From 9351f2c2e8af0c3bf1280f9696f1459db2819005 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 10 Mar 2015 01:42:04 +0000 Subject: [PATCH] in progress --- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 105 ++++---- .../src/org/forester/archaeopteryx/MainFrame.java | 266 ++++++++++++-------- 2 files changed, 222 insertions(+), 149 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 22ade3b..f6c26cf 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -47,6 +47,7 @@ import org.forester.sdi.GSDIR; import org.forester.sdi.SDIException; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; +import org.forester.util.WindowsUtils; // Use like this: // 0 ) ) { - JOptionPane.showMessageDialog( this, - "Wrote image to: " + file_written_to, - "Graphics Export", - JOptionPane.INFORMATION_MESSAGE ); + void setCurrentDir( final File current_dir ) { + _current_dir = current_dir; + } + + File getCurrentDir() { + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( ForesterUtil.isWindows() ) { + try { + _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); + } + catch ( final Exception e ) { + _current_dir = null; + } } - else { - JOptionPane.showMessageDialog( this, - "There was an unknown problem when attempting to write to an image file: \"" - + file_name + "\"", - "Error", - JOptionPane.ERROR_MESSAGE ); + } + if ( ( _current_dir == null ) || !_current_dir.canRead() ) { + if ( System.getProperty( "user.home" ) != null ) { + _current_dir = new File( System.getProperty( "user.home" ) ); + } + else if ( System.getProperty( "user.dir" ) != null ) { + _current_dir = new File( System.getProperty( "user.dir" ) ); } } - _contentpane.repaint(); + return _current_dir; } + + void buildFileMenu() { @@ -467,10 +464,23 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { } // else if ( o == _write_to_pdf_item ) { - writeToPdf( _mainpanel.getCurrentPhylogeny() ); + // writeToPdf( _mainpanel.getCurrentPhylogeny() ); + final File curr_dir =MainFrame.writeToPdf( _mainpanel.getCurrentPhylogeny(), + getMainPanel(), + _writetopdf_filechooser, + _current_dir, + getContentPane(), + this ); + + + if ( curr_dir != null ) { + setCurrentDir( curr_dir ); + } + } else if ( o == _write_to_jpg_item ) { + writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG ); } else if ( o == _write_to_gif_item ) { @@ -618,6 +628,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { @Override public void init() { + _writetopdf_filechooser = new JFileChooser(); final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL ); AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename ); final Configuration configuration = new Configuration( config_filename, true, true, true ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 5fddabb..f544c43 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -625,16 +625,67 @@ public abstract class MainFrame extends JFrame implements ActionListener { writeAllToFile(); } else if ( o == _write_to_jpg_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG ); + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.JPG, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } } else if ( o == _write_to_gif_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF ); + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.GIF, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } else if ( o == _write_to_tif_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF ); + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.TIFF, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + } else if ( o == _write_to_bmp_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP ); + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.BMP, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } + + } + else if ( o == _write_to_png_item ) { + final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), + GraphicsExportType.PNG, + _mainpanel, + _writetographics_filechooser, + this, + getContentPane(), + _current_dir ); + if ( new_dir != null ) { + setCurrentDir( new_dir ); + } } else if ( o == _print_item ) { print( getCurrentTreePanel(), getOptions(), this ); @@ -642,9 +693,7 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _save_item ) { writeToFile( _mainpanel.getCurrentPhylogeny() ); } - else if ( o == _write_to_png_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG ); - } + else if ( o == _graphics_export_visible_only_cbmi ) { updateOptions( getOptions() ); } @@ -875,11 +924,11 @@ 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; @@ -911,12 +960,12 @@ 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; @@ -1105,8 +1154,8 @@ 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, @@ -1118,8 +1167,8 @@ 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 ); } } @@ -1178,8 +1227,8 @@ 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, @@ -1189,8 +1238,8 @@ 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 ); } } @@ -1324,10 +1373,10 @@ 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; } } @@ -1377,8 +1426,8 @@ 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() ) { @@ -1524,20 +1573,20 @@ 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 ); } @@ -1548,7 +1597,7 @@ 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() ); } @@ -1562,14 +1611,14 @@ 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() ) { @@ -1583,9 +1632,9 @@ 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 ); } @@ -1599,14 +1648,14 @@ 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 ) ) { @@ -1672,8 +1721,8 @@ public abstract class MainFrame extends JFrame implements ActionListener { title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title; } showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions() - .getNhConversionSupportValueStyle() ), - title ); + .getNhConversionSupportValueStyle() ), + title ); } } @@ -1723,40 +1772,44 @@ public abstract class MainFrame extends JFrame implements ActionListener { return exception; } - void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) { - _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), - _mainpanel.getCurrentTreePanel().getHeight() ); + static void writePhylogenyToGraphicsFile( final String file_name, + final GraphicsExportType type, + final MainPanel mp, + final Component comp, + final Container contentpane ) { + mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(), + mp.getCurrentTreePanel().getHeight() ); String file_written_to = ""; boolean error = false; try { file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name, - _mainpanel.getCurrentTreePanel().getWidth(), - _mainpanel.getCurrentTreePanel().getHeight(), - _mainpanel.getCurrentTreePanel(), - _mainpanel.getControlPanel(), + mp.getCurrentTreePanel().getWidth(), + mp.getCurrentTreePanel().getHeight(), + mp.getCurrentTreePanel(), + mp.getControlPanel(), type, - getOptions() ); + mp.getOptions() ); } catch ( final IOException e ) { error = true; - JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); + JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); } if ( !error ) { if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) { - JOptionPane.showMessageDialog( this, + JOptionPane.showMessageDialog( comp, "Wrote image to: " + file_written_to, "Graphics Export", JOptionPane.INFORMATION_MESSAGE ); } else { - JOptionPane.showMessageDialog( this, + 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(); + contentpane.repaint(); } void writeToFile( final Phylogeny t ) { @@ -1850,53 +1903,62 @@ public abstract class MainFrame extends JFrame implements ActionListener { } } - void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) { + static File writeToGraphicsFile( final Phylogeny t, + final GraphicsExportType type, + final MainPanel mp, + final JFileChooser writetographics_filechooser, + final Component component, + final Container contentpane, + final File current_dir ) { + File new_dir = null; if ( ( t == null ) || t.isEmpty() ) { - return; + return null; } String initial_filename = ""; - if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { - initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString(); + if ( mp.getCurrentTreePanel().getTreeFile() != null ) { + initial_filename = mp.getCurrentTreePanel().getTreeFile().toString(); } if ( initial_filename.indexOf( '.' ) > 0 ) { initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); } initial_filename = initial_filename + "." + type; - _writetographics_filechooser.setSelectedFile( new File( initial_filename ) ); - final File my_dir = getCurrentDir(); + writetographics_filechooser.setSelectedFile( new File( initial_filename ) ); + final File my_dir = current_dir; if ( my_dir != null ) { - _writetographics_filechooser.setCurrentDirectory( my_dir ); + writetographics_filechooser.setCurrentDirectory( my_dir ); } - final int result = _writetographics_filechooser.showSaveDialog( _contentpane ); - File file = _writetographics_filechooser.getSelectedFile(); - setCurrentDir( _writetographics_filechooser.getCurrentDirectory() ); + final int result = writetographics_filechooser.showSaveDialog( contentpane ); + File file = writetographics_filechooser.getSelectedFile(); + //setCurrentDir( writetographics_filechooser.getCurrentDirectory() ); + new_dir = writetographics_filechooser.getCurrentDirectory(); if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) { file = new File( file.toString() + "." + type ); } if ( file.exists() ) { - final int i = JOptionPane.showConfirmDialog( this, + final int i = JOptionPane.showConfirmDialog( component, file + " already exists. Overwrite?", "Warning", JOptionPane.OK_CANCEL_OPTION, JOptionPane.WARNING_MESSAGE ); if ( i != JOptionPane.OK_OPTION ) { - return; + return null; } else { try { file.delete(); } catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, + JOptionPane.showMessageDialog( component, "Failed to delete: " + file, "Error", JOptionPane.WARNING_MESSAGE ); } } } - writePhylogenyToGraphicsFile( file.toString(), type ); + writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane ); } + return new_dir; } static File writeToPdf( final Phylogeny t, @@ -1953,10 +2015,10 @@ 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(); @@ -1975,7 +2037,7 @@ 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(); @@ -2002,7 +2064,7 @@ 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 ); } @@ -2027,11 +2089,11 @@ 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; @@ -2073,10 +2135,10 @@ 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(); @@ -2093,8 +2155,8 @@ 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(); @@ -2299,11 +2361,11 @@ 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; @@ -2446,7 +2508,7 @@ 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..." ); -- 1.7.10.2