import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.filechooser.FileFilter;
+import javax.swing.plaf.synth.SynthLookAndFeel;
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
-import org.forester.archaeopteryx.Util.GraphicsExportType;
import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
import org.forester.archaeopteryx.tools.GoAnnotation;
import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.io.writers.SequenceWriter;
import org.forester.msa.Msa;
import org.forester.util.BasicTableParser;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
-import org.forester.util.ForesterUtil.PhylogenyNodeField;
-import org.forester.util.ForesterUtil.TAXONOMY_EXTRACTION;
import org.forester.util.WindowsUtils;
class DefaultFilter extends FileFilter {
public final class MainFrameApplication extends MainFrame {
- private final static int FRAME_X_SIZE = 800;
- private final static int FRAME_Y_SIZE = 800;
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";
+ private final static int FRAME_X_SIZE = 800;
+ private final static int FRAME_Y_SIZE = 800;
// Filters for the file-open dialog (classes defined in this file)
- private final static NHFilter nhfilter = new NHFilter();
- private final static NHXFilter nhxfilter = new NHXFilter();
- private final static XMLFilter xmlfilter = new XMLFilter();
- private final static TolFilter tolfilter = new TolFilter();
- private final static NexusFilter nexusfilter = new NexusFilter();
- private final static PdfFilter pdffilter = new PdfFilter();
- private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
- private final static MsaFileFilter msafilter = new MsaFileFilter();
- private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
- private final static DefaultFilter defaultfilter = new DefaultFilter();
- private static final long serialVersionUID = -799735726778865234L;
+ private final static NHFilter nhfilter = new NHFilter();
+ private final static NHXFilter nhxfilter = new NHXFilter();
+ private final static XMLFilter xmlfilter = new XMLFilter();
+ private final static TolFilter tolfilter = new TolFilter();
+ private final static NexusFilter nexusfilter = new NexusFilter();
+ private final static PdfFilter pdffilter = new PdfFilter();
+ private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();
+ private final static MsaFileFilter msafilter = new MsaFileFilter();
+ private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();
+ private final static DefaultFilter defaultfilter = new DefaultFilter();
+ private static final long serialVersionUID = -799735726778865234L;
private final JFileChooser _values_filechooser;
private final JFileChooser _open_filechooser;
private final JFileChooser _msa_filechooser;
private File _current_dir;
private ButtonGroup _radio_group_1;
// Others:
- double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
+ double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;
// Phylogeny Inference menu
private JMenu _inference_menu;
private JMenuItem _inference_from_msa_item;
private JMenuItem _inference_from_seqs_item;
// Phylogeny Inference
- private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
- private Msa _msa = null;
- private File _msa_file = null;
- private List<Sequence> _seqs = null;
- private File _seqs_file = null;
+ private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;
+ private Msa _msa = null;
+ private File _msa_file = null;
+ private List<Sequence> _seqs = null;
+ private File _seqs_file = null;
// expression values menu:
JMenuItem _read_values_jmi;
throw new IllegalArgumentException( "configuration is null" );
}
try {
- if ( _configuration.isUseNativeUI() ) {
- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+ boolean synth_exception = false;
+ if ( Constants.__SYNTH_LF ) {
+ try {
+ final SynthLookAndFeel synth = new SynthLookAndFeel();
+ synth.load( MainFrameApplication.class.getResourceAsStream( "/resources/synth_look_and_feel_1.xml" ),
+ MainFrameApplication.class );
+ UIManager.setLookAndFeel( synth );
+ }
+ catch ( final Exception ex ) {
+ synth_exception = true;
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+ "could not create synth look and feel: "
+ + ex.getLocalizedMessage() );
+ }
}
- else {
- UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
+ if ( !Constants.__SYNTH_LF || synth_exception ) {
+ if ( _configuration.isUseNativeUI() ) {
+ UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+ }
+ else {
+ UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
+ }
}
//UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
}
catch ( final UnsupportedLookAndFeelException e ) {
- Util.dieWithSystemError( "UnsupportedLookAndFeelException: " + e.toString() );
+ AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
}
catch ( final ClassNotFoundException e ) {
- Util.dieWithSystemError( "ClassNotFoundException: " + e.toString() );
+ AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
}
catch ( final InstantiationException e ) {
- Util.dieWithSystemError( "InstantiationException: " + e.toString() );
+ AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
}
catch ( final IllegalAccessException e ) {
- Util.dieWithSystemError( "IllegalAccessException: " + e.toString() );
+ AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
}
catch ( final Exception e ) {
- Util.dieWithSystemError( e.toString() );
+ AptxUtil.dieWithSystemError( e.toString() );
}
// hide until everything is ready
setVisible( false );
// addKeyListener( this );
setVisible( true );
if ( ( phys != null ) && ( phys.length > 0 ) ) {
- Util.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
+ AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
validate();
getMainPanel().getControlPanel().showWholeAll();
getMainPanel().getControlPanel().showWhole();
System.gc();
}
+ private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
+ _configuration = config;
+ if ( _configuration == null ) {
+ throw new IllegalArgumentException( "configuration is null" );
+ }
+ setVisible( false );
+ setOptions( Options.createInstance( _configuration ) );
+ _mainpanel = new MainPanel( _configuration, this );
+ _open_filechooser = null;
+ _open_filechooser_for_species_tree = null;
+ _save_filechooser = null;
+ _writetopdf_filechooser = null;
+ _writetographics_filechooser = null;
+ _msa_filechooser = null;
+ _seqs_filechooser = null;
+ _values_filechooser = null;
+ _jmenubar = new JMenuBar();
+ buildFileMenu();
+ buildTypeMenu();
+ _contentpane = getContentPane();
+ _contentpane.setLayout( new BorderLayout() );
+ _contentpane.add( _mainpanel, BorderLayout.CENTER );
+ // App is this big
+ setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
+ // The window listener
+ setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
+ addWindowListener( new WindowAdapter() {
+
+ @Override
+ public void windowClosing( final WindowEvent e ) {
+ exit();
+ }
+ } );
+ // setVisible( true );
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {
+ AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
+ validate();
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ }
+ //activateSaveAllIfNeeded();
+ // ...and its children
+ _contentpane.repaint();
+ }
+
private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
// Reads the config file (false, false => not url, not applet):
- this( phys, new Configuration( config_file, false, false ), title );
+ this( phys, new Configuration( config_file, false, false, true ), title );
}
@Override
}
obtainDetailedTaxonomicInformation();
}
+ else if ( o == _obtain_detailed_taxonomic_information_deleting_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ obtainDetailedTaxonomicInformationDelete();
+ }
else if ( o == _obtain_uniprot_seq_information_jmi ) {
obtainUniProtSequenceInformation();
}
_contentpane.repaint();
}
catch ( final Exception ex ) {
- Util.unexpectedException( ex );
+ AptxUtil.unexpectedException( ex );
}
catch ( final Error err ) {
- Util.unexpectedError( err );
+ AptxUtil.unexpectedError( err );
}
}
customizeJMenuItem( _root_min_cost_l_item );
customizeJMenuItem( _load_species_tree_item );
_analysis_menu.addSeparator();
- _analysis_menu.add( _lineage_inference = new JMenuItem( "Infer Ancestor Taxonomies" ) );
+ _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
customizeJMenuItem( _lineage_inference );
_lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
_jmenubar.add( _analysis_menu );
_save_all_item.setEnabled( false );
_file_jmenu.addSeparator();
_file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
- if ( Util.canWriteFormat( "tif" ) || Util.canWriteFormat( "tiff" ) || Util.canWriteFormat( "TIF" ) ) {
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
_file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
}
_file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
_file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
- if ( Util.canWriteFormat( "gif" ) ) {
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {
_file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
}
- if ( Util.canWriteFormat( "bmp" ) ) {
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {
_file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
}
_file_jmenu.addSeparator();
@Override
public void stateChanged( final ChangeEvent e ) {
- MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getCurrentTreePanel() );
+ MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
MainFrame
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
_uniform_cladograms_rbmi,
_ext_node_dependent_cladogram_rbmi,
_label_direction_cbmi );
+ MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
+ MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
+ MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
}
} );
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
- //
_options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) );
_options_jmenu
.add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
_options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
_options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
_options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
- //
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
customizeJMenuItem( _print_size_mi );
customizeJMenuItem( _choose_pdf_width_mi );
customizeJMenuItem( _overview_placment_mi );
- //TODO FIXME ~~
customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() );
customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
customizeJMenuItem( _choose_node_size_mi );
- //TODO FIXME ~~
customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
_tools_menu = createMenu( "Tools", getConfiguration() );
_tools_menu.add( _confcolor_item = new JMenuItem( "Colorize Branches Depending on Confidence" ) );
customizeJMenuItem( _confcolor_item );
+ _tools_menu.add( _color_rank_jmi = new JMenuItem( "Colorize Subtrees via Taxonomic Rank" ) );
+ customizeJMenuItem( _color_rank_jmi );
+ _color_rank_jmi.setToolTipText( "for example, at \"Class\" level, colorize mammal specific subtree red" );
_tools_menu.add( _taxcolor_item = new JMenuItem( "Taxonomy Colorize Branches" ) );
customizeJMenuItem( _taxcolor_item );
_tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete Branch Colors" ) );
customizeJMenuItem( _infer_common_sn_names_item );
_tools_menu.addSeparator();
_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)" );
_tools_menu
+ .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)" );
+ _tools_menu
.add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
_obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
JOptionPane.ERROR_MESSAGE );
return;
}
- final Phylogeny phy = _mainpanel.getCurrentPhylogeny().copy();
final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,
_mainpanel.getCurrentTreePanel(),
- phy );
+ _mainpanel.getCurrentPhylogeny()
+ .copy() );
new Thread( inferrer ).start();
}
System.exit( 0 );
}
+ public void end() {
+ _mainpanel.terminate();
+ _contentpane.removeAll();
+ setVisible( false );
+ dispose();
+ }
+
private void extractTaxCodeFromNodeNames() {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
final PhylogenyNode n = it.next();
final String name = n.getName().trim();
if ( !ForesterUtil.isEmpty( name ) ) {
- final String code = ForesterUtil.extractTaxonomyCodeFromNodeName( name,
- false,
- TAXONOMY_EXTRACTION.YES );
+ final String code = ParserUtils
+ .extractTaxonomyCodeFromNodeName( name, false, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
if ( !ForesterUtil.isEmpty( code ) ) {
PhylogenyMethods.setTaxonomyCode( n, code );
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- ForesterUtil.transferNodeNameToField( phy, PhylogenyNodeField.SEQUENCE_NAME );
+ PhylogenyMethods.transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME );
}
}
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- ForesterUtil.transferNodeNameToField( phy, PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME );
+ PhylogenyMethods.transferNodeNameToField( phy,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME );
}
}
}
phy.setRoot( node );
phy.setRooted( true );
phys[ 0 ] = phy;
- Util.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
+ AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
_mainpanel.getControlPanel().showWhole();
_mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
_mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
}
}
+ private void obtainDetailedTaxonomicInformationDelete() {
+ if ( getCurrentTreePanel() != null ) {
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( ( phy != null ) && !phy.isEmpty() ) {
+ final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ true );
+ new Thread( t ).start();
+ }
+ }
+ }
+
private void obtainUniProtSequenceInformation() {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
try {
final NHXParser nhx = new NHXParser();
setSpecialOptionsForNhxParser( nhx );
- phys = ForesterUtil.readPhylogenies( nhx, file );
+ phys = PhylogenyMethods.readPhylogenies( nhx, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
try {
final PhyloXmlParser xml_parser = createPhyloXmlParser();
- phys = ForesterUtil.readPhylogenies( xml_parser, file );
+ phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
}
catch ( final Exception e ) {
exception = true;
}
else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
- phys = ForesterUtil.readPhylogenies( new TolParser(), file );
+ phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
}
catch ( final Exception e ) {
exception = true;
try {
final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
setSpecialOptionsForNexParser( nex );
- phys = ForesterUtil.readPhylogenies( nex, file );
+ phys = PhylogenyMethods.readPhylogenies( nex, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final PhylogenyParser parser = ForesterUtil
+ final PhylogenyParser parser = ParserUtils
.createParserDependingOnFileType( file, getConfiguration()
.isValidatePhyloXmlAgainstSchema() );
if ( parser instanceof NexusPhylogeniesParser ) {
else if ( parser instanceof PhyloXmlParser ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
}
- phys = ForesterUtil.readPhylogenies( parser, file );
+ phys = PhylogenyMethods.readPhylogenies( parser, file );
}
catch ( final Exception e ) {
exception = true;
if ( nhx_or_nexus ) {
for( final Phylogeny phy : phys ) {
if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
- ForesterUtil.transferInternalNodeNamesToConfidence( phy );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
one_desc = true;
}
}
}
- Util.addPhylogeniesToTabs( phys,
- file.getName(),
- file.getAbsolutePath(),
- getConfiguration(),
- getMainPanel() );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ file.getName(),
+ file.getAbsolutePath(),
+ getConfiguration(),
+ getMainPanel() );
_mainpanel.getControlPanel().showWhole();
if ( nhx_or_nexus && one_desc ) {
JOptionPane
parser = new TolParser();
}
else {
- parser = ForesterUtil.createParserDependingOnUrlContents( url, getConfiguration()
+ parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
.isValidatePhyloXmlAgainstSchema() );
}
if ( parser instanceof NexusPhylogeniesParser ) {
if ( ( phys != null ) && ( phys.length > 0 ) ) {
if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
for( final Phylogeny phy : phys ) {
- ForesterUtil.transferInternalNodeNamesToConfidence( phy );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
}
- Util.addPhylogeniesToTabs( phys,
- new File( url.getFile() ).getName(),
- new File( url.getFile() ).toString(),
- getConfiguration(),
- getMainPanel() );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( url.getFile() ).getName(),
+ new File( url.getFile() ).toString(),
+ getConfiguration(),
+ getMainPanel() );
_mainpanel.getControlPanel().showWhole();
}
}
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
try {
- final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
}
else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
- final Phylogeny[] trees = ForesterUtil.readPhylogenies( new TolParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
- ForesterUtil.TAXONOMY_EXTRACTION te = ForesterUtil.TAXONOMY_EXTRACTION.NO;
+ PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
if ( getOptions().isExtractPfamTaxonomyCodesInNhParsing() ) {
- te = ForesterUtil.TAXONOMY_EXTRACTION.YES;
+ te = PhylogenyMethods.TAXONOMY_EXTRACTION.YES;
}
nhx.setTaxonomyExtraction( te );
}
return exception;
}
- private void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
+ void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
_mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
_mainpanel.getCurrentTreePanel().getHeight(),
true );
String file_written_to = "";
boolean error = false;
try {
- file_written_to = Util.writePhylogenyToGraphicsFile( file_name,
- _mainpanel.getCurrentTreePanel().getWidth(),
- _mainpanel.getCurrentTreePanel().getHeight(),
- _mainpanel.getCurrentTreePanel(),
- _mainpanel.getControlPanel(),
- type,
- getOptions() );
+ 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;
return new MainFrameApplication( phys, config, title );
}
+ public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
+ return new MainFrameApplication( phys, config );
+ }
+
static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
return new MainFrameApplication( phys, config_file_name, title );
}
git://source.jalview.org / jalview.git / blobdiff