFORMATION_MESSAGE ); + + " tree(s) from [" + url + "]", 80 ), + "Success", + JOptionPane.INFORMATION_MESSAGE ); } catch ( final Exception e ) { // Not important if this fails, do nothing.