import org.forester.sdi.SDIException;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
+import org.forester.util.WindowsUtils;
// Use like this:
// <applet archive="forester.jar"
private JCheckBoxMenuItem _right_line_up_domains_cbmi;
private JCheckBoxMenuItem _line_up_renderable_data_cbmi;
// file menu:
- JMenuItem _open_item;
- JMenuItem _open_url_item;
- JMenuItem _save_item;
- JMenuItem _save_all_item;
- JMenuItem _close_item;
- JMenuItem _exit_item;
- JMenuItem _new_item;
- JMenuItem _print_item;
- JMenuItem _write_to_pdf_item;
- JMenuItem _write_to_jpg_item;
- JMenuItem _write_to_gif_item;
- JMenuItem _write_to_tif_item;
- JMenuItem _write_to_png_item;
- JMenuItem _write_to_bmp_item;
- JMenu _file_jmenu;
+ private JMenuItem _open_item;
+ private JMenuItem _open_url_item;
+ private JMenuItem _save_item;
+ private JMenuItem _save_all_item;
+ private JMenuItem _close_item;
+ private JMenuItem _exit_item;
+ private JMenuItem _new_item;
+ private JMenuItem _print_item;
+ private JMenuItem _write_to_pdf_item;
+ private JMenuItem _write_to_jpg_item;
+ private JMenuItem _write_to_gif_item;
+ private JMenuItem _write_to_tif_item;
+ private JMenuItem _write_to_png_item;
+ private JMenuItem _write_to_bmp_item;
+ private JMenu _file_jmenu;
+ private JFileChooser _writetopdf_filechooser;
+ private File _current_dir;
+ private JFileChooser _save_filechooser;
+ private JFileChooser _writetographics_filechooser;
- void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
- _mainpanel.getCurrentTreePanel().getHeight() );
- String file_written_to = "";
- boolean error = false;
- try {
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,
- _mainpanel.getCurrentTreePanel().getWidth(),
- _mainpanel.getCurrentTreePanel().getHeight(),
- _mainpanel.getCurrentTreePanel(),
- _mainpanel.getControlPanel(),
- type,
- getOptions() );
- }
- catch ( final IOException e ) {
- error = true;
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );
- }
- if ( !error ) {
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {
- JOptionPane.showMessageDialog( this,
- "Wrote image to: " + file_written_to,
- "Graphics Export",
- JOptionPane.INFORMATION_MESSAGE );
+ 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() {
}
//
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 ) {
@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 );
writeAllToFile();\r
}\r
else if ( o == _write_to_jpg_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );\r
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
+ GraphicsExportType.JPG,\r
+ _mainpanel,\r
+ _writetographics_filechooser,\r
+ this,\r
+ getContentPane(),\r
+ _current_dir );\r
+ if ( new_dir != null ) {\r
+ setCurrentDir( new_dir );\r
+ }\r
}\r
else if ( o == _write_to_gif_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );\r
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
+ GraphicsExportType.GIF,\r
+ _mainpanel,\r
+ _writetographics_filechooser,\r
+ this,\r
+ getContentPane(),\r
+ _current_dir );\r
+ if ( new_dir != null ) {\r
+ setCurrentDir( new_dir );\r
+ }\r
+ \r
}\r
else if ( o == _write_to_tif_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF );\r
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
+ GraphicsExportType.TIFF,\r
+ _mainpanel,\r
+ _writetographics_filechooser,\r
+ this,\r
+ getContentPane(),\r
+ _current_dir );\r
+ if ( new_dir != null ) {\r
+ setCurrentDir( new_dir );\r
+ }\r
+ \r
}\r
else if ( o == _write_to_bmp_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP );\r
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
+ GraphicsExportType.BMP,\r
+ _mainpanel,\r
+ _writetographics_filechooser,\r
+ this,\r
+ getContentPane(),\r
+ _current_dir );\r
+ if ( new_dir != null ) {\r
+ setCurrentDir( new_dir );\r
+ }\r
+ \r
+ }\r
+ else if ( o == _write_to_png_item ) {\r
+ final File new_dir = writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(),\r
+ GraphicsExportType.PNG,\r
+ _mainpanel,\r
+ _writetographics_filechooser,\r
+ this,\r
+ getContentPane(),\r
+ _current_dir );\r
+ if ( new_dir != null ) {\r
+ setCurrentDir( new_dir );\r
+ }\r
}\r
else if ( o == _print_item ) {\r
print( getCurrentTreePanel(), getOptions(), this );\r
else if ( o == _save_item ) {\r
writeToFile( _mainpanel.getCurrentPhylogeny() );\r
}\r
- else if ( o == _write_to_png_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );\r
- }\r
+ \r
else if ( o == _graphics_export_visible_only_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
"Please enter the default line width for PDF export.\n"\r
+ "[current value: "\r
+ getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
+ "Line Width for PDF Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintLineWidth() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
float f = 0.0f;\r
+ Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
+ Constants.US_LETTER_SIZE_X + ", "\r
+ Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
+ "Default Size for Graphics Export",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getPrintSizeX() + ", "\r
+ + getOptions().getPrintSizeY() );\r
if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
boolean success = true;\r
int x = 0;\r
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "GSDI successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
+ gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDI successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ "GSDI successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
\r
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.WARNING_MESSAGE );\r
+ "GSDIR successfully completed",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
+ gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"\r
+ "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"\r
+ "Number of polytomies in species tree used: " + poly + "\n",\r
- "GSDIR successfully completed",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ "GSDIR successfully completed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
\r
if ( getCurrentTreePanel() != null ) {\r
if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
- "Operation can not be exectuted on a sub-tree",\r
- JOptionPane.WARNING_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",\r
+ "Operation can not be exectuted on a sub-tree",\r
+ JOptionPane.WARNING_MESSAGE );\r
return true;\r
}\r
}\r
JOptionPane.showMessageDialog( comp,\r
"There was an unknown problem when attempting to write to PDF file: \""\r
+ file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
if ( !opts.isPrintUsingActualSize() ) {\r
void updateOptions( final Options options ) {\r
options.setAntialiasScreen( ( _screen_antialias_cbmi != null ) && _screen_antialias_cbmi.isSelected() );\r
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )\r
- && _background_gradient_cbmi.isSelected() );\r
+ && _background_gradient_cbmi.isSelected() );\r
options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );\r
options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )\r
- && _show_annotation_ref_source.isSelected() );\r
+ && _show_annotation_ref_source.isSelected() );\r
options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )\r
- && _abbreviate_scientific_names.isSelected() );\r
+ && _abbreviate_scientific_names.isSelected() );\r
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )\r
- && _color_labels_same_as_parent_branch.isSelected() );\r
+ && _color_labels_same_as_parent_branch.isSelected() );\r
options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )\r
- && _show_default_node_shapes_internal_cbmi.isSelected() );\r
+ && _show_default_node_shapes_internal_cbmi.isSelected() );\r
options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )\r
- && _show_default_node_shapes_external_cbmi.isSelected() );\r
+ && _show_default_node_shapes_external_cbmi.isSelected() );\r
options.setShowDefaultNodeShapesForMarkedNodes( ( _show_default_node_shapes_for_marked_cbmi != null )\r
- && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
+ && _show_default_node_shapes_for_marked_cbmi.isSelected() );\r
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {\r
options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP );\r
}\r
options.setCladogramType( CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
}\r
options.setSearchCaseSensitive( ( _search_case_senstive_cbmi != null )\r
- && _search_case_senstive_cbmi.isSelected() );\r
+ && _search_case_senstive_cbmi.isSelected() );\r
if ( ( _show_scale_cbmi != null ) && _show_scale_cbmi.isEnabled() ) {\r
options.setShowScale( _show_scale_cbmi.isSelected() );\r
}\r
}\r
options.setShowOverview( ( _show_overview_cbmi != null ) && _show_overview_cbmi.isSelected() );\r
options.setShowConfidenceStddev( ( _show_confidence_stddev_cbmi != null )\r
- && _show_confidence_stddev_cbmi.isSelected() );\r
+ && _show_confidence_stddev_cbmi.isSelected() );\r
if ( ( _color_by_taxonomic_group_cbmi != null ) && _color_by_taxonomic_group_cbmi.isEnabled() ) {\r
options.setColorByTaxonomicGroup( _color_by_taxonomic_group_cbmi.isSelected() );\r
}\r
options.setPrintUsingActualSize( ( _print_using_actual_size_cbmi != null )\r
- && ( _print_using_actual_size_cbmi.isSelected() ) );\r
+ && ( _print_using_actual_size_cbmi.isSelected() ) );\r
options.setGraphicsExportUsingActualSize( ( _graphics_export_using_actual_size_cbmi != null )\r
- && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
+ && ( _graphics_export_using_actual_size_cbmi.isSelected() ) );\r
options.setAntialiasPrint( ( _antialias_print_cbmi != null ) && _antialias_print_cbmi.isSelected() );\r
if ( ( _use_brackets_for_conf_in_nh_export_cbmi != null )\r
&& _use_brackets_for_conf_in_nh_export_cbmi.isSelected() ) {\r
options.setNhConversionSupportValueStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );\r
}\r
options.setPrintBlackAndWhite( ( _print_black_and_white_cbmi != null )\r
- && _print_black_and_white_cbmi.isSelected() );\r
+ && _print_black_and_white_cbmi.isSelected() );\r
options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )\r
- && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
+ && _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );\r
if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {\r
options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );\r
}\r
options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );\r
}\r
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )\r
- && _replace_underscores_cbmi.isSelected() );\r
+ && _replace_underscores_cbmi.isSelected() );\r
options.setAllowErrorsInDistanceToParent( ( _allow_errors_in_distance_to_parent_cbmi != null )\r
- && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
+ && _allow_errors_in_distance_to_parent_cbmi.isSelected() );\r
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )\r
- && _search_whole_words_only_cbmi.isSelected() );\r
+ && _search_whole_words_only_cbmi.isSelected() );\r
options.setSearchWithRegex( ( _search_with_regex_cbmi != null ) && _search_with_regex_cbmi.isSelected() );\r
options.setInverseSearchResult( ( _inverse_search_result_cbmi != null )\r
- && _inverse_search_result_cbmi.isSelected() );\r
+ && _inverse_search_result_cbmi.isSelected() );\r
if ( _graphics_export_visible_only_cbmi != null ) {\r
options.setGraphicsExportVisibleOnly( _graphics_export_visible_only_cbmi.isSelected() );\r
if ( _graphics_export_visible_only_cbmi.isSelected() && ( _graphics_export_using_actual_size_cbmi != null ) ) {\r
title = "\"" + getMainPanel().getCurrentPhylogeny().getName() + "\" in " + title;\r
}\r
showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshire( getOptions()\r
- .getNhConversionSupportValueStyle() ),\r
- title );\r
+ .getNhConversionSupportValueStyle() ),\r
+ title );\r
}\r
}\r
\r
return exception;\r
}\r
\r
- void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight() );\r
+ static void writePhylogenyToGraphicsFile( final String file_name,\r
+ final GraphicsExportType type,\r
+ final MainPanel mp,\r
+ final Component comp,\r
+ final Container contentpane ) {\r
+ mp.getCurrentTreePanel().calcParametersForPainting( mp.getCurrentTreePanel().getWidth(),\r
+ mp.getCurrentTreePanel().getHeight() );\r
String file_written_to = "";\r
boolean error = false;\r
try {\r
file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
- _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getControlPanel(),\r
+ mp.getCurrentTreePanel().getWidth(),\r
+ mp.getCurrentTreePanel().getHeight(),\r
+ mp.getCurrentTreePanel(),\r
+ mp.getControlPanel(),\r
type,\r
- getOptions() );\r
+ mp.getOptions() );\r
}\r
catch ( final IOException e ) {\r
error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
+ JOptionPane.showMessageDialog( comp, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
}\r
if ( !error ) {\r
if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
+ JOptionPane.showMessageDialog( comp,\r
"Wrote image to: " + file_written_to,\r
"Graphics Export",\r
JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
- JOptionPane.showMessageDialog( this,\r
+ JOptionPane.showMessageDialog( comp,\r
"There was an unknown problem when attempting to write to an image file: \""\r
+ file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
+ "Error",\r
+ JOptionPane.ERROR_MESSAGE );\r
}\r
}\r
- _contentpane.repaint();\r
+ contentpane.repaint();\r
}\r
\r
void writeToFile( final Phylogeny t ) {\r
}\r
}\r
\r
- void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {\r
+ static File writeToGraphicsFile( final Phylogeny t,\r
+ final GraphicsExportType type,\r
+ final MainPanel mp,\r
+ final JFileChooser writetographics_filechooser,\r
+ final Component component,\r
+ final Container contentpane,\r
+ final File current_dir ) {\r
+ File new_dir = null;\r
if ( ( t == null ) || t.isEmpty() ) {\r
- return;\r
+ return null;\r
}\r
String initial_filename = "";\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
+ if ( mp.getCurrentTreePanel().getTreeFile() != null ) {\r
+ initial_filename = mp.getCurrentTreePanel().getTreeFile().toString();\r
}\r
if ( initial_filename.indexOf( '.' ) > 0 ) {\r
initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
}\r
initial_filename = initial_filename + "." + type;\r
- _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = getCurrentDir();\r
+ writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
+ final File my_dir = current_dir;\r
if ( my_dir != null ) {\r
- _writetographics_filechooser.setCurrentDirectory( my_dir );\r
+ writetographics_filechooser.setCurrentDirectory( my_dir );\r
}\r
- final int result = _writetographics_filechooser.showSaveDialog( _contentpane );\r
- File file = _writetographics_filechooser.getSelectedFile();\r
- setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );\r
+ final int result = writetographics_filechooser.showSaveDialog( contentpane );\r
+ File file = writetographics_filechooser.getSelectedFile();\r
+ //setCurrentDir( writetographics_filechooser.getCurrentDirectory() );\r
+ new_dir = writetographics_filechooser.getCurrentDirectory();\r
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
file = new File( file.toString() + "." + type );\r
}\r
if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
+ final int i = JOptionPane.showConfirmDialog( component,\r
file + " already exists. Overwrite?",\r
"Warning",\r
JOptionPane.OK_CANCEL_OPTION,\r
JOptionPane.WARNING_MESSAGE );\r
if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
+ return null;\r
}\r
else {\r
try {\r
file.delete();\r
}\r
catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
+ JOptionPane.showMessageDialog( component,\r
"Failed to delete: " + file,\r
"Error",\r
JOptionPane.WARNING_MESSAGE );\r
}\r
}\r
}\r
- writePhylogenyToGraphicsFile( file.toString(), type );\r
+ writePhylogenyToGraphicsFile( file.toString(), type, mp, component, contentpane );\r
}\r
+ return new_dir;\r
}\r
\r
static File writeToPdf( final Phylogeny t,\r
}\r
if ( ( nodes == null ) || nodes.isEmpty() ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select nodes, either via direct selection or via the \"Search\" function",\r
- "No nodes selected for annotation",\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "Need to select nodes, either via direct selection or via the \"Search\" function",\r
+ "No nodes selected for annotation",\r
+ JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
final Phylogeny phy = getMainPanel().getCurrentPhylogeny();\r
my_panel,\r
"Enter the sequence annotation(s) for the "\r
+ nodes.size() + " selected nodes",\r
- JOptionPane.OK_CANCEL_OPTION );\r
+ JOptionPane.OK_CANCEL_OPTION );\r
if ( result == JOptionPane.OK_OPTION ) {\r
String ref = ref_field.getText();\r
String desc = desc_filed.getText();\r
for( final PhylogenyNode n : nodes ) {\r
ForesterUtil.ensurePresenceOfSequence( n );\r
final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()\r
- : new Annotation( ref );\r
+ : new Annotation( ref );\r
if ( !ForesterUtil.isEmpty( desc ) ) {\r
ann.setDesc( desc );\r
}\r
.showInputDialog( this,\r
"Please enter the minimum for confidence values to be displayed.\n"\r
+ "[current value: " + getOptions().getMinConfidenceValue() + "]\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getMinConfidenceValue() );\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getOptions().getMinConfidenceValue() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
double m = 0.0;\r
}\r
if ( ( nodes == null ) || nodes.isEmpty() ) {\r
JOptionPane\r
- .showMessageDialog( this,\r
- "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
- "No external nodes selected to " + function.toLowerCase(),\r
- JOptionPane.ERROR_MESSAGE );\r
+ .showMessageDialog( this,\r
+ "Need to select external nodes, either via direct selection or via the \"Search\" function",\r
+ "No external nodes selected to " + function.toLowerCase(),\r
+ JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
final int todo = nodes.size();\r
return;\r
}\r
final int result = JOptionPane.showConfirmDialog( null, function + " " + todo\r
- + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
- + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
+ + " external node(s), from a total of " + ext + " external nodes," + "\nresulting in tree with " + res\r
+ + " nodes?", function + " external nodes", JOptionPane.OK_CANCEL_OPTION );\r
if ( result == JOptionPane.OK_OPTION ) {\r
if ( !delete ) {\r
final List<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();\r
"Please enter the default size for node shapes.\n"\r
+ "[current value: "\r
+ options.getDefaultNodeShapeSize() + "]\n",\r
- "Node Shape Size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- options.getDefaultNodeShapeSize() );\r
+ "Node Shape Size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ options.getDefaultNodeShapeSize() );\r
if ( !ForesterUtil.isEmpty( s ) ) {\r
boolean success = true;\r
double m = 0.0;\r
static void setTextColorChooseMenuItem( final JMenuItem mi, final TreePanel tree_panel ) {\r
if ( ( tree_panel != null ) && ( tree_panel.getTreeColorSet() != null ) ) {\r
mi.setText( "Select Color Scheme... (current: " + tree_panel.getTreeColorSet().getCurrentColorSchemeName()\r
- + ")" );\r
+ + ")" );\r
}\r
else {\r
mi.setText( "Select Color Scheme..." );\r
git://source.jalview.org / jalview.git / commitdiff