import javax.swing.WindowConstants;\r
import javax.swing.event.ChangeEvent;\r
import javax.swing.event.ChangeListener;\r
-import javax.swing.filechooser.FileFilter;\r
import javax.swing.plaf.synth.SynthLookAndFeel;\r
\r
import org.forester.analysis.TaxonomyDataManager;\r
import org.forester.phylogeny.PhylogenyNode;\r
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
import org.forester.phylogeny.data.Confidence;\r
+import org.forester.phylogeny.data.PhylogenyDataUtil;\r
+import org.forester.phylogeny.data.Sequence;\r
import org.forester.phylogeny.data.Taxonomy;\r
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;\r
import org.forester.phylogeny.factories.PhylogenyFactory;\r
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
-import org.forester.sequence.Sequence;\r
+import org.forester.sequence.MolecularSequence;\r
import org.forester.util.BasicDescriptiveStatistics;\r
import org.forester.util.BasicTable;\r
import org.forester.util.BasicTableParser;\r
import org.forester.util.DescriptiveStatistics;\r
import org.forester.util.ForesterUtil;\r
-import org.forester.util.WindowsUtils;\r
\r
public final class MainFrameApplication extends MainFrame {\r
\r
- static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
- static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
- private final static int FRAME_X_SIZE = 800;\r
- private final static int FRAME_Y_SIZE = 800;\r
+ public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
+ return new MainFrameApplication( phys, config );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
+ return new MainFrameApplication( phys, config, title );\r
+ }\r
+\r
+ public static MainFrame createInstance( final Phylogeny[] phys,\r
+ final Configuration config,\r
+ final String title,\r
+ final File current_dir ) {\r
+ return new MainFrameApplication( phys, config, title, current_dir );\r
+ }\r
+\r
+ static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
+ return new MainFrameApplication( phys, config_file_name, title );\r
+ }\r
+\r
+ static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
+ if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
+ JOptionPane\r
+ .showMessageDialog( null,\r
+ ForesterUtil\r
+ .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
+ 80 ),\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies";\r
+ static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information";\r
+ private final static int FRAME_X_SIZE = 800;\r
+ private final static int FRAME_Y_SIZE = 800;\r
// Filters for the file-open dialog (classes defined in this file)\r
- private final static NHFilter nhfilter = new NHFilter();\r
- private final static NHXFilter nhxfilter = new NHXFilter();\r
- private final static XMLFilter xmlfilter = new XMLFilter();\r
- private final static TolFilter tolfilter = new TolFilter();\r
- private final static NexusFilter nexusfilter = new NexusFilter();\r
- private final static PdfFilter pdffilter = new PdfFilter();\r
- private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter();\r
- private final static MsaFileFilter msafilter = new MsaFileFilter();\r
- private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();\r
- private final static DefaultFilter defaultfilter = new DefaultFilter();\r
- private static final long serialVersionUID = -799735726778865234L;\r
- private final JFileChooser _values_filechooser;\r
- private final JFileChooser _sequences_filechooser;\r
- private final JFileChooser _open_filechooser;\r
- private final JFileChooser _msa_filechooser;\r
- private final JFileChooser _seqs_pi_filechooser;\r
- private final JFileChooser _open_filechooser_for_species_tree;\r
- private final JFileChooser _save_filechooser;\r
- private final JFileChooser _writetopdf_filechooser;\r
- private final JFileChooser _writetographics_filechooser;\r
+ private static final long serialVersionUID = -799735726778865234L;\r
+ private static final boolean PREPROCESS_TREES = false;\r
+ private final JFileChooser _values_filechooser;\r
+ private final JFileChooser _sequences_filechooser;\r
+ private final JFileChooser _open_filechooser;\r
+ private final JFileChooser _msa_filechooser;\r
+ private final JFileChooser _seqs_pi_filechooser;\r
+ private final JFileChooser _open_filechooser_for_species_tree;\r
// Application-only print menu items\r
- private JMenuItem _print_item;\r
- private JMenuItem _write_to_pdf_item;\r
- private JMenuItem _write_to_jpg_item;\r
- private JMenuItem _write_to_gif_item;\r
- private JMenuItem _write_to_tif_item;\r
- private JMenuItem _write_to_png_item;\r
- private JMenuItem _write_to_bmp_item;\r
- private File _current_dir;\r
- private ButtonGroup _radio_group_1;\r
- private ButtonGroup _radio_group_2;\r
+ private JMenuItem _collapse_below_threshold;\r
+ private JMenuItem _collapse_below_branch_length;\r
+ private ButtonGroup _radio_group_1;\r
+ private ButtonGroup _radio_group_2;\r
// Others:\r
- double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
+ double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
+ double _min_not_collapse_bl = 0.001;\r
// Phylogeny Inference menu\r
- private JMenu _inference_menu;\r
- private JMenuItem _inference_from_msa_item;\r
- private JMenuItem _inference_from_seqs_item;\r
+ private JMenu _inference_menu;\r
+ private JMenuItem _inference_from_msa_item;\r
+ private JMenuItem _inference_from_seqs_item;\r
// Phylogeny Inference\r
- private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;\r
- private Msa _msa = null;\r
- private File _msa_file = null;\r
- private List<Sequence> _seqs = null;\r
- private File _seqs_file = null;\r
- JMenuItem _read_values_jmi;\r
- JMenuItem _read_seqs_jmi;\r
+ private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;\r
+ private Msa _msa = null;\r
+ private File _msa_file = null;\r
+ private List<MolecularSequence> _seqs = null;\r
+ private File _seqs_file = null;\r
+ JMenuItem _read_values_jmi;\r
+ JMenuItem _read_seqs_jmi;\r
\r
private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {\r
_configuration = config;\r
_open_filechooser = new JFileChooser();\r
_open_filechooser.setCurrentDirectory( new File( "." ) );\r
_open_filechooser.setMultiSelectionEnabled( false );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );\r
- _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );\r
+ _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter );\r
_open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() );\r
- _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter );\r
+ _open_filechooser.setFileFilter( MainFrame.defaultfilter );\r
_open_filechooser_for_species_tree = new JFileChooser();\r
_open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) );\r
_open_filechooser_for_species_tree.setMultiSelectionEnabled( false );\r
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter );\r
- _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter );\r
- _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter );\r
+ _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter );\r
+ _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter );\r
+ _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter );\r
_save_filechooser = new JFileChooser();\r
_save_filechooser.setCurrentDirectory( new File( "." ) );\r
_save_filechooser.setMultiSelectionEnabled( false );\r
- _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter );\r
- _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter );\r
- _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter );\r
+ _save_filechooser.setFileFilter( MainFrame.xmlfilter );\r
+ _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter );\r
+ _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter );\r
_save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() );\r
_writetopdf_filechooser = new JFileChooser();\r
- _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter );\r
+ _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter );\r
_writetographics_filechooser = new JFileChooser();\r
- _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter );\r
+ _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter );\r
// Msa:\r
_msa_filechooser = new JFileChooser();\r
_msa_filechooser.setName( "Read Multiple Sequence Alignment File" );\r
_msa_filechooser.setCurrentDirectory( new File( "." ) );\r
_msa_filechooser.setMultiSelectionEnabled( false );\r
_msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() );\r
- _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter );\r
+ _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter );\r
// Seqs:\r
_seqs_pi_filechooser = new JFileChooser();\r
_seqs_pi_filechooser.setName( "Read Sequences File" );\r
_seqs_pi_filechooser.setCurrentDirectory( new File( "." ) );\r
_seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
_seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() );\r
- _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter );\r
+ _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter );\r
// Expression\r
_values_filechooser = new JFileChooser();\r
_values_filechooser.setCurrentDirectory( new File( "." ) );\r
_mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()\r
.getWidth(),\r
_mainpanel.getCurrentTreePanel()\r
- .getHeight(),\r
- getOptions().isAllowFontSizeChange() );\r
+ .getHeight() );\r
}\r
}\r
} );\r
if ( o == _open_url_item ) {\r
readPhylogeniesFromURL();\r
}\r
- else if ( o == _save_item ) {\r
- writeToFile( _mainpanel.getCurrentPhylogeny() );\r
- // If subtree currently displayed, save it, instead of complete\r
- // tree.\r
- }\r
else if ( o == _new_item ) {\r
newTree();\r
}\r
else if ( o == _close_item ) {\r
closeCurrentPane();\r
}\r
- else if ( o == _write_to_pdf_item ) {\r
- writeToPdf( _mainpanel.getCurrentPhylogeny() );\r
- }\r
else if ( o == _write_to_jpg_item ) {\r
writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG );\r
}\r
- else if ( o == _write_to_png_item ) {\r
- writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG );\r
- }\r
else if ( o == _write_to_gif_item ) {\r
writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF );\r
}\r
else if ( o == _extract_tax_code_from_node_names_jmi ) {\r
extractTaxDataFromNodeNames();\r
}\r
- else if ( o == _graphics_export_visible_only_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _antialias_print_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_black_and_white_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_using_actual_size_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _graphics_export_using_actual_size_cbmi ) {\r
- updateOptions( getOptions() );\r
- }\r
- else if ( o == _print_size_mi ) {\r
- choosePrintSize();\r
- }\r
- else if ( o == _choose_pdf_width_mi ) {\r
- choosePdfWidth();\r
- }\r
else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) {\r
updateOptions( getOptions() );\r
}\r
}\r
collapseBelowThreshold();\r
}\r
+ else if ( o == _collapse_below_branch_length ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ collapseBelowBranchLengthThreshold();\r
+ }\r
else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )\r
|| ( o == _extract_taxonomy_agressive_rbmi ) ) {\r
if ( _replace_underscores_cbmi != null ) {\r
}\r
}\r
\r
- public void end() {\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- }\r
-\r
- @Override\r
- public MainPanel getMainPanel() {\r
- return _mainpanel;\r
- }\r
-\r
- public Msa getMsa() {\r
- return _msa;\r
- }\r
-\r
- public File getMsaFile() {\r
- return _msa_file;\r
- }\r
-\r
- public List<Sequence> getSeqs() {\r
- return _seqs;\r
- }\r
-\r
- public File getSeqsFile() {\r
- return _seqs_file;\r
- }\r
-\r
- public void readMsaFromFile() {\r
- // Set an initial directory if none set yet\r
+ private void addExpressionValuesFromFile() {\r
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Need to load evolutionary tree first",\r
+ "Can Not Read Expression Values",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return;\r
+ }\r
final File my_dir = getCurrentDir();\r
- _msa_filechooser.setMultiSelectionEnabled( false );\r
- // Open file-open dialog and set current directory\r
if ( my_dir != null ) {\r
- _msa_filechooser.setCurrentDirectory( my_dir );\r
+ _values_filechooser.setCurrentDirectory( my_dir );\r
}\r
- final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the msa\r
- final File file = _msa_filechooser.getSelectedFile();\r
- setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setMsaFile( null );\r
- setMsa( null );\r
- Msa msa = null;\r
+ final int result = _values_filechooser.showOpenDialog( _contentpane );\r
+ final File file = _values_filechooser.getSelectedFile();\r
+ if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ BasicTable<String> t = null;\r
try {\r
- final InputStream is = new FileInputStream( file );\r
- if ( FastaParser.isLikelyFasta( file ) ) {\r
- msa = FastaParser.parseMsa( is );\r
+ t = BasicTableParser.parse( file, '\t' );\r
+ if ( t.getNumberOfColumns() < 2 ) {\r
+ t = BasicTableParser.parse( file, ',' );\r
}\r
- else {\r
- msa = GeneralMsaParser.parse( is );\r
+ if ( t.getNumberOfColumns() < 2 ) {\r
+ t = BasicTableParser.parse( file, ' ' );\r
}\r
}\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence alignment format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
catch ( final IOException e ) {\r
- setArrowCursor();\r
JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence alignment",\r
+ e.getMessage(),\r
+ "Could Not Read Expression Value Table",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
- catch ( final IllegalArgumentException e ) {\r
- setArrowCursor();\r
+ if ( t.getNumberOfColumns() < 2 ) {\r
JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
+ "Table contains " + t.getNumberOfColumns() + " column(s)",\r
+ "Problem with Expression Value Table",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
+ if ( t.getNumberOfRows() < 1 ) {\r
JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence alignment",\r
+ "Table contains zero rows",\r
+ "Problem with Expression Value Table",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
- if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {\r
JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment is empty",\r
- "Illegal Multiple Sequence Alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ "Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
+ + phy.getNumberOfExternalNodes() + " external nodes",\r
+ "Warning",\r
+ JOptionPane.WARNING_MESSAGE );\r
}\r
- if ( msa.getNumberOfSequences() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 3 sequences",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
+ int not_found = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
+ final PhylogenyNode node = iter.next();\r
+ final String node_name = node.getName();\r
+ if ( !ForesterUtil.isEmpty( node_name ) ) {\r
+ int row = -1;\r
+ try {\r
+ row = t.findRow( node_name );\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ JOptionPane\r
+ .showMessageDialog( this,\r
+ e.getMessage(),\r
+ "Error Mapping Node Identifiers to Expression Value Identifiers",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( row < 0 ) {\r
+ if ( node.isExternal() ) {\r
+ not_found++;\r
+ }\r
+ continue;\r
+ }\r
+ final List<Double> l = new ArrayList<Double>();\r
+ for( int col = 1; col < t.getNumberOfColumns(); ++col ) {\r
+ double d = -100;\r
+ try {\r
+ d = Double.parseDouble( t.getValueAsString( col, row ) );\r
+ }\r
+ catch ( final NumberFormatException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Could not parse \"" + t.getValueAsString( col, row )\r
+ + "\" into a decimal value",\r
+ "Issue with Expression Value Table",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ stats.addValue( d );\r
+ l.add( d );\r
+ }\r
+ if ( !l.isEmpty() ) {\r
+ if ( node.getNodeData().getProperties() != null ) {\r
+ node.getNodeData().getProperties()\r
+ .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
+ }\r
+ node.getNodeData().setVector( l );\r
+ }\r
+ }\r
}\r
- if ( msa.getLength() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence alignment needs to contain at least 2 residues",\r
- "Illegal multiple sequence alignment",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ if ( not_found > 0 ) {\r
+ JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
+ + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
}\r
- System.gc();\r
- setMsaFile( _msa_filechooser.getSelectedFile() );\r
- setMsa( msa );\r
+ getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
}\r
}\r
\r
- public void readSeqsFromFileforPI() {\r
- // Set an initial directory if none set yet\r
+ private void addSequencesFromFile() {\r
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Need to load evolutionary tree first",\r
+ "Can Not Read Sequences",\r
+ JOptionPane.WARNING_MESSAGE );\r
+ return;\r
+ }\r
final File my_dir = getCurrentDir();\r
- _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
- // Open file-open dialog and set current directory\r
if ( my_dir != null ) {\r
- _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
+ _sequences_filechooser.setCurrentDirectory( my_dir );\r
}\r
- final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
- // All done: get the seqs\r
- final File file = _seqs_pi_filechooser.getSelectedFile();\r
- setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
+ final int result = _sequences_filechooser.showOpenDialog( _contentpane );\r
+ final File file = _sequences_filechooser.getSelectedFile();\r
+ List<MolecularSequence> seqs = null;\r
if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- setSeqsFile( null );\r
- setSeqs( null );\r
- List<Sequence> seqs = null;\r
try {\r
if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
seqs = FastaParser.parse( new FileInputStream( file ) );\r
- for( final Sequence seq : seqs ) {\r
- System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
- }\r
}\r
else {\r
- //TODO error\r
+ JOptionPane.showMessageDialog( this,\r
+ "Format does not appear to be Fasta",\r
+ "Multiple sequence file format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
}\r
catch ( final MsaFormatException e ) {\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
- catch ( final IllegalArgumentException e ) {\r
+ catch ( final Exception e ) {\r
setArrowCursor();\r
+ e.printStackTrace();\r
JOptionPane.showMessageDialog( this,\r
e.getLocalizedMessage(),\r
"Unexpected error during reading of multiple sequence file",\r
JOptionPane.ERROR_MESSAGE );\r
return;\r
}\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
JOptionPane.showMessageDialog( this,\r
"Multiple sequence file is empty",\r
- "Illegal multiple sequence file",\r
+ "Empty multiple sequence file",\r
JOptionPane.ERROR_MESSAGE );\r
+ setArrowCursor();\r
return;\r
}\r
- if ( seqs.size() < 4 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file needs to contain at least 3 sequences",\r
- "Illegal multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ }\r
+ if ( seqs != null ) {\r
+ for( final MolecularSequence seq : seqs ) {\r
+ System.out.println( seq.getIdentifier() );\r
+ }\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ int total_counter = 0;\r
+ int attached_counter = 0;\r
+ for( final MolecularSequence seq : seqs ) {\r
+ ++total_counter;\r
+ final String seq_name = seq.getIdentifier();\r
+ if ( !ForesterUtil.isEmpty( seq_name ) ) {\r
+ List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodesViaSequenceSymbol( seq_name );\r
+ }\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodesViaGeneName( seq_name );\r
+ }\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodes( seq_name );\r
+ }\r
+ if ( nodes.size() > 1 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Sequence name \"" + seq_name + "\" is not unique",\r
+ "Sequence name not unique",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ setArrowCursor();\r
+ return;\r
+ }\r
+ final String[] a = seq_name.split( "\\s" );\r
+ if ( nodes.isEmpty() && ( a.length > 1 ) ) {\r
+ final String seq_name_split = a[ 0 ];\r
+ nodes = phy.getNodesViaSequenceName( seq_name_split );\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodesViaSequenceSymbol( seq_name_split );\r
+ }\r
+ if ( nodes.isEmpty() ) {\r
+ nodes = phy.getNodes( seq_name_split );\r
+ }\r
+ if ( nodes.size() > 1 ) {\r
+ JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
+ + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
+ setArrowCursor();\r
+ return;\r
+ }\r
+ }\r
+ if ( nodes.size() == 1 ) {\r
+ ++attached_counter;\r
+ final PhylogenyNode n = nodes.get( 0 );\r
+ if ( !n.getNodeData().isHasSequence() ) {\r
+ n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );\r
+ }\r
+ n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );\r
+ if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {\r
+ n.getNodeData().getSequence().setName( seq_name );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if ( attached_counter > 0 ) {\r
+ int ext_nodes = 0;\r
+ int ext_nodes_with_seq = 0;\r
+ for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
+ ++ext_nodes;\r
+ final PhylogenyNode n = iter.next();\r
+ if ( n.getNodeData().isHasSequence()\r
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {\r
+ ++ext_nodes_with_seq;\r
+ }\r
+ }\r
+ final String s;\r
+ if ( ext_nodes == ext_nodes_with_seq ) {\r
+ s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";\r
+ }\r
+ else {\r
+ s = ext_nodes_with_seq + " out of " + ext_nodes\r
+ + " external nodes now have a molecular sequence attached to them.";\r
+ }\r
+ if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Attached all " + total_counter + " sequences to tree nodes.\n" + s,\r
+ "All sequences attached",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
+ + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
+ + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
+ }\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
+ + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
}\r
- // if ( msa.getLength() < 2 ) {\r
- // JOptionPane.showMessageDialog( this,\r
- // "Multiple sequence alignment needs to contain at least 2 residues",\r
- // "Illegal multiple sequence file",\r
- // JOptionPane.ERROR_MESSAGE );\r
- // return;\r
- // }\r
- System.gc();\r
- setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
- setSeqs( seqs );\r
}\r
}\r
\r
.setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );\r
MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame\r
.createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
- setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
- setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
- MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),\r
- _show_scale_cbmi,\r
- _show_branch_length_values_cbmi,\r
- _non_lined_up_cladograms_rbmi,\r
- _uniform_cladograms_rbmi,\r
- _ext_node_dependent_cladogram_rbmi,\r
- _label_direction_cbmi );\r
+ MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
+ MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
+ MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );\r
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
+ try {\r
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();\r
+ getMainPanel().getControlPanel().setVisibilityOfX();\r
+ }\r
+ catch ( final Exception ignore ) {\r
+ // do nothing, not important.\r
+ }\r
}\r
} );\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );\r
_radio_group_1.add( _uniform_cladograms_rbmi );\r
_radio_group_1.add( _non_lined_up_cladograms_rbmi );\r
- ///////\r
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
_options_jmenu\r
- .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );\r
- _options_jmenu\r
.add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
_options_jmenu\r
.add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+ _options_jmenu\r
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );\r
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );\r
+ _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );\r
}\r
_options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );\r
_options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );\r
_options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );\r
_options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );\r
_options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );\r
- ///////\r
+ _options_jmenu.addSeparator();\r
+ _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) );\r
_options_jmenu.addSeparator();\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) );\r
_options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) );\r
_options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) );\r
+ _options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );\r
+ _search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );\r
_options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );\r
_options_jmenu.addSeparator();\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),\r
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );\r
_options_jmenu\r
.add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );\r
- //\r
_options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );\r
_options_jmenu\r
.add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );\r
_radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );\r
_radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );\r
_radio_group_2.add( _extract_taxonomy_agressive_rbmi );\r
- // \r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );\r
_options_jmenu\r
.add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );\r
.isShowDefaultNodeShapesExternal() );\r
customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()\r
.isShowDefaultNodeShapesInternal() );\r
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()\r
+ .isShowDefaultNodeShapesForMarkedNodes() );\r
customizeJMenuItem( _cycle_node_shape_mi );\r
customizeJMenuItem( _cycle_node_fill_mi );\r
customizeJMenuItem( _choose_node_size_mi );\r
+ customizeJMenuItem( _cycle_data_return );\r
customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );\r
customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );\r
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );\r
getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
- customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );\r
customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
customizeCheckBoxMenuItem( _label_direction_cbmi,\r
getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r
customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );\r
customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()\r
.isReplaceUnderscoresInNhParsing() );\r
+ customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );\r
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );\r
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );\r
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );\r
.getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
.getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );\r
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );\r
_jmenubar.add( _options_jmenu );\r
}\r
\r
customizeJMenuItem( _delete_selected_nodes_item );\r
_tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );\r
_delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );\r
- \r
customizeJMenuItem( _delete_not_selected_nodes_item );\r
_tools_menu.addSeparator();\r
_tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );\r
customizeJMenuItem( _collapse_species_specific_subtrees );\r
+ _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );\r
_tools_menu\r
.add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
customizeJMenuItem( _collapse_below_threshold );\r
_collapse_below_threshold\r
- .setToolTipText( "To 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)" );\r
+ .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)" );\r
+ //\r
+ _tools_menu\r
+ .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
+ customizeJMenuItem( _collapse_below_branch_length );\r
+ _collapse_below_branch_length\r
+ .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
+ //\r
_tools_menu.addSeparator();\r
_tools_menu\r
.add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
exit();\r
}\r
\r
- void executeLineageInference() {\r
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
- return;\r
- }\r
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Phylogeny is not rooted.",\r
- "Cannot infer ancestral taxonomies",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ private void closeCurrentPane() {\r
+ if ( getMainPanel().getCurrentTreePanel() != null ) {\r
+ if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
+ final int r = JOptionPane.showConfirmDialog( this,\r
+ "Close tab despite potentially unsaved changes?",\r
+ "Close Tab?",\r
+ JOptionPane.YES_NO_OPTION );\r
+ if ( r != JOptionPane.YES_OPTION ) {\r
+ return;\r
+ }\r
+ }\r
+ getMainPanel().closeCurrentPane();\r
+ activateSaveAllIfNeeded();\r
}\r
- final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getCurrentPhylogeny()\r
- .copy() );\r
- new Thread( inferrer ).start();\r
- }\r
-\r
- void exit() {\r
- removeAllTextFrames();\r
- _mainpanel.terminate();\r
- _contentpane.removeAll();\r
- setVisible( false );\r
- dispose();\r
- System.exit( 0 );\r
}\r
\r
- void readPhylogeniesFromURL() {\r
- URL url = null;\r
- Phylogeny[] phys = null;\r
- final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";\r
- final String url_string = JOptionPane.showInputDialog( this,\r
- message,\r
- "Use URL/webservice to obtain a phylogeny",\r
- JOptionPane.QUESTION_MESSAGE );\r
- boolean nhx_or_nexus = false;\r
- if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {\r
- try {\r
- url = new URL( url_string );\r
- PhylogenyParser parser = null;\r
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {\r
- parser = new TolParser();\r
- }\r
- else {\r
- parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
- .isValidatePhyloXmlAgainstSchema() );\r
- }\r
- if ( parser instanceof NexusPhylogeniesParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- else if ( parser instanceof NHXParser ) {\r
- nhx_or_nexus = true;\r
- }\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setWaitCursor();\r
- }\r
- else {\r
- _mainpanel.setWaitCursor();\r
+ private void collapse( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
+ double min_support = Double.MAX_VALUE;\r
+ boolean conf_present = false;\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ final List<Confidence> c = n.getBranchData().getConfidences();\r
+ if ( ( c != null ) && ( c.size() > 0 ) ) {\r
+ conf_present = true;\r
+ double max = 0;\r
+ for( final Confidence confidence : c ) {\r
+ if ( confidence.getValue() > max ) {\r
+ max = confidence.getValue();\r
+ }\r
+ }\r
+ if ( max < getMinNotCollapseConfidenceValue() ) {\r
+ to_be_removed.add( n );\r
+ }\r
+ if ( max < min_support ) {\r
+ min_support = max;\r
+ }\r
}\r
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
- phys = factory.create( url.openStream(), parser );\r
}\r
- catch ( final MalformedURLException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),\r
- "Malformed URL",\r
- JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ if ( conf_present ) {\r
+ for( final PhylogenyNode node : to_be_removed ) {\r
+ PhylogenyMethods.removeNode( node, phy );\r
}\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not read from " + url + "\n"\r
- + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Failed to read URL",\r
- JOptionPane.ERROR_MESSAGE );\r
+ if ( to_be_removed.size() > 0 ) {\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
+ getCurrentTreePanel().calculateLongestExtNodeInfo();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().setEdited( true );\r
+ getCurrentTreePanel().repaint();\r
+ repaint();\r
}\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
- "Unexpected Exception",\r
- JOptionPane.ERROR_MESSAGE );\r
- }\r
- finally {\r
- if ( _mainpanel.getCurrentTreePanel() != null ) {\r
- _mainpanel.getCurrentTreePanel().setArrowCursor();\r
- }\r
- else {\r
- _mainpanel.setArrowCursor();\r
- }\r
- }\r
- if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
- if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
- for( final Phylogeny phy : phys ) {\r
- \r
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
- }\r
- }\r
- AptxUtil.addPhylogeniesToTabs( phys,\r
- new File( url.getFile() ).getName(),\r
- new File( url.getFile() ).toString(),\r
- getConfiguration(),\r
- getMainPanel() );\r
- _mainpanel.getControlPanel().showWhole();\r
- }\r
- }\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
- }\r
-\r
- void setMsa( final Msa msa ) {\r
- _msa = msa;\r
- }\r
-\r
- void setMsaFile( final File msa_file ) {\r
- _msa_file = msa_file;\r
- }\r
-\r
- void setSeqs( final List<Sequence> seqs ) {\r
- _seqs = seqs;\r
- }\r
-\r
- void setSeqsFile( final File seqs_file ) {\r
- _seqs_file = seqs_file;\r
- }\r
-\r
- void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {\r
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- true );\r
- String file_written_to = "";\r
- boolean error = false;\r
- try {\r
- file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name,\r
- _mainpanel.getCurrentTreePanel().getWidth(),\r
- _mainpanel.getCurrentTreePanel().getHeight(),\r
- _mainpanel.getCurrentTreePanel(),\r
- _mainpanel.getControlPanel(),\r
- type,\r
- getOptions() );\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Wrote image to: " + file_written_to,\r
- "Graphics Export",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ if ( to_be_removed.size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
+ + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
- JOptionPane.showMessageDialog( this,\r
- "There was an unknown problem when attempting to write to an image file: \""\r
- + file_name + "\"",\r
- "Error",\r
- JOptionPane.ERROR_MESSAGE );\r
+ JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
+ + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
- _contentpane.repaint();\r
- }\r
-\r
- private void addExpressionValuesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
+ else {\r
JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Expression Values",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _values_filechooser.setCurrentDirectory( my_dir );\r
+ "No branch collapsed because no confidence values present",\r
+ "No confidence values present",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
- final int result = _values_filechooser.showOpenDialog( _contentpane );\r
- final File file = _values_filechooser.getSelectedFile();\r
- if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- BasicTable<String> t = null;\r
- try {\r
- t = BasicTableParser.parse( file, '\t' );\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ',' );\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- t = BasicTableParser.parse( file, ' ' );\r
- }\r
- }\r
- catch ( final IOException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- e.getMessage(),\r
- "Could Not Read Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfColumns() < 2 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfColumns() + " column(s)",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( t.getNumberOfRows() < 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains zero rows",\r
- "Problem with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
+ }\r
+\r
+ private void collapseBelowBranchLengthThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Table contains " + t.getNumberOfRows() + " rows, but tree contains "\r
- + phy.getNumberOfExternalNodes() + " external nodes",\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();\r
- int not_found = 0;\r
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {\r
- final PhylogenyNode node = iter.next();\r
- final String node_name = node.getName();\r
- if ( !ForesterUtil.isEmpty( node_name ) ) {\r
- int row = -1;\r
- try {\r
- row = t.findRow( node_name );\r
- }\r
- catch ( final IllegalArgumentException e ) {\r
- JOptionPane\r
- .showMessageDialog( this,\r
- e.getMessage(),\r
- "Error Mapping Node Identifiers to Expression Value Identifiers",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( row < 0 ) {\r
- if ( node.isExternal() ) {\r
- not_found++;\r
- }\r
- continue;\r
- }\r
- final List<Double> l = new ArrayList<Double>();\r
- for( int col = 1; col < t.getNumberOfColumns(); ++col ) {\r
- double d = -100;\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum branch length value\n",\r
+ "Minimal Branch Length Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseBlValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
try {\r
- d = Double.parseDouble( t.getValueAsString( col, row ) );\r
+ m = Double.parseDouble( m_str );\r
}\r
- catch ( final NumberFormatException e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Could not parse \"" + t.getValueAsString( col, row )\r
- + "\" into a decimal value",\r
- "Issue with Expression Value Table",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
}\r
- stats.addValue( d );\r
- l.add( d );\r
}\r
- if ( !l.isEmpty() ) {\r
- if ( node.getNodeData().getProperties() != null ) {\r
- node.getNodeData().getProperties()\r
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );\r
- }\r
- node.getNodeData().setVector( l );\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseBlValue( m );\r
+ collapseBl( phy );\r
}\r
}\r
}\r
- if ( not_found > 0 ) {\r
- JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found\r
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );\r
- }\r
- getCurrentTreePanel().setStatisticsForExpressionValues( stats );\r
}\r
}\r
\r
- private void addSequencesFromFile() {\r
- if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Need to load evolutionary tree first",\r
- "Can Not Read Sequences",\r
- JOptionPane.WARNING_MESSAGE );\r
- return;\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _sequences_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _sequences_filechooser.showOpenDialog( _contentpane );\r
- final File file = _sequences_filechooser.getSelectedFile();\r
- List<Sequence> seqs = null;\r
- if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- try {\r
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
- seqs = FastaParser.parse( new FileInputStream( file ) );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this,\r
- "Format does not appear to be Fasta",\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- }\r
- catch ( final MsaFormatException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Multiple sequence file format error",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final IOException e ) {\r
- setArrowCursor();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Failed to read multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- catch ( final Exception e ) {\r
- setArrowCursor();\r
- e.printStackTrace();\r
- JOptionPane.showMessageDialog( this,\r
- e.getLocalizedMessage(),\r
- "Unexpected error during reading of multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- return;\r
- }\r
- if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Multiple sequence file is empty",\r
- "Empty multiple sequence file",\r
- JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- }\r
- if ( seqs != null ) {\r
- for( final Sequence seq : seqs ) {\r
- System.out.println( seq.getIdentifier() );\r
- }\r
+ private void collapseBelowThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- int total_counter = 0;\r
- int attached_counter = 0;\r
- for( final Sequence seq : seqs ) {\r
- ++total_counter;\r
- final String seq_name = seq.getIdentifier();\r
- if ( !ForesterUtil.isEmpty( seq_name ) ) {\r
- List<PhylogenyNode> nodes = phy.getNodesViaSequenceName( seq_name );\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaSequenceSymbol( seq_name );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaGeneName( seq_name );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodes( seq_name );\r
- }\r
- if ( nodes.size() > 1 ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Sequence name \"" + seq_name + "\" is not unique",\r
- "Sequence name not unique",\r
- JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- final String[] a = seq_name.split( "\\s" );\r
- if ( nodes.isEmpty() && ( a.length > 1 ) ) {\r
- final String seq_name_split = a[ 0 ];\r
- nodes = phy.getNodesViaSequenceName( seq_name_split );\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodesViaSequenceSymbol( seq_name_split );\r
- }\r
- if ( nodes.isEmpty() ) {\r
- nodes = phy.getNodes( seq_name_split );\r
- }\r
- if ( nodes.size() > 1 ) {\r
- JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split\r
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );\r
- setArrowCursor();\r
- return;\r
- }\r
- }\r
- if ( nodes.size() == 1 ) {\r
- ++attached_counter;\r
- final PhylogenyNode n = nodes.get( 0 );\r
- if ( !n.getNodeData().isHasSequence() ) {\r
- n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane.showInputDialog( this,\r
+ "Please enter the minimum confidence value\n",\r
+ "Minimal Confidence Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseConfidenceValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
}\r
- n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );\r
- if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {\r
- n.getNodeData().getSequence().setName( seq_name );\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
}\r
}\r
- }\r
- }\r
- if ( attached_counter > 0 ) {\r
- int ext_nodes = 0;\r
- int ext_nodes_with_seq = 0;\r
- for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {\r
- ++ext_nodes;\r
- final PhylogenyNode n = iter.next();\r
- if ( n.getNodeData().isHasSequence()\r
- && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {\r
- ++ext_nodes_with_seq;\r
- }\r
- }\r
- final String s;\r
- if ( ext_nodes == ext_nodes_with_seq ) {\r
- s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them.";\r
- }\r
- else {\r
- s = ext_nodes_with_seq + " out of " + ext_nodes\r
- + " external nodes now have a molecular sequence attached to them.";\r
- }\r
- if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Attached all " + total_counter + " sequences to tree nodes.\n" + s,\r
- "All sequences attached",\r
- JOptionPane.INFORMATION_MESSAGE );\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "Attached " + attached_counter\r
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter\r
- + " sequences attached", JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- else {\r
- JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter\r
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );\r
- }\r
- }\r
- }\r
-\r
- private void choosePdfWidth() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the default line width for PDF export.\n"\r
- + "[current value: "\r
- + getOptions().getPrintLineWidth() + "]\n",\r
- "Line Width for PDF Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintLineWidth() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- float f = 0.0f;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- f = Float.parseFloat( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( f > 0.0 ) ) {\r
- getOptions().setPrintLineWidth( f );\r
- }\r
- }\r
- }\r
-\r
- private void choosePrintSize() {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter values for width and height,\nseparated by a comma.\n"\r
- + "[current values: "\r
- + getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() + "]\n"\r
- + "[A4: " + Constants.A4_SIZE_X + ", "\r
- + Constants.A4_SIZE_Y + "]\n" + "[US Letter: "\r
- + Constants.US_LETTER_SIZE_X + ", "\r
- + Constants.US_LETTER_SIZE_Y + "]",\r
- "Default Size for Graphics Export",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getOptions().getPrintSizeX() + ", "\r
- + getOptions().getPrintSizeY() );\r
- if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) {\r
- boolean success = true;\r
- int x = 0;\r
- int y = 0;\r
- final String[] str_ary = s.split( "," );\r
- if ( str_ary.length == 2 ) {\r
- final String x_str = str_ary[ 0 ].trim();\r
- final String y_str = str_ary[ 1 ].trim();\r
- if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) {\r
- try {\r
- x = Integer.parseInt( x_str );\r
- y = Integer.parseInt( y_str );\r
- }\r
- catch ( final Exception ex ) {\r
+ else {\r
success = false;\r
}\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseConfidenceValue( m );\r
+ collapse( phy );\r
+ }\r
}\r
- else {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( x > 1 ) && ( y > 1 ) ) {\r
- getOptions().setPrintSizeX( x );\r
- getOptions().setPrintSizeY( y );\r
}\r
}\r
}\r
\r
- private void closeCurrentPane() {\r
- if ( getMainPanel().getCurrentTreePanel() != null ) {\r
- if ( getMainPanel().getCurrentTreePanel().isEdited() ) {\r
- final int r = JOptionPane.showConfirmDialog( this,\r
- "Close tab despite potentially unsaved changes?",\r
- "Close Tab?",\r
- JOptionPane.YES_NO_OPTION );\r
- if ( r != JOptionPane.YES_OPTION ) {\r
- return;\r
- }\r
- }\r
- getMainPanel().closeCurrentPane();\r
- activateSaveAllIfNeeded();\r
- }\r
- }\r
-\r
- private void collapse( final Phylogeny phy, final double m ) {\r
+ private void collapseBl( final Phylogeny phy ) {\r
final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
- double min_support = Double.MAX_VALUE;\r
- boolean conf_present = false;\r
+ double min_bl = Double.MAX_VALUE;\r
+ boolean bl_present = false;\r
while ( it.hasNext() ) {\r
final PhylogenyNode n = it.next();\r
if ( !n.isExternal() && !n.isRoot() ) {\r
- final List<Confidence> c = n.getBranchData().getConfidences();\r
- if ( ( c != null ) && ( c.size() > 0 ) ) {\r
- conf_present = true;\r
- double max = 0;\r
- for( final Confidence confidence : c ) {\r
- if ( confidence.getValue() > max ) {\r
- max = confidence.getValue();\r
- }\r
- }\r
- if ( max < getMinNotCollapseConfidenceValue() ) {\r
+ final double bl = n.getDistanceToParent();\r
+ if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {\r
+ bl_present = true;\r
+ if ( bl < getMinNotCollapseBlValue() ) {\r
to_be_removed.add( n );\r
}\r
- if ( max < min_support ) {\r
- min_support = max;\r
+ if ( bl < min_bl ) {\r
+ min_bl = bl;\r
}\r
}\r
}\r
}\r
- if ( conf_present ) {\r
+ if ( bl_present ) {\r
for( final PhylogenyNode node : to_be_removed ) {\r
PhylogenyMethods.removeNode( node, phy );\r
}\r
}\r
if ( to_be_removed.size() > 0 ) {\r
JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
- + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "\r
+ + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "\r
+ to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
}\r
else {\r
- JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "\r
- + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );\r
+ JOptionPane.showMessageDialog( this,\r
+ "No branch collapsed,\nminimum branch length is " + min_bl,\r
+ "No branch collapsed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
else {\r
JOptionPane.showMessageDialog( this,\r
- "No branch collapsed because no confidence values present",\r
- "No confidence values present",\r
+ "No branch collapsed because no branch length values present",\r
+ "No branch length values present",\r
JOptionPane.INFORMATION_MESSAGE );\r
}\r
}\r
\r
- private void collapseBelowThreshold() {\r
- if ( getCurrentTreePanel() != null ) {\r
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
- if ( ( phy != null ) && !phy.isEmpty() ) {\r
- final String s = ( String ) JOptionPane.showInputDialog( this,\r
- "Please enter the minimum confidence value\n",\r
- "Minimal Confidence Value",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- null,\r
- getMinNotCollapseConfidenceValue() );\r
- if ( !ForesterUtil.isEmpty( s ) ) {\r
- boolean success = true;\r
- double m = 0.0;\r
- final String m_str = s.trim();\r
- if ( !ForesterUtil.isEmpty( m_str ) ) {\r
- try {\r
- m = Double.parseDouble( m_str );\r
- }\r
- catch ( final Exception ex ) {\r
- success = false;\r
- }\r
- }\r
- else {\r
- success = false;\r
- }\r
- if ( success && ( m >= 0.0 ) ) {\r
- setMinNotCollapseConfidenceValue( m );\r
- collapse( phy, m );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
private PhyloXmlParser createPhyloXmlParser() {\r
PhyloXmlParser xml_parser = null;\r
if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) {\r
return xml_parser;\r
}\r
\r
+ public void end() {\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ }\r
+\r
+ void executeLineageInference() {\r
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {\r
+ return;\r
+ }\r
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Phylogeny is not rooted.",\r
+ "Cannot infer ancestral taxonomies",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this,\r
+ _mainpanel.getCurrentTreePanel(),\r
+ _mainpanel.getCurrentPhylogeny()\r
+ .copy() );\r
+ new Thread( inferrer ).start();\r
+ }\r
+\r
private void executePhyleneticInference( final boolean from_unaligned_seqs ) {\r
final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this,\r
getPhylogeneticInferenceOptions(),\r
}\r
}\r
\r
+ void exit() {\r
+ removeAllTextFrames();\r
+ _mainpanel.terminate();\r
+ _contentpane.removeAll();\r
+ setVisible( false );\r
+ dispose();\r
+ // System.exit( 0 ); //TODO reconfirm that this is OK, then remove.\r
+ }\r
+\r
private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException {\r
final StringBuilder sb = new StringBuilder();\r
final StringBuilder sb_failed = new StringBuilder();\r
}\r
}\r
\r
- private ControlPanel getControlPanel() {\r
- return getMainPanel().getControlPanel();\r
+ @Override\r
+ public MainPanel getMainPanel() {\r
+ return _mainpanel;\r
}\r
\r
- private File getCurrentDir() {\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( ForesterUtil.isWindows() ) {\r
- try {\r
- _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );\r
- }\r
- catch ( final Exception e ) {\r
- _current_dir = null;\r
- }\r
- }\r
- }\r
- if ( ( _current_dir == null ) || !_current_dir.canRead() ) {\r
- if ( System.getProperty( "user.home" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.home" ) );\r
- }\r
- else if ( System.getProperty( "user.dir" ) != null ) {\r
- _current_dir = new File( System.getProperty( "user.dir" ) );\r
- }\r
- }\r
- return _current_dir;\r
+ private double getMinNotCollapseBlValue() {\r
+ return _min_not_collapse_bl;\r
}\r
\r
private double getMinNotCollapseConfidenceValue() {\r
return _min_not_collapse;\r
}\r
\r
+ public Msa getMsa() {\r
+ return _msa;\r
+ }\r
+\r
+ public File getMsaFile() {\r
+ return _msa_file;\r
+ }\r
+\r
private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {\r
if ( _phylogenetic_inference_options == null ) {\r
_phylogenetic_inference_options = new PhylogeneticInferenceOptions();\r
return _phylogenetic_inference_options;\r
}\r
\r
+ public List<MolecularSequence> getSeqs() {\r
+ return _seqs;\r
+ }\r
+\r
+ public File getSeqsFile() {\r
+ return _seqs_file;\r
+ }\r
+\r
private boolean isUnsavedDataPresent() {\r
final List<TreePanel> tps = getMainPanel().getTreePanels();\r
for( final TreePanel tp : tps ) {\r
}\r
}\r
\r
+ private void preProcessTreesUponReading( final Phylogeny[] phys ) {\r
+ for( final Phylogeny phy : phys ) {\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( n.isExternal() ) {\r
+ if ( n.getNodeData().isHasSequence() ) {\r
+ final Sequence s = n.getNodeData().getSequence();\r
+ if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {\r
+ if ( ( s.getAccession() != null )\r
+ && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {\r
+ s.setGeneName( s.getAccession().getValue() );\r
+ }\r
+ else if ( !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ s.setGeneName( n.getName() );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
private void print() {\r
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null )\r
|| getCurrentTreePanel().getPhylogeny().isEmpty() ) {\r
}\r
if ( !getOptions().isPrintUsingActualSize() ) {\r
getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80,\r
- getOptions().getPrintSizeY() - 140,\r
- true );\r
+ getOptions().getPrintSizeY() - 140 );\r
getCurrentTreePanel().resetPreferredSize();\r
getCurrentTreePanel().repaint();\r
}\r
}\r
}\r
\r
- private void printPhylogenyToPdf( final String file_name ) {\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(),\r
- getOptions().getPrintSizeY(),\r
- true );\r
- getCurrentTreePanel().resetPreferredSize();\r
- getCurrentTreePanel().repaint();\r
+ public void readMsaFromFile() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _msa_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _msa_filechooser.setCurrentDirectory( my_dir );\r
}\r
- String pdf_written_to = "";\r
- boolean error = false;\r
- try {\r
- if ( getOptions().isPrintUsingActualSize() ) {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name,\r
- getCurrentTreePanel(),\r
- getCurrentTreePanel().getWidth(),\r
- getCurrentTreePanel().getHeight() );\r
+ final int result = _msa_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the msa\r
+ final File file = _msa_filechooser.getSelectedFile();\r
+ setCurrentDir( _msa_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setMsaFile( null );\r
+ setMsa( null );\r
+ Msa msa = null;\r
+ try {\r
+ final InputStream is = new FileInputStream( file );\r
+ if ( FastaParser.isLikelyFasta( file ) ) {\r
+ msa = FastaParser.parseMsa( is );\r
+ }\r
+ else {\r
+ msa = GeneralMsaParser.parse( is );\r
+ }\r
}\r
- else {\r
- pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions()\r
- .getPrintSizeX(), getOptions().getPrintSizeY() );\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence alignment format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- }\r
- catch ( final IOException e ) {\r
- error = true;\r
- JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE );\r
- }\r
- if ( !error ) {\r
- if ( !ForesterUtil.isEmpty( pdf_written_to ) ) {\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
JOptionPane.showMessageDialog( this,\r
- "Wrote PDF to: " + pdf_written_to,\r
- "Information",\r
- JOptionPane.INFORMATION_MESSAGE );\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- else {\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
JOptionPane.showMessageDialog( this,\r
- "There was an unknown problem when attempting to write to PDF file: \""\r
- + file_name + "\"",\r
- "Error",\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
JOptionPane.ERROR_MESSAGE );\r
+ return;\r
}\r
- }\r
- if ( !getOptions().isPrintUsingActualSize() ) {\r
- getControlPanel().showWhole();\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment is empty",\r
+ "Illegal Multiple Sequence Alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getNumberOfSequences() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( msa.getLength() < 2 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence alignment needs to contain at least 2 residues",\r
+ "Illegal multiple sequence alignment",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ System.gc();\r
+ setMsaFile( _msa_filechooser.getSelectedFile() );\r
+ setMsa( msa );\r
}\r
}\r
\r
else {\r
_mainpanel.setWaitCursor();\r
}\r
- if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter )\r
- || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) {\r
+ if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter )\r
+ || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) {\r
try {\r
final NHXParser nhx = new NHXParser();\r
setSpecialOptionsForNhxParser( nhx );\r
exceptionOccuredDuringOpenFile( e );\r
}\r
}\r
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
+ else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) {\r
warnIfNotPhyloXmlValidation( getConfiguration() );\r
try {\r
final PhyloXmlParser xml_parser = createPhyloXmlParser();\r
exceptionOccuredDuringOpenFile( e );\r
}\r
}\r
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {\r
+ else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) {\r
try {\r
phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
}\r
exceptionOccuredDuringOpenFile( e );\r
}\r
}\r
- else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {\r
+ else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) {\r
try {\r
final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();\r
setSpecialOptionsForNexParser( nex );\r
}\r
}\r
}\r
+ if ( PREPROCESS_TREES ) {\r
+ preProcessTreesUponReading( phys );\r
+ }\r
AptxUtil.addPhylogeniesToTabs( phys,\r
file.getName(),\r
file.getAbsolutePath(),\r
}\r
}\r
}\r
- activateSaveAllIfNeeded();\r
- System.gc();\r
+ activateSaveAllIfNeeded();\r
+ System.gc();\r
+ }\r
+\r
+ void readPhylogeniesFromURL() {\r
+ URL url = null;\r
+ Phylogeny[] phys = null;\r
+ final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";\r
+ final String url_string = JOptionPane.showInputDialog( this,\r
+ message,\r
+ "Use URL/webservice to obtain a phylogeny",\r
+ JOptionPane.QUESTION_MESSAGE );\r
+ boolean nhx_or_nexus = false;\r
+ if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {\r
+ try {\r
+ url = new URL( url_string );\r
+ PhylogenyParser parser = null;\r
+ if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {\r
+ parser = new TolParser();\r
+ }\r
+ else {\r
+ parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()\r
+ .isValidatePhyloXmlAgainstSchema() );\r
+ }\r
+ if ( parser instanceof NexusPhylogeniesParser ) {\r
+ nhx_or_nexus = true;\r
+ }\r
+ else if ( parser instanceof NHXParser ) {\r
+ nhx_or_nexus = true;\r
+ }\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().setWaitCursor();\r
+ }\r
+ else {\r
+ _mainpanel.setWaitCursor();\r
+ }\r
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();\r
+ phys = factory.create( url.openStream(), parser );\r
+ }\r
+ catch ( final MalformedURLException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Malformed URL: " + url + "\n" + e.getLocalizedMessage(),\r
+ "Malformed URL",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ catch ( final IOException e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Could not read from " + url + "\n"\r
+ + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Failed to read URL",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ catch ( final Exception e ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),\r
+ "Unexpected Exception",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ }\r
+ finally {\r
+ if ( _mainpanel.getCurrentTreePanel() != null ) {\r
+ _mainpanel.getCurrentTreePanel().setArrowCursor();\r
+ }\r
+ else {\r
+ _mainpanel.setArrowCursor();\r
+ }\r
+ }\r
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
+ if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
+ for( final Phylogeny phy : phys ) {\r
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
+ }\r
+ }\r
+ AptxUtil.addPhylogeniesToTabs( phys,\r
+ new File( url.getFile() ).getName(),\r
+ new File( url.getFile() ).toString(),\r
+ getConfiguration(),\r
+ getMainPanel() );\r
+ _mainpanel.getControlPanel().showWhole();\r
+ }\r
+ }\r
+ activateSaveAllIfNeeded();\r
+ System.gc();\r
+ }\r
+\r
+ public void readSeqsFromFileforPI() {\r
+ // Set an initial directory if none set yet\r
+ final File my_dir = getCurrentDir();\r
+ _seqs_pi_filechooser.setMultiSelectionEnabled( false );\r
+ // Open file-open dialog and set current directory\r
+ if ( my_dir != null ) {\r
+ _seqs_pi_filechooser.setCurrentDirectory( my_dir );\r
+ }\r
+ final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane );\r
+ // All done: get the seqs\r
+ final File file = _seqs_pi_filechooser.getSelectedFile();\r
+ setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() );\r
+ if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
+ setSeqsFile( null );\r
+ setSeqs( null );\r
+ List<MolecularSequence> seqs = null;\r
+ try {\r
+ if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
+ seqs = FastaParser.parse( new FileInputStream( file ) );\r
+ for( final MolecularSequence seq : seqs ) {\r
+ System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
+ }\r
+ }\r
+ else {\r
+ //TODO error\r
+ }\r
+ }\r
+ catch ( final MsaFormatException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Multiple sequence file format error",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IOException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Failed to read multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final IllegalArgumentException e ) {\r
+ setArrowCursor();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ catch ( final Exception e ) {\r
+ setArrowCursor();\r
+ e.printStackTrace();\r
+ JOptionPane.showMessageDialog( this,\r
+ e.getLocalizedMessage(),\r
+ "Unexpected error during reading of multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( ( seqs == null ) || ( seqs.size() < 1 ) ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file is empty",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ if ( seqs.size() < 4 ) {\r
+ JOptionPane.showMessageDialog( this,\r
+ "Multiple sequence file needs to contain at least 3 sequences",\r
+ "Illegal multiple sequence file",\r
+ JOptionPane.ERROR_MESSAGE );\r
+ return;\r
+ }\r
+ // if ( msa.getLength() < 2 ) {\r
+ // JOptionPane.showMessageDialog( this,\r
+ // "Multiple sequence alignment needs to contain at least 2 residues",\r
+ // "Illegal multiple sequence file",\r
+ // JOptionPane.ERROR_MESSAGE );\r
+ // return;\r
+ // }\r
+ System.gc();\r
+ setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );\r
+ setSeqs( seqs );\r
+ }\r
}\r
\r
private void readSpeciesTreeFromFile() {\r
final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane );\r
final File file = _open_filechooser_for_species_tree.getSelectedFile();\r
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
+ if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {\r
try {\r
final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser\r
.createPhyloXmlParserXsdValidating(), file );\r
exceptionOccuredDuringOpenFile( e );\r
}\r
}\r
- else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {\r
+ else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) {\r
try {\r
final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );\r
t = trees[ 0 ];\r
}\r
}\r
\r
- private void setCurrentDir( final File current_dir ) {\r
- _current_dir = current_dir;\r
+ private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
+ _min_not_collapse_bl = min_not_collapse_bl;\r
}\r
\r
private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) {\r
_min_not_collapse = min_not_collapse;\r
}\r
\r
+ void setMsa( final Msa msa ) {\r
+ _msa = msa;\r
+ }\r
+\r
+ void setMsaFile( final File msa_file ) {\r
+ _msa_file = msa_file;\r
+ }\r
+\r
private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
_phylogenetic_inference_options = phylogenetic_inference_options;\r
}\r
\r
+ void setSeqs( final List<MolecularSequence> seqs ) {\r
+ _seqs = seqs;\r
+ }\r
+\r
+ void setSeqsFile( final File seqs_file ) {\r
+ _seqs_file = seqs_file;\r
+ }\r
+\r
private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) {\r
nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );\r
nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() );\r
}\r
}\r
}\r
-\r
- private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
- }\r
- return exception;\r
- }\r
-\r
- private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
- }\r
- return exception;\r
- }\r
-\r
- private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) {\r
- try {\r
- final PhylogenyWriter writer = new PhylogenyWriter();\r
- writer.toPhyloXML( file, t, 0 );\r
- }\r
- catch ( final Exception e ) {\r
- exception = true;\r
- exceptionOccuredDuringSaveAs( e );\r
- }\r
- return exception;\r
- }\r
-\r
- private void writeToFile( final Phylogeny t ) {\r
- if ( t == null ) {\r
- return;\r
- }\r
- String initial_filename = null;\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- try {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath();\r
- }\r
- catch ( final IOException e ) {\r
- initial_filename = null;\r
- }\r
- }\r
- if ( !ForesterUtil.isEmpty( initial_filename ) ) {\r
- _save_filechooser.setSelectedFile( new File( initial_filename ) );\r
- }\r
- else {\r
- _save_filechooser.setSelectedFile( new File( "" ) );\r
- }\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _save_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _save_filechooser.showSaveDialog( _contentpane );\r
- final File file = _save_filechooser.getSelectedFile();\r
- setCurrentDir( _save_filechooser.getCurrentDirectory() );\r
- boolean exception = false;\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists.\nOverwrite?",\r
- "Overwrite?",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.QUESTION_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- else {\r
- final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX );\r
- try {\r
- ForesterUtil.copyFile( file, to );\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to create backup copy " + to,\r
- "Failed to Create Backup Copy",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Failed to Delete",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
- else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // "*.*":\r
- else {\r
- final String file_name = file.getName().trim().toLowerCase();\r
- if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tree" ) ) {\r
- exception = writeAsNewHampshire( t, exception, file );\r
- }\r
- else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) {\r
- exception = writeAsNexus( t, exception, file );\r
- }\r
- // XML is default:\r
- else {\r
- exception = writeAsPhyloXml( t, exception, file );\r
- }\r
- }\r
- if ( !exception ) {\r
- getMainPanel().setTitleOfSelectedTab( file.getName() );\r
- getMainPanel().getCurrentTreePanel().setTreeFile( file );\r
- getMainPanel().getCurrentTreePanel().setEdited( false );\r
- }\r
- }\r
- }\r
-\r
- private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return;\r
- }\r
- String initial_filename = "";\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + "." + type;\r
- _writetographics_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _writetographics_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _writetographics_filechooser.showSaveDialog( _contentpane );\r
- File file = _writetographics_filechooser.getSelectedFile();\r
- setCurrentDir( _writetographics_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) {\r
- file = new File( file.toString() + "." + type );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "Warning",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- else {\r
- try {\r
- file.delete();\r
- }\r
- catch ( final Exception e ) {\r
- JOptionPane.showMessageDialog( this,\r
- "Failed to delete: " + file,\r
- "Error",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
- }\r
- writePhylogenyToGraphicsFile( file.toString(), type );\r
- }\r
- }\r
-\r
- private void writeToPdf( final Phylogeny t ) {\r
- if ( ( t == null ) || t.isEmpty() ) {\r
- return;\r
- }\r
- String initial_filename = "";\r
- if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) {\r
- initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString();\r
- }\r
- if ( initial_filename.indexOf( '.' ) > 0 ) {\r
- initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) );\r
- }\r
- initial_filename = initial_filename + ".pdf";\r
- _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) );\r
- final File my_dir = getCurrentDir();\r
- if ( my_dir != null ) {\r
- _writetopdf_filechooser.setCurrentDirectory( my_dir );\r
- }\r
- final int result = _writetopdf_filechooser.showSaveDialog( _contentpane );\r
- File file = _writetopdf_filechooser.getSelectedFile();\r
- setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() );\r
- if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
- if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) {\r
- file = new File( file.toString() + ".pdf" );\r
- }\r
- if ( file.exists() ) {\r
- final int i = JOptionPane.showConfirmDialog( this,\r
- file + " already exists. Overwrite?",\r
- "WARNING",\r
- JOptionPane.OK_CANCEL_OPTION,\r
- JOptionPane.WARNING_MESSAGE );\r
- if ( i != JOptionPane.OK_OPTION ) {\r
- return;\r
- }\r
- }\r
- printPhylogenyToPdf( file.toString() );\r
- }\r
- }\r
-\r
- public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {\r
- return new MainFrameApplication( phys, config );\r
- }\r
-\r
- public static MainFrame createInstance( final Phylogeny[] phys,\r
- final Configuration config,\r
- final String title,\r
- final File current_dir ) {\r
- return new MainFrameApplication( phys, config, title, current_dir );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) {\r
- return new MainFrameApplication( phys, config, title );\r
- }\r
-\r
- static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {\r
- return new MainFrameApplication( phys, config_file_name, title );\r
- }\r
-\r
- static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "\r
- + o.getPrintSizeY() + ")" );\r
- }\r
-\r
- static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) {\r
- mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" );\r
- }\r
-\r
- static void warnIfNotPhyloXmlValidation( final Configuration c ) {\r
- if ( !c.isValidatePhyloXmlAgainstSchema() ) {\r
- JOptionPane\r
- .showMessageDialog( null,\r
- ForesterUtil\r
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",\r
- 80 ),\r
- "Warning",\r
- JOptionPane.WARNING_MESSAGE );\r
- }\r
- }\r
} // MainFrameApplication.\r
-\r
-class DefaultFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" )\r
- || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" )\r
- || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" )\r
- || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" )\r
- || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" )\r
- || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" )\r
- || file_name.endsWith( ".con" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)";\r
- }\r
-}\r
-\r
-class GraphicsFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" )\r
- || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)";\r
- }\r
-}\r
-\r
-class MsaFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" )\r
- || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)";\r
- }\r
-}\r
-\r
-class NexusFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" )\r
- || file_name.endsWith( ".tre" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Nexus files (*.nex, *.nexus, *.nx, *.tre)";\r
- }\r
-} // NexusFilter\r
-\r
-class NHFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" )\r
- || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" )\r
- || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" )\r
- || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)";\r
- }\r
-} // NHFilter\r
-\r
-class NHXFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".nhx" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "NHX files (*.nhx) [deprecated]";\r
- }\r
-}\r
-\r
-class PdfFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "PDF files (*.pdf)";\r
- }\r
-} // PdfFilter\r
-\r
-class SequencesFileFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" )\r
- || file_name.endsWith( ".seqs" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )";\r
- }\r
-}\r
-\r
-class TolFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f\r
- .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) );\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "Tree of Life files (*.tol, *.tolxml)";\r
- }\r
-} // TolFilter\r
-\r
-class XMLFilter extends FileFilter {\r
-\r
- @Override\r
- public boolean accept( final File f ) {\r
- final String file_name = f.getName().trim().toLowerCase();\r
- return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" )\r
- || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory();\r
- }\r
-\r
- @Override\r
- public String getDescription() {\r
- return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)";\r
- }\r
-} // XMLFilter\r
git://source.jalview.org / jalview.git / blobdiff