X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=2588e959dc985fbcf06a4a0274bfd890c0c26a92;hb=9351f2c2e8af0c3bf1280f9696f1459db2819005;hp=57c2cb4eb3d2e54532d6b64e119b07a1555c067f;hpb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 57c2cb4..2588e95 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -57,7 +57,6 @@ import javax.swing.UnsupportedLookAndFeelException; import javax.swing.WindowConstants; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; -import javax.swing.filechooser.FileFilter; import javax.swing.plaf.synth.SynthLookAndFeel; import org.forester.analysis.TaxonomyDataManager; @@ -105,64 +104,72 @@ import org.forester.util.BasicTable; import org.forester.util.BasicTableParser; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterUtil; -import org.forester.util.WindowsUtils; public final class MainFrameApplication extends MainFrame { - static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies"; - static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information"; - private final static int FRAME_X_SIZE = 800; - private final static int FRAME_Y_SIZE = 800; + public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) { + return new MainFrameApplication( phys, config ); + } + + static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) { + return new MainFrameApplication( phys, config, title ); + } + + public static MainFrame createInstance( final Phylogeny[] phys, + final Configuration config, + final String title, + final File current_dir ) { + return new MainFrameApplication( phys, config, title, current_dir ); + } + + static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) { + return new MainFrameApplication( phys, config_file_name, title ); + } + + static void warnIfNotPhyloXmlValidation( final Configuration c ) { + if ( !c.isValidatePhyloXmlAgainstSchema() ) { + JOptionPane + .showMessageDialog( null, + ForesterUtil + .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]", + 80 ), + "Warning", + JOptionPane.WARNING_MESSAGE ); + } + } + static final String INFER_ANCESTOR_TAXONOMIES = "Infer Ancestor Taxonomies"; + static final String OBTAIN_DETAILED_TAXONOMIC_INFORMATION = "Obtain Detailed Taxonomic Information"; + private final static int FRAME_X_SIZE = 800; + private final static int FRAME_Y_SIZE = 800; // Filters for the file-open dialog (classes defined in this file) - private final static NHFilter nhfilter = new NHFilter(); - private final static NHXFilter nhxfilter = new NHXFilter(); - private final static XMLFilter xmlfilter = new XMLFilter(); - private final static TolFilter tolfilter = new TolFilter(); - private final static NexusFilter nexusfilter = new NexusFilter(); - private final static PdfFilter pdffilter = new PdfFilter(); - private final static GraphicsFileFilter graphicsfilefilter = new GraphicsFileFilter(); - private final static MsaFileFilter msafilter = new MsaFileFilter(); - private final static SequencesFileFilter seqsfilter = new SequencesFileFilter(); - private final static DefaultFilter defaultfilter = new DefaultFilter(); - private static final long serialVersionUID = -799735726778865234L; - private static final boolean PREPROCESS_TREES = false; - private final JFileChooser _values_filechooser; - private final JFileChooser _sequences_filechooser; - private final JFileChooser _open_filechooser; - private final JFileChooser _msa_filechooser; - private final JFileChooser _seqs_pi_filechooser; - private final JFileChooser _open_filechooser_for_species_tree; - private final JFileChooser _save_filechooser; - private final JFileChooser _writetopdf_filechooser; - private final JFileChooser _writetographics_filechooser; + private static final long serialVersionUID = -799735726778865234L; + private static final boolean PREPROCESS_TREES = false; + private final JFileChooser _values_filechooser; + private final JFileChooser _sequences_filechooser; + private final JFileChooser _open_filechooser; + private final JFileChooser _msa_filechooser; + private final JFileChooser _seqs_pi_filechooser; + private final JFileChooser _open_filechooser_for_species_tree; // Application-only print menu items - private JMenuItem _print_item; - private JMenuItem _write_to_pdf_item; - private JMenuItem _write_to_jpg_item; - private JMenuItem _write_to_gif_item; - private JMenuItem _write_to_tif_item; - private JMenuItem _write_to_png_item; - private JMenuItem _write_to_bmp_item; - private JMenuItem _collapse_below_threshold; - private JMenuItem _collapse_below_branch_length; - private File _current_dir; - private ButtonGroup _radio_group_1; - private ButtonGroup _radio_group_2; + private JMenuItem _collapse_below_threshold; + private JMenuItem _collapse_below_branch_length; + private ButtonGroup _radio_group_1; + private ButtonGroup _radio_group_2; // Others: - double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT; - double _min_not_collapse_bl = 0.001; + double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT; + double _min_not_collapse_bl = 0.001; // Phylogeny Inference menu - private JMenu _inference_menu; - private JMenuItem _inference_from_msa_item; - private JMenuItem _inference_from_seqs_item; + private JMenu _inference_menu; + private JMenuItem _inference_from_msa_item; + private JMenuItem _inference_from_seqs_item; // Phylogeny Inference - private PhylogeneticInferenceOptions _phylogenetic_inference_options = null; - private Msa _msa = null; - private File _msa_file = null; - private List _seqs = null; - private File _seqs_file = null; - JMenuItem _read_values_jmi; - JMenuItem _read_seqs_jmi; + private PhylogeneticInferenceOptions _phylogenetic_inference_options = null; + private Msa _msa = null; + private File _msa_file = null; + private List _seqs = null; + private File _seqs_file = null; + JMenuItem _read_values_jmi; + JMenuItem _read_seqs_jmi; private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) { _configuration = config; @@ -277,44 +284,44 @@ public final class MainFrameApplication extends MainFrame { _open_filechooser = new JFileChooser(); _open_filechooser.setCurrentDirectory( new File( "." ) ); _open_filechooser.setMultiSelectionEnabled( false ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.xmlfilter ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter ); - _open_filechooser.addChoosableFileFilter( MainFrameApplication.tolfilter ); + _open_filechooser.addChoosableFileFilter( MainFrame.xmlfilter ); + _open_filechooser.addChoosableFileFilter( MainFrame.nhxfilter ); + _open_filechooser.addChoosableFileFilter( MainFrame.nhfilter ); + _open_filechooser.addChoosableFileFilter( MainFrame.nexusfilter ); + _open_filechooser.addChoosableFileFilter( MainFrame.tolfilter ); _open_filechooser.addChoosableFileFilter( _open_filechooser.getAcceptAllFileFilter() ); - _open_filechooser.setFileFilter( MainFrameApplication.defaultfilter ); + _open_filechooser.setFileFilter( MainFrame.defaultfilter ); _open_filechooser_for_species_tree = new JFileChooser(); _open_filechooser_for_species_tree.setCurrentDirectory( new File( "." ) ); _open_filechooser_for_species_tree.setMultiSelectionEnabled( false ); - _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.xmlfilter ); - _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrameApplication.tolfilter ); - _open_filechooser_for_species_tree.setFileFilter( MainFrameApplication.xmlfilter ); + _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.xmlfilter ); + _open_filechooser_for_species_tree.addChoosableFileFilter( MainFrame.tolfilter ); + _open_filechooser_for_species_tree.setFileFilter( MainFrame.xmlfilter ); _save_filechooser = new JFileChooser(); _save_filechooser.setCurrentDirectory( new File( "." ) ); _save_filechooser.setMultiSelectionEnabled( false ); - _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter ); - _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter ); - _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter ); + _save_filechooser.setFileFilter( MainFrame.xmlfilter ); + _save_filechooser.addChoosableFileFilter( MainFrame.nhfilter ); + _save_filechooser.addChoosableFileFilter( MainFrame.nexusfilter ); _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); _writetopdf_filechooser = new JFileChooser(); - _writetopdf_filechooser.addChoosableFileFilter( MainFrameApplication.pdffilter ); + _writetopdf_filechooser.addChoosableFileFilter( MainFrame.pdffilter ); _writetographics_filechooser = new JFileChooser(); - _writetographics_filechooser.addChoosableFileFilter( MainFrameApplication.graphicsfilefilter ); + _writetographics_filechooser.addChoosableFileFilter( MainFrame.graphicsfilefilter ); // Msa: _msa_filechooser = new JFileChooser(); _msa_filechooser.setName( "Read Multiple Sequence Alignment File" ); _msa_filechooser.setCurrentDirectory( new File( "." ) ); _msa_filechooser.setMultiSelectionEnabled( false ); _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() ); - _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter ); + _msa_filechooser.addChoosableFileFilter( MainFrame.msafilter ); // Seqs: _seqs_pi_filechooser = new JFileChooser(); _seqs_pi_filechooser.setName( "Read Sequences File" ); _seqs_pi_filechooser.setCurrentDirectory( new File( "." ) ); _seqs_pi_filechooser.setMultiSelectionEnabled( false ); _seqs_pi_filechooser.addChoosableFileFilter( _seqs_pi_filechooser.getAcceptAllFileFilter() ); - _seqs_pi_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter ); + _seqs_pi_filechooser.addChoosableFileFilter( MainFrame.seqsfilter ); // Expression _values_filechooser = new JFileChooser(); _values_filechooser.setCurrentDirectory( new File( "." ) ); @@ -425,41 +432,14 @@ public final class MainFrameApplication extends MainFrame { if ( o == _open_url_item ) { readPhylogeniesFromURL(); } - else if ( o == _save_item ) { - writeToFile( _mainpanel.getCurrentPhylogeny() ); - // If subtree currently displayed, save it, instead of complete - // tree. - } else if ( o == _new_item ) { newTree(); } - else if ( o == _save_all_item ) { - writeAllToFile(); - } + else if ( o == _close_item ) { closeCurrentPane(); } - else if ( o == _write_to_pdf_item ) { - writeToPdf( _mainpanel.getCurrentPhylogeny() ); - } - else if ( o == _write_to_jpg_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.JPG ); - } - else if ( o == _write_to_png_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.PNG ); - } - else if ( o == _write_to_gif_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.GIF ); - } - else if ( o == _write_to_tif_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.TIFF ); - } - else if ( o == _write_to_bmp_item ) { - writeToGraphicsFile( _mainpanel.getCurrentPhylogeny(), GraphicsExportType.BMP ); - } - else if ( o == _print_item ) { - print(); - } + else if ( o == _load_species_tree_item ) { readSpeciesTreeFromFile(); } @@ -509,27 +489,6 @@ public final class MainFrameApplication extends MainFrame { else if ( o == _extract_tax_code_from_node_names_jmi ) { extractTaxDataFromNodeNames(); } - else if ( o == _graphics_export_visible_only_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _antialias_print_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _print_black_and_white_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _print_using_actual_size_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _graphics_export_using_actual_size_cbmi ) { - updateOptions( getOptions() ); - } - else if ( o == _print_size_mi ) { - choosePrintSize(); - } - else if ( o == _choose_pdf_width_mi ) { - choosePdfWidth(); - } else if ( o == _internal_number_are_confidence_for_nh_parsing_cbmi ) { updateOptions( getOptions() ); } @@ -580,144 +539,144 @@ public final class MainFrameApplication extends MainFrame { } } - public void end() { - _mainpanel.terminate(); - _contentpane.removeAll(); - setVisible( false ); - dispose(); - } - - @Override - public MainPanel getMainPanel() { - return _mainpanel; - } - - public Msa getMsa() { - return _msa; - } - - public File getMsaFile() { - return _msa_file; - } - - public List getSeqs() { - return _seqs; - } - - public File getSeqsFile() { - return _seqs_file; - } - - public void readMsaFromFile() { - // Set an initial directory if none set yet + private void addExpressionValuesFromFile() { + if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { + JOptionPane.showMessageDialog( this, + "Need to load evolutionary tree first", + "Can Not Read Expression Values", + JOptionPane.WARNING_MESSAGE ); + return; + } final File my_dir = getCurrentDir(); - _msa_filechooser.setMultiSelectionEnabled( false ); - // Open file-open dialog and set current directory if ( my_dir != null ) { - _msa_filechooser.setCurrentDirectory( my_dir ); + _values_filechooser.setCurrentDirectory( my_dir ); } - final int result = _msa_filechooser.showOpenDialog( _contentpane ); - // All done: get the msa - final File file = _msa_filechooser.getSelectedFile(); - setCurrentDir( _msa_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { - setMsaFile( null ); - setMsa( null ); - Msa msa = null; + final int result = _values_filechooser.showOpenDialog( _contentpane ); + final File file = _values_filechooser.getSelectedFile(); + if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) { + BasicTable t = null; try { - final InputStream is = new FileInputStream( file ); - if ( FastaParser.isLikelyFasta( file ) ) { - msa = FastaParser.parseMsa( is ); + t = BasicTableParser.parse( file, '\t' ); + if ( t.getNumberOfColumns() < 2 ) { + t = BasicTableParser.parse( file, ',' ); } - else { - msa = GeneralMsaParser.parse( is ); + if ( t.getNumberOfColumns() < 2 ) { + t = BasicTableParser.parse( file, ' ' ); } } - catch ( final MsaFormatException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Multiple sequence alignment format error", - JOptionPane.ERROR_MESSAGE ); - return; - } catch ( final IOException e ) { - setArrowCursor(); JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Failed to read multiple sequence alignment", + e.getMessage(), + "Could Not Read Expression Value Table", JOptionPane.ERROR_MESSAGE ); return; } - catch ( final IllegalArgumentException e ) { - setArrowCursor(); + if ( t.getNumberOfColumns() < 2 ) { JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence alignment", + "Table contains " + t.getNumberOfColumns() + " column(s)", + "Problem with Expression Value Table", JOptionPane.ERROR_MESSAGE ); return; } - catch ( final Exception e ) { - setArrowCursor(); - e.printStackTrace(); + if ( t.getNumberOfRows() < 1 ) { JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence alignment", + "Table contains zero rows", + "Problem with Expression Value Table", JOptionPane.ERROR_MESSAGE ); return; } - if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) { JOptionPane.showMessageDialog( this, - "Multiple sequence alignment is empty", - "Illegal Multiple Sequence Alignment", - JOptionPane.ERROR_MESSAGE ); - return; + "Table contains " + t.getNumberOfRows() + " rows, but tree contains " + + phy.getNumberOfExternalNodes() + " external nodes", + "Warning", + JOptionPane.WARNING_MESSAGE ); } - if ( msa.getNumberOfSequences() < 4 ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence alignment needs to contain at least 3 sequences", - "Illegal multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; + final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); + int not_found = 0; + for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { + final PhylogenyNode node = iter.next(); + final String node_name = node.getName(); + if ( !ForesterUtil.isEmpty( node_name ) ) { + int row = -1; + try { + row = t.findRow( node_name ); + } + catch ( final IllegalArgumentException e ) { + JOptionPane + .showMessageDialog( this, + e.getMessage(), + "Error Mapping Node Identifiers to Expression Value Identifiers", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( row < 0 ) { + if ( node.isExternal() ) { + not_found++; + } + continue; + } + final List l = new ArrayList(); + for( int col = 1; col < t.getNumberOfColumns(); ++col ) { + double d = -100; + try { + d = Double.parseDouble( t.getValueAsString( col, row ) ); + } + catch ( final NumberFormatException e ) { + JOptionPane.showMessageDialog( this, + "Could not parse \"" + t.getValueAsString( col, row ) + + "\" into a decimal value", + "Issue with Expression Value Table", + JOptionPane.ERROR_MESSAGE ); + return; + } + stats.addValue( d ); + l.add( d ); + } + if ( !l.isEmpty() ) { + if ( node.getNodeData().getProperties() != null ) { + node.getNodeData().getProperties() + .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); + } + node.getNodeData().setVector( l ); + } + } } - if ( msa.getLength() < 2 ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence alignment needs to contain at least 2 residues", - "Illegal multiple sequence alignment", - JOptionPane.ERROR_MESSAGE ); - return; + if ( not_found > 0 ) { + JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found + + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE ); } - System.gc(); - setMsaFile( _msa_filechooser.getSelectedFile() ); - setMsa( msa ); + getCurrentTreePanel().setStatisticsForExpressionValues( stats ); } } - public void readSeqsFromFileforPI() { - // Set an initial directory if none set yet + private void addSequencesFromFile() { + if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { + JOptionPane.showMessageDialog( this, + "Need to load evolutionary tree first", + "Can Not Read Sequences", + JOptionPane.WARNING_MESSAGE ); + return; + } final File my_dir = getCurrentDir(); - _seqs_pi_filechooser.setMultiSelectionEnabled( false ); - // Open file-open dialog and set current directory if ( my_dir != null ) { - _seqs_pi_filechooser.setCurrentDirectory( my_dir ); + _sequences_filechooser.setCurrentDirectory( my_dir ); } - final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane ); - // All done: get the seqs - final File file = _seqs_pi_filechooser.getSelectedFile(); - setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() ); + final int result = _sequences_filechooser.showOpenDialog( _contentpane ); + final File file = _sequences_filechooser.getSelectedFile(); + List seqs = null; if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { - setSeqsFile( null ); - setSeqs( null ); - List seqs = null; try { if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { seqs = FastaParser.parse( new FileInputStream( file ) ); - for( final MolecularSequence seq : seqs ) { - System.out.println( SequenceWriter.toFasta( seq, 60 ) ); - } } else { - //TODO error + JOptionPane.showMessageDialog( this, + "Format does not appear to be Fasta", + "Multiple sequence file format error", + JOptionPane.ERROR_MESSAGE ); + return; } } catch ( final MsaFormatException e ) { @@ -736,14 +695,6 @@ public final class MainFrameApplication extends MainFrame { JOptionPane.ERROR_MESSAGE ); return; } - catch ( final IllegalArgumentException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } catch ( final Exception e ) { setArrowCursor(); e.printStackTrace(); @@ -756,27 +707,106 @@ public final class MainFrameApplication extends MainFrame { if ( ( seqs == null ) || ( seqs.size() < 1 ) ) { JOptionPane.showMessageDialog( this, "Multiple sequence file is empty", - "Illegal multiple sequence file", + "Empty multiple sequence file", JOptionPane.ERROR_MESSAGE ); + setArrowCursor(); return; } - if ( seqs.size() < 4 ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence file needs to contain at least 3 sequences", - "Illegal multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; + } + if ( seqs != null ) { + for( final MolecularSequence seq : seqs ) { + System.out.println( seq.getIdentifier() ); + } + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + int total_counter = 0; + int attached_counter = 0; + for( final MolecularSequence seq : seqs ) { + ++total_counter; + final String seq_name = seq.getIdentifier(); + if ( !ForesterUtil.isEmpty( seq_name ) ) { + List nodes = phy.getNodesViaSequenceName( seq_name ); + if ( nodes.isEmpty() ) { + nodes = phy.getNodesViaSequenceSymbol( seq_name ); + } + if ( nodes.isEmpty() ) { + nodes = phy.getNodesViaGeneName( seq_name ); + } + if ( nodes.isEmpty() ) { + nodes = phy.getNodes( seq_name ); + } + if ( nodes.size() > 1 ) { + JOptionPane.showMessageDialog( this, + "Sequence name \"" + seq_name + "\" is not unique", + "Sequence name not unique", + JOptionPane.ERROR_MESSAGE ); + setArrowCursor(); + return; + } + final String[] a = seq_name.split( "\\s" ); + if ( nodes.isEmpty() && ( a.length > 1 ) ) { + final String seq_name_split = a[ 0 ]; + nodes = phy.getNodesViaSequenceName( seq_name_split ); + if ( nodes.isEmpty() ) { + nodes = phy.getNodesViaSequenceSymbol( seq_name_split ); + } + if ( nodes.isEmpty() ) { + nodes = phy.getNodes( seq_name_split ); + } + if ( nodes.size() > 1 ) { + JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split + + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE ); + setArrowCursor(); + return; + } + } + if ( nodes.size() == 1 ) { + ++attached_counter; + final PhylogenyNode n = nodes.get( 0 ); + if ( !n.getNodeData().isHasSequence() ) { + n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() ); + } + n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() ); + if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { + n.getNodeData().getSequence().setName( seq_name ); + } + } + } + } + if ( attached_counter > 0 ) { + int ext_nodes = 0; + int ext_nodes_with_seq = 0; + for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) { + ++ext_nodes; + final PhylogenyNode n = iter.next(); + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { + ++ext_nodes_with_seq; + } + } + final String s; + if ( ext_nodes == ext_nodes_with_seq ) { + s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them."; + } + else { + s = ext_nodes_with_seq + " out of " + ext_nodes + + " external nodes now have a molecular sequence attached to them."; + } + if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) { + JOptionPane.showMessageDialog( this, + "Attached all " + total_counter + " sequences to tree nodes.\n" + s, + "All sequences attached", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane.showMessageDialog( this, "Attached " + attached_counter + + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter + + " sequences attached", JOptionPane.WARNING_MESSAGE ); + } + } + else { + JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter + + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE ); } - // if ( msa.getLength() < 2 ) { - // JOptionPane.showMessageDialog( this, - // "Multiple sequence alignment needs to contain at least 2 residues", - // "Illegal multiple sequence file", - // JOptionPane.ERROR_MESSAGE ); - // return; - // } - System.gc(); - setSeqsFile( _seqs_pi_filechooser.getSelectedFile() ); - setSeqs( seqs ); } } @@ -877,10 +907,11 @@ public final class MainFrameApplication extends MainFrame { .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() ); MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) ); - setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); - setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); + MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() ); + MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() ); MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() ); MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() ); + MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() ); MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() ); try { getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB(); @@ -931,6 +962,8 @@ public final class MainFrameApplication extends MainFrame { _options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) ); _options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) ); _options_jmenu.addSeparator(); + _options_jmenu.add( _cycle_data_return = new JMenuItem( "Cycle Data Return" ) ); + _options_jmenu.addSeparator(); _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( SEARCH_SUBHEADER ), getConfiguration() ) ); _options_jmenu.add( _search_case_senstive_cbmi = new JCheckBoxMenuItem( SEARCH_CASE_SENSITIVE_LABEL ) ); _options_jmenu.add( _search_whole_words_only_cbmi = new JCheckBoxMenuItem( SEARCH_TERMS_ONLY_LABEL ) ); @@ -997,6 +1030,7 @@ public final class MainFrameApplication extends MainFrame { customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); + customizeJMenuItem( _cycle_data_return ); customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() ); customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() ); customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() ); @@ -1167,527 +1201,152 @@ public final class MainFrameApplication extends MainFrame { exit(); } - void executeLineageInference() { - if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) { - return; - } - if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { - JOptionPane.showMessageDialog( this, - "Phylogeny is not rooted.", - "Cannot infer ancestral taxonomies", - JOptionPane.ERROR_MESSAGE ); - return; + private void closeCurrentPane() { + if ( getMainPanel().getCurrentTreePanel() != null ) { + if ( getMainPanel().getCurrentTreePanel().isEdited() ) { + final int r = JOptionPane.showConfirmDialog( this, + "Close tab despite potentially unsaved changes?", + "Close Tab?", + JOptionPane.YES_NO_OPTION ); + if ( r != JOptionPane.YES_OPTION ) { + return; + } + } + getMainPanel().closeCurrentPane(); + activateSaveAllIfNeeded(); } - final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this, - _mainpanel.getCurrentTreePanel(), - _mainpanel.getCurrentPhylogeny() - .copy() ); - new Thread( inferrer ).start(); - } - - void exit() { - removeAllTextFrames(); - _mainpanel.terminate(); - _contentpane.removeAll(); - setVisible( false ); - dispose(); - System.exit( 0 ); } - void readPhylogeniesFromURL() { - URL url = null; - Phylogeny[] phys = null; - final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\""; - final String url_string = JOptionPane.showInputDialog( this, - message, - "Use URL/webservice to obtain a phylogeny", - JOptionPane.QUESTION_MESSAGE ); - boolean nhx_or_nexus = false; - if ( ( url_string != null ) && ( url_string.length() > 0 ) ) { - try { - url = new URL( url_string ); - PhylogenyParser parser = null; - if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) { - parser = new TolParser(); - } - else { - parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration() - .isValidatePhyloXmlAgainstSchema() ); - } - if ( parser instanceof NexusPhylogeniesParser ) { - nhx_or_nexus = true; - } - else if ( parser instanceof NHXParser ) { - nhx_or_nexus = true; - } - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().setWaitCursor(); - } - else { - _mainpanel.setWaitCursor(); + private void collapse( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + final List to_be_removed = new ArrayList(); + double min_support = Double.MAX_VALUE; + boolean conf_present = false; + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( !n.isExternal() && !n.isRoot() ) { + final List c = n.getBranchData().getConfidences(); + if ( ( c != null ) && ( c.size() > 0 ) ) { + conf_present = true; + double max = 0; + for( final Confidence confidence : c ) { + if ( confidence.getValue() > max ) { + max = confidence.getValue(); + } + } + if ( max < getMinNotCollapseConfidenceValue() ) { + to_be_removed.add( n ); + } + if ( max < min_support ) { + min_support = max; + } } - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - phys = factory.create( url.openStream(), parser ); } - catch ( final MalformedURLException e ) { - JOptionPane.showMessageDialog( this, - "Malformed URL: " + url + "\n" + e.getLocalizedMessage(), - "Malformed URL", - JOptionPane.ERROR_MESSAGE ); + } + if ( conf_present ) { + for( final PhylogenyNode node : to_be_removed ) { + PhylogenyMethods.removeNode( node, phy ); } - catch ( final IOException e ) { - JOptionPane.showMessageDialog( this, - "Could not read from " + url + "\n" - + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), - "Failed to read URL", - JOptionPane.ERROR_MESSAGE ); + if ( to_be_removed.size() > 0 ) { + phy.externalNodesHaveChanged(); + phy.clearHashIdToNodeMap(); + phy.recalculateNumberOfExternalDescendants( true ); + getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); + getCurrentTreePanel().calculateLongestExtNodeInfo(); + getCurrentTreePanel().setNodeInPreorderToNull(); + getCurrentTreePanel().recalculateMaxDistanceToRoot(); + getCurrentTreePanel().resetPreferredSize(); + getCurrentTreePanel().setEdited( true ); + getCurrentTreePanel().repaint(); + repaint(); } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), - "Unexpected Exception", - JOptionPane.ERROR_MESSAGE ); - } - finally { - if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - else { - _mainpanel.setArrowCursor(); - } - } - if ( ( phys != null ) && ( phys.length > 0 ) ) { - if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) { - for( final Phylogeny phy : phys ) { - PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" ); - } - } - AptxUtil.addPhylogeniesToTabs( phys, - new File( url.getFile() ).getName(), - new File( url.getFile() ).toString(), - getConfiguration(), - getMainPanel() ); - _mainpanel.getControlPanel().showWhole(); - } - } - activateSaveAllIfNeeded(); - System.gc(); - } - - void setMsa( final Msa msa ) { - _msa = msa; - } - - void setMsaFile( final File msa_file ) { - _msa_file = msa_file; - } - - void setSeqs( final List seqs ) { - _seqs = seqs; - } - - void setSeqsFile( final File seqs_file ) { - _seqs_file = seqs_file; - } - - void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) { - _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), - _mainpanel.getCurrentTreePanel().getHeight() ); - String file_written_to = ""; - boolean error = false; - try { - file_written_to = AptxUtil.writePhylogenyToGraphicsFile( file_name, - _mainpanel.getCurrentTreePanel().getWidth(), - _mainpanel.getCurrentTreePanel().getHeight(), - _mainpanel.getCurrentTreePanel(), - _mainpanel.getControlPanel(), - type, - getOptions() ); - } - catch ( final IOException e ) { - error = true; - JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); - } - if ( !error ) { - if ( ( file_written_to != null ) && ( file_written_to.length() > 0 ) ) { - JOptionPane.showMessageDialog( this, - "Wrote image to: " + file_written_to, - "Graphics Export", - JOptionPane.INFORMATION_MESSAGE ); + if ( to_be_removed.size() > 0 ) { + JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() + + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed " + + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); } else { - JOptionPane.showMessageDialog( this, - "There was an unknown problem when attempting to write to an image file: \"" - + file_name + "\"", - "Error", - JOptionPane.ERROR_MESSAGE ); + JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is " + + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE ); } } - _contentpane.repaint(); - } - - private void addExpressionValuesFromFile() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { + else { JOptionPane.showMessageDialog( this, - "Need to load evolutionary tree first", - "Can Not Read Expression Values", - JOptionPane.WARNING_MESSAGE ); - return; - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _values_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _values_filechooser.showOpenDialog( _contentpane ); - final File file = _values_filechooser.getSelectedFile(); - if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - BasicTable t = null; - try { - t = BasicTableParser.parse( file, '\t' ); - if ( t.getNumberOfColumns() < 2 ) { - t = BasicTableParser.parse( file, ',' ); - } - if ( t.getNumberOfColumns() < 2 ) { - t = BasicTableParser.parse( file, ' ' ); - } - } - catch ( final IOException e ) { - JOptionPane.showMessageDialog( this, - e.getMessage(), - "Could Not Read Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( t.getNumberOfColumns() < 2 ) { - JOptionPane.showMessageDialog( this, - "Table contains " + t.getNumberOfColumns() + " column(s)", - "Problem with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( t.getNumberOfRows() < 1 ) { - JOptionPane.showMessageDialog( this, - "Table contains zero rows", - "Problem with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) { - JOptionPane.showMessageDialog( this, - "Table contains " + t.getNumberOfRows() + " rows, but tree contains " - + phy.getNumberOfExternalNodes() + " external nodes", - "Warning", - JOptionPane.WARNING_MESSAGE ); - } - final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); - int not_found = 0; - for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); - final String node_name = node.getName(); - if ( !ForesterUtil.isEmpty( node_name ) ) { - int row = -1; - try { - row = t.findRow( node_name ); - } - catch ( final IllegalArgumentException e ) { - JOptionPane - .showMessageDialog( this, - e.getMessage(), - "Error Mapping Node Identifiers to Expression Value Identifiers", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( row < 0 ) { - if ( node.isExternal() ) { - not_found++; - } - continue; - } - final List l = new ArrayList(); - for( int col = 1; col < t.getNumberOfColumns(); ++col ) { - double d = -100; - try { - d = Double.parseDouble( t.getValueAsString( col, row ) ); - } - catch ( final NumberFormatException e ) { - JOptionPane.showMessageDialog( this, - "Could not parse \"" + t.getValueAsString( col, row ) - + "\" into a decimal value", - "Issue with Expression Value Table", - JOptionPane.ERROR_MESSAGE ); - return; - } - stats.addValue( d ); - l.add( d ); - } - if ( !l.isEmpty() ) { - if ( node.getNodeData().getProperties() != null ) { - node.getNodeData().getProperties() - .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF ); - } - node.getNodeData().setVector( l ); - } - } - } - if ( not_found > 0 ) { - JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found - + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE ); - } - getCurrentTreePanel().setStatisticsForExpressionValues( stats ); + "No branch collapsed because no confidence values present", + "No confidence values present", + JOptionPane.INFORMATION_MESSAGE ); } } - private void addSequencesFromFile() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { - JOptionPane.showMessageDialog( this, - "Need to load evolutionary tree first", - "Can Not Read Sequences", - JOptionPane.WARNING_MESSAGE ); - return; - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _sequences_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _sequences_filechooser.showOpenDialog( _contentpane ); - final File file = _sequences_filechooser.getSelectedFile(); - List seqs = null; - if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { - try { - if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { - seqs = FastaParser.parse( new FileInputStream( file ) ); - } - else { - JOptionPane.showMessageDialog( this, - "Format does not appear to be Fasta", - "Multiple sequence file format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - } - catch ( final MsaFormatException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Multiple sequence file format error", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final IOException e ) { - setArrowCursor(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Failed to read multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - catch ( final Exception e ) { - setArrowCursor(); - e.printStackTrace(); - JOptionPane.showMessageDialog( this, - e.getLocalizedMessage(), - "Unexpected error during reading of multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - return; - } - if ( ( seqs == null ) || ( seqs.size() < 1 ) ) { - JOptionPane.showMessageDialog( this, - "Multiple sequence file is empty", - "Empty multiple sequence file", - JOptionPane.ERROR_MESSAGE ); - setArrowCursor(); - return; - } - } - if ( seqs != null ) { - for( final MolecularSequence seq : seqs ) { - System.out.println( seq.getIdentifier() ); - } + private void collapseBelowBranchLengthThreshold() { + if ( getCurrentTreePanel() != null ) { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - int total_counter = 0; - int attached_counter = 0; - for( final MolecularSequence seq : seqs ) { - ++total_counter; - final String seq_name = seq.getIdentifier(); - if ( !ForesterUtil.isEmpty( seq_name ) ) { - List nodes = phy.getNodesViaSequenceName( seq_name ); - if ( nodes.isEmpty() ) { - nodes = phy.getNodesViaSequenceSymbol( seq_name ); - } - if ( nodes.isEmpty() ) { - nodes = phy.getNodesViaGeneName( seq_name ); - } - if ( nodes.isEmpty() ) { - nodes = phy.getNodes( seq_name ); - } - if ( nodes.size() > 1 ) { - JOptionPane.showMessageDialog( this, - "Sequence name \"" + seq_name + "\" is not unique", - "Sequence name not unique", - JOptionPane.ERROR_MESSAGE ); - setArrowCursor(); - return; - } - final String[] a = seq_name.split( "\\s" ); - if ( nodes.isEmpty() && ( a.length > 1 ) ) { - final String seq_name_split = a[ 0 ]; - nodes = phy.getNodesViaSequenceName( seq_name_split ); - if ( nodes.isEmpty() ) { - nodes = phy.getNodesViaSequenceSymbol( seq_name_split ); - } - if ( nodes.isEmpty() ) { - nodes = phy.getNodes( seq_name_split ); + if ( ( phy != null ) && !phy.isEmpty() ) { + final String s = ( String ) JOptionPane + .showInputDialog( this, + "Please enter the minimum branch length value\n", + "Minimal Branch Length Value", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getMinNotCollapseBlValue() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + double m = 0.0; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + m = Double.parseDouble( m_str ); } - if ( nodes.size() > 1 ) { - JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split - + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE ); - setArrowCursor(); - return; + catch ( final Exception ex ) { + success = false; } } - if ( nodes.size() == 1 ) { - ++attached_counter; - final PhylogenyNode n = nodes.get( 0 ); - if ( !n.getNodeData().isHasSequence() ) { - n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() ); - } - n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() ); - if ( ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { - n.getNodeData().getSequence().setName( seq_name ); - } + else { + success = false; } - } - } - if ( attached_counter > 0 ) { - int ext_nodes = 0; - int ext_nodes_with_seq = 0; - for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) { - ++ext_nodes; - final PhylogenyNode n = iter.next(); - if ( n.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { - ++ext_nodes_with_seq; + if ( success && ( m >= 0.0 ) ) { + setMinNotCollapseBlValue( m ); + collapseBl( phy ); } } - final String s; - if ( ext_nodes == ext_nodes_with_seq ) { - s = "All " + ext_nodes_with_seq + " external nodes now have a molecular sequence attached to them."; - } - else { - s = ext_nodes_with_seq + " out of " + ext_nodes - + " external nodes now have a molecular sequence attached to them."; - } - if ( ( attached_counter == total_counter ) && ( ext_nodes == ext_nodes_with_seq ) ) { - JOptionPane.showMessageDialog( this, - "Attached all " + total_counter + " sequences to tree nodes.\n" + s, - "All sequences attached", - JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, "Attached " + attached_counter - + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter - + " sequences attached", JOptionPane.WARNING_MESSAGE ); - } - } - else { - JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter - + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE ); - } - } - } - - private void choosePdfWidth() { - final String s = ( String ) JOptionPane.showInputDialog( this, - "Please enter the default line width for PDF export.\n" - + "[current value: " - + getOptions().getPrintLineWidth() + "]\n", - "Line Width for PDF Export", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getPrintLineWidth() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - float f = 0.0f; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - f = Float.parseFloat( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( f > 0.0 ) ) { - getOptions().setPrintLineWidth( f ); } } } - private void choosePrintSize() { - final String s = ( String ) JOptionPane.showInputDialog( this, - "Please enter values for width and height,\nseparated by a comma.\n" - + "[current values: " - + getOptions().getPrintSizeX() + ", " - + getOptions().getPrintSizeY() + "]\n" - + "[A4: " + Constants.A4_SIZE_X + ", " - + Constants.A4_SIZE_Y + "]\n" + "[US Letter: " - + Constants.US_LETTER_SIZE_X + ", " - + Constants.US_LETTER_SIZE_Y + "]", - "Default Size for Graphics Export", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getOptions().getPrintSizeX() + ", " - + getOptions().getPrintSizeY() ); - if ( !ForesterUtil.isEmpty( s ) && ( s.indexOf( ',' ) > 0 ) ) { - boolean success = true; - int x = 0; - int y = 0; - final String[] str_ary = s.split( "," ); - if ( str_ary.length == 2 ) { - final String x_str = str_ary[ 0 ].trim(); - final String y_str = str_ary[ 1 ].trim(); - if ( !ForesterUtil.isEmpty( x_str ) && !ForesterUtil.isEmpty( y_str ) ) { - try { - x = Integer.parseInt( x_str ); - y = Integer.parseInt( y_str ); + private void collapseBelowThreshold() { + if ( getCurrentTreePanel() != null ) { + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + if ( ( phy != null ) && !phy.isEmpty() ) { + final String s = ( String ) JOptionPane.showInputDialog( this, + "Please enter the minimum confidence value\n", + "Minimal Confidence Value", + JOptionPane.QUESTION_MESSAGE, + null, + null, + getMinNotCollapseConfidenceValue() ); + if ( !ForesterUtil.isEmpty( s ) ) { + boolean success = true; + double m = 0.0; + final String m_str = s.trim(); + if ( !ForesterUtil.isEmpty( m_str ) ) { + try { + m = Double.parseDouble( m_str ); + } + catch ( final Exception ex ) { + success = false; + } } - catch ( final Exception ex ) { + else { success = false; } - } - else { - success = false; - } - } - else { - success = false; - } - if ( success && ( x > 1 ) && ( y > 1 ) ) { - getOptions().setPrintSizeX( x ); - getOptions().setPrintSizeY( y ); - } - } - } - - private void closeCurrentPane() { - if ( getMainPanel().getCurrentTreePanel() != null ) { - if ( getMainPanel().getCurrentTreePanel().isEdited() ) { - final int r = JOptionPane.showConfirmDialog( this, - "Close tab despite potentially unsaved changes?", - "Close Tab?", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.YES_OPTION ) { - return; + if ( success && ( m >= 0.0 ) ) { + setMinNotCollapseConfidenceValue( m ); + collapse( phy ); + } } } - getMainPanel().closeCurrentPane(); - activateSaveAllIfNeeded(); } } @@ -1749,139 +1408,6 @@ public final class MainFrameApplication extends MainFrame { } } - private void collapse( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - final List to_be_removed = new ArrayList(); - double min_support = Double.MAX_VALUE; - boolean conf_present = false; - while ( it.hasNext() ) { - final PhylogenyNode n = it.next(); - if ( !n.isExternal() && !n.isRoot() ) { - final List c = n.getBranchData().getConfidences(); - if ( ( c != null ) && ( c.size() > 0 ) ) { - conf_present = true; - double max = 0; - for( final Confidence confidence : c ) { - if ( confidence.getValue() > max ) { - max = confidence.getValue(); - } - } - if ( max < getMinNotCollapseConfidenceValue() ) { - to_be_removed.add( n ); - } - if ( max < min_support ) { - min_support = max; - } - } - } - } - if ( conf_present ) { - for( final PhylogenyNode node : to_be_removed ) { - PhylogenyMethods.removeNode( node, phy ); - } - if ( to_be_removed.size() > 0 ) { - phy.externalNodesHaveChanged(); - phy.clearHashIdToNodeMap(); - phy.recalculateNumberOfExternalDescendants( true ); - getCurrentTreePanel().resetNodeIdToDistToLeafMap(); - getCurrentTreePanel().updateSetOfCollapsedExternalNodes(); - getCurrentTreePanel().calculateLongestExtNodeInfo(); - getCurrentTreePanel().setNodeInPreorderToNull(); - getCurrentTreePanel().recalculateMaxDistanceToRoot(); - getCurrentTreePanel().resetPreferredSize(); - getCurrentTreePanel().setEdited( true ); - getCurrentTreePanel().repaint(); - repaint(); - } - if ( to_be_removed.size() > 0 ) { - JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() - + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed " - + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE ); - } - else { - JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is " - + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE ); - } - } - else { - JOptionPane.showMessageDialog( this, - "No branch collapsed because no confidence values present", - "No confidence values present", - JOptionPane.INFORMATION_MESSAGE ); - } - } - - private void collapseBelowThreshold() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final String s = ( String ) JOptionPane.showInputDialog( this, - "Please enter the minimum confidence value\n", - "Minimal Confidence Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getMinNotCollapseConfidenceValue() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - setMinNotCollapseConfidenceValue( m ); - collapse( phy ); - } - } - } - } - } - - private void collapseBelowBranchLengthThreshold() { - if ( getCurrentTreePanel() != null ) { - final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); - if ( ( phy != null ) && !phy.isEmpty() ) { - final String s = ( String ) JOptionPane - .showInputDialog( this, - "Please enter the minimum branch length value\n", - "Minimal Branch Length Value", - JOptionPane.QUESTION_MESSAGE, - null, - null, - getMinNotCollapseBlValue() ); - if ( !ForesterUtil.isEmpty( s ) ) { - boolean success = true; - double m = 0.0; - final String m_str = s.trim(); - if ( !ForesterUtil.isEmpty( m_str ) ) { - try { - m = Double.parseDouble( m_str ); - } - catch ( final Exception ex ) { - success = false; - } - } - else { - success = false; - } - if ( success && ( m >= 0.0 ) ) { - setMinNotCollapseBlValue( m ); - collapseBl( phy ); - } - } - } - } - } - private PhyloXmlParser createPhyloXmlParser() { PhyloXmlParser xml_parser = null; if ( getConfiguration().isValidatePhyloXmlAgainstSchema() ) { @@ -1901,6 +1427,31 @@ public final class MainFrameApplication extends MainFrame { return xml_parser; } + public void end() { + _mainpanel.terminate(); + _contentpane.removeAll(); + setVisible( false ); + dispose(); + } + + void executeLineageInference() { + if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) { + return; + } + if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) { + JOptionPane.showMessageDialog( this, + "Phylogeny is not rooted.", + "Cannot infer ancestral taxonomies", + JOptionPane.ERROR_MESSAGE ); + return; + } + final AncestralTaxonomyInferrer inferrer = new AncestralTaxonomyInferrer( this, + _mainpanel.getCurrentTreePanel(), + _mainpanel.getCurrentPhylogeny() + .copy() ); + new Thread( inferrer ).start(); + } + private void executePhyleneticInference( final boolean from_unaligned_seqs ) { final PhyloInferenceDialog dialog = new PhyloInferenceDialog( this, getPhylogeneticInferenceOptions(), @@ -1938,6 +1489,15 @@ public final class MainFrameApplication extends MainFrame { } } + void exit() { + removeAllTextFrames(); + _mainpanel.terminate(); + _contentpane.removeAll(); + setVisible( false ); + dispose(); + // System.exit( 0 ); //TODO reconfirm that this is OK, then remove. + } + private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException { final StringBuilder sb = new StringBuilder(); final StringBuilder sb_failed = new StringBuilder(); @@ -2001,38 +1561,25 @@ public final class MainFrameApplication extends MainFrame { } } - private ControlPanel getControlPanel() { - return getMainPanel().getControlPanel(); + @Override + public MainPanel getMainPanel() { + return _mainpanel; } - private File getCurrentDir() { - if ( ( _current_dir == null ) || !_current_dir.canRead() ) { - if ( ForesterUtil.isWindows() ) { - try { - _current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() ); - } - catch ( final Exception e ) { - _current_dir = null; - } - } - } - if ( ( _current_dir == null ) || !_current_dir.canRead() ) { - if ( System.getProperty( "user.home" ) != null ) { - _current_dir = new File( System.getProperty( "user.home" ) ); - } - else if ( System.getProperty( "user.dir" ) != null ) { - _current_dir = new File( System.getProperty( "user.dir" ) ); - } - } - return _current_dir; + private double getMinNotCollapseBlValue() { + return _min_not_collapse_bl; } private double getMinNotCollapseConfidenceValue() { return _min_not_collapse; } - private double getMinNotCollapseBlValue() { - return _min_not_collapse_bl; + public Msa getMsa() { + return _msa; + } + + public File getMsaFile() { + return _msa_file; } private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() { @@ -2042,6 +1589,14 @@ public final class MainFrameApplication extends MainFrame { return _phylogenetic_inference_options; } + public List getSeqs() { + return _seqs; + } + + public File getSeqsFile() { + return _seqs_file; + } + private boolean isUnsavedDataPresent() { final List tps = getMainPanel().getTreePanels(); for( final TreePanel tp : tps ) { @@ -2136,81 +1691,114 @@ public final class MainFrameApplication extends MainFrame { } } - private void print() { - if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) - || getCurrentTreePanel().getPhylogeny().isEmpty() ) { - return; - } - if ( !getOptions().isPrintUsingActualSize() ) { - getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80, - getOptions().getPrintSizeY() - 140 ); - getCurrentTreePanel().resetPreferredSize(); - getCurrentTreePanel().repaint(); - } - final String job_name = Constants.PRG_NAME; - boolean error = false; - String printer_name = null; - try { - printer_name = Printer.print( getCurrentTreePanel(), job_name ); - } - catch ( final Exception e ) { - error = true; - JOptionPane.showMessageDialog( this, e.getMessage(), "Printing Error", JOptionPane.ERROR_MESSAGE ); - } - if ( !error && ( printer_name != null ) ) { - String msg = "Printing data sent to printer"; - if ( printer_name.length() > 1 ) { - msg += " [" + printer_name + "]"; - } - JOptionPane.showMessageDialog( this, msg, "Printing...", JOptionPane.INFORMATION_MESSAGE ); - } - if ( !getOptions().isPrintUsingActualSize() ) { - getControlPanel().showWhole(); - } - } + private void preProcessTreesUponReading( final Phylogeny[] phys ) { + for( final Phylogeny phy : phys ) { + if ( ( phy != null ) && !phy.isEmpty() ) { + for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + if ( n.isExternal() ) { + if ( n.getNodeData().isHasSequence() ) { + final Sequence s = n.getNodeData().getSequence(); + if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) { + if ( ( s.getAccession() != null ) + && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) { + s.setGeneName( s.getAccession().getValue() ); + } + else if ( !ForesterUtil.isEmpty( n.getName() ) ) { + s.setGeneName( n.getName() ); + } + } + } + } + } + } + } + } + + - private void printPhylogenyToPdf( final String file_name ) { - if ( !getOptions().isPrintUsingActualSize() ) { - getCurrentTreePanel() - .calcParametersForPainting( getOptions().getPrintSizeX(), getOptions().getPrintSizeY() ); - getCurrentTreePanel().resetPreferredSize(); - getCurrentTreePanel().repaint(); + public void readMsaFromFile() { + // Set an initial directory if none set yet + final File my_dir = getCurrentDir(); + _msa_filechooser.setMultiSelectionEnabled( false ); + // Open file-open dialog and set current directory + if ( my_dir != null ) { + _msa_filechooser.setCurrentDirectory( my_dir ); } - String pdf_written_to = ""; - boolean error = false; - try { - if ( getOptions().isPrintUsingActualSize() ) { - pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, - getCurrentTreePanel(), - getCurrentTreePanel().getWidth(), - getCurrentTreePanel().getHeight() ); + final int result = _msa_filechooser.showOpenDialog( _contentpane ); + // All done: get the msa + final File file = _msa_filechooser.getSelectedFile(); + setCurrentDir( _msa_filechooser.getCurrentDirectory() ); + if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { + setMsaFile( null ); + setMsa( null ); + Msa msa = null; + try { + final InputStream is = new FileInputStream( file ); + if ( FastaParser.isLikelyFasta( file ) ) { + msa = FastaParser.parseMsa( is ); + } + else { + msa = GeneralMsaParser.parse( is ); + } } - else { - pdf_written_to = PdfExporter.writePhylogenyToPdf( file_name, getCurrentTreePanel(), getOptions() - .getPrintSizeX(), getOptions().getPrintSizeY() ); + catch ( final MsaFormatException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Multiple sequence alignment format error", + JOptionPane.ERROR_MESSAGE ); + return; } - } - catch ( final IOException e ) { - error = true; - JOptionPane.showMessageDialog( this, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE ); - } - if ( !error ) { - if ( !ForesterUtil.isEmpty( pdf_written_to ) ) { + catch ( final IOException e ) { + setArrowCursor(); JOptionPane.showMessageDialog( this, - "Wrote PDF to: " + pdf_written_to, - "Information", - JOptionPane.INFORMATION_MESSAGE ); + e.getLocalizedMessage(), + "Failed to read multiple sequence alignment", + JOptionPane.ERROR_MESSAGE ); + return; } - else { + catch ( final IllegalArgumentException e ) { + setArrowCursor(); JOptionPane.showMessageDialog( this, - "There was an unknown problem when attempting to write to PDF file: \"" - + file_name + "\"", - "Error", + e.getLocalizedMessage(), + "Unexpected error during reading of multiple sequence alignment", JOptionPane.ERROR_MESSAGE ); + return; } - } - if ( !getOptions().isPrintUsingActualSize() ) { - getControlPanel().showWhole(); + catch ( final Exception e ) { + setArrowCursor(); + e.printStackTrace(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Unexpected error during reading of multiple sequence alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( ( msa == null ) || ( msa.getNumberOfSequences() < 1 ) ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence alignment is empty", + "Illegal Multiple Sequence Alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( msa.getNumberOfSequences() < 4 ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence alignment needs to contain at least 3 sequences", + "Illegal multiple sequence alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( msa.getLength() < 2 ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence alignment needs to contain at least 2 residues", + "Illegal multiple sequence alignment", + JOptionPane.ERROR_MESSAGE ); + return; + } + System.gc(); + setMsaFile( _msa_filechooser.getSelectedFile() ); + setMsa( msa ); } } @@ -2238,8 +1826,8 @@ public final class MainFrameApplication extends MainFrame { else { _mainpanel.setWaitCursor(); } - if ( ( _open_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) - || ( _open_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) ) { + if ( ( _open_filechooser.getFileFilter() == MainFrame.nhfilter ) + || ( _open_filechooser.getFileFilter() == MainFrame.nhxfilter ) ) { try { final NHXParser nhx = new NHXParser(); setSpecialOptionsForNhxParser( nhx ); @@ -2251,7 +1839,7 @@ public final class MainFrameApplication extends MainFrame { exceptionOccuredDuringOpenFile( e ); } } - else if ( _open_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) { + else if ( _open_filechooser.getFileFilter() == MainFrame.xmlfilter ) { warnIfNotPhyloXmlValidation( getConfiguration() ); try { final PhyloXmlParser xml_parser = createPhyloXmlParser(); @@ -2262,7 +1850,7 @@ public final class MainFrameApplication extends MainFrame { exceptionOccuredDuringOpenFile( e ); } } - else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) { + else if ( _open_filechooser.getFileFilter() == MainFrame.tolfilter ) { try { phys = PhylogenyMethods.readPhylogenies( new TolParser(), file ); } @@ -2271,7 +1859,7 @@ public final class MainFrameApplication extends MainFrame { exceptionOccuredDuringOpenFile( e ); } } - else if ( _open_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) { + else if ( _open_filechooser.getFileFilter() == MainFrame.nexusfilter ) { try { final NexusPhylogeniesParser nex = new NexusPhylogeniesParser(); setSpecialOptionsForNexParser( nex ); @@ -2354,27 +1942,170 @@ public final class MainFrameApplication extends MainFrame { System.gc(); } - private void preProcessTreesUponReading( final Phylogeny[] phys ) { - for( final Phylogeny phy : phys ) { - if ( ( phy != null ) && !phy.isEmpty() ) { - for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( n.isExternal() ) { - if ( n.getNodeData().isHasSequence() ) { - final Sequence s = n.getNodeData().getSequence(); - if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) { - if ( ( s.getAccession() != null ) - && !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) { - s.setGeneName( s.getAccession().getValue() ); - } - else if ( !ForesterUtil.isEmpty( n.getName() ) ) { - s.setGeneName( n.getName() ); - } - } - } + void readPhylogeniesFromURL() { + URL url = null; + Phylogeny[] phys = null; + final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\""; + final String url_string = JOptionPane.showInputDialog( this, + message, + "Use URL/webservice to obtain a phylogeny", + JOptionPane.QUESTION_MESSAGE ); + boolean nhx_or_nexus = false; + if ( ( url_string != null ) && ( url_string.length() > 0 ) ) { + try { + url = new URL( url_string ); + PhylogenyParser parser = null; + if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) { + parser = new TolParser(); + } + else { + parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration() + .isValidatePhyloXmlAgainstSchema() ); + } + if ( parser instanceof NexusPhylogeniesParser ) { + nhx_or_nexus = true; + } + else if ( parser instanceof NHXParser ) { + nhx_or_nexus = true; + } + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().setWaitCursor(); + } + else { + _mainpanel.setWaitCursor(); + } + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + phys = factory.create( url.openStream(), parser ); + } + catch ( final MalformedURLException e ) { + JOptionPane.showMessageDialog( this, + "Malformed URL: " + url + "\n" + e.getLocalizedMessage(), + "Malformed URL", + JOptionPane.ERROR_MESSAGE ); + } + catch ( final IOException e ) { + JOptionPane.showMessageDialog( this, + "Could not read from " + url + "\n" + + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), + "Failed to read URL", + JOptionPane.ERROR_MESSAGE ); + } + catch ( final Exception e ) { + JOptionPane.showMessageDialog( this, + ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ), + "Unexpected Exception", + JOptionPane.ERROR_MESSAGE ); + } + finally { + if ( _mainpanel.getCurrentTreePanel() != null ) { + _mainpanel.getCurrentTreePanel().setArrowCursor(); + } + else { + _mainpanel.setArrowCursor(); + } + } + if ( ( phys != null ) && ( phys.length > 0 ) ) { + if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) { + for( final Phylogeny phy : phys ) { + PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" ); + } + } + AptxUtil.addPhylogeniesToTabs( phys, + new File( url.getFile() ).getName(), + new File( url.getFile() ).toString(), + getConfiguration(), + getMainPanel() ); + _mainpanel.getControlPanel().showWhole(); + } + } + activateSaveAllIfNeeded(); + System.gc(); + } + + public void readSeqsFromFileforPI() { + // Set an initial directory if none set yet + final File my_dir = getCurrentDir(); + _seqs_pi_filechooser.setMultiSelectionEnabled( false ); + // Open file-open dialog and set current directory + if ( my_dir != null ) { + _seqs_pi_filechooser.setCurrentDirectory( my_dir ); + } + final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane ); + // All done: get the seqs + final File file = _seqs_pi_filechooser.getSelectedFile(); + setCurrentDir( _seqs_pi_filechooser.getCurrentDirectory() ); + if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) { + setSeqsFile( null ); + setSeqs( null ); + List seqs = null; + try { + if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) { + seqs = FastaParser.parse( new FileInputStream( file ) ); + for( final MolecularSequence seq : seqs ) { + System.out.println( SequenceWriter.toFasta( seq, 60 ) ); } } + else { + //TODO error + } + } + catch ( final MsaFormatException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Multiple sequence file format error", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final IOException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Failed to read multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final IllegalArgumentException e ) { + setArrowCursor(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Unexpected error during reading of multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + catch ( final Exception e ) { + setArrowCursor(); + e.printStackTrace(); + JOptionPane.showMessageDialog( this, + e.getLocalizedMessage(), + "Unexpected error during reading of multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( ( seqs == null ) || ( seqs.size() < 1 ) ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence file is empty", + "Illegal multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; } + if ( seqs.size() < 4 ) { + JOptionPane.showMessageDialog( this, + "Multiple sequence file needs to contain at least 3 sequences", + "Illegal multiple sequence file", + JOptionPane.ERROR_MESSAGE ); + return; + } + // if ( msa.getLength() < 2 ) { + // JOptionPane.showMessageDialog( this, + // "Multiple sequence alignment needs to contain at least 2 residues", + // "Illegal multiple sequence file", + // JOptionPane.ERROR_MESSAGE ); + // return; + // } + System.gc(); + setSeqsFile( _seqs_pi_filechooser.getSelectedFile() ); + setSeqs( seqs ); } } @@ -2389,7 +2120,7 @@ public final class MainFrameApplication extends MainFrame { final int result = _open_filechooser_for_species_tree.showOpenDialog( _contentpane ); final File file = _open_filechooser_for_species_tree.getSelectedFile(); if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) { + if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) { try { final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser .createPhyloXmlParserXsdValidating(), file ); @@ -2400,7 +2131,7 @@ public final class MainFrameApplication extends MainFrame { exceptionOccuredDuringOpenFile( e ); } } - else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) { + else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.tolfilter ) { try { final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file ); t = trees[ 0 ]; @@ -2483,22 +2214,34 @@ public final class MainFrameApplication extends MainFrame { } } - private void setCurrentDir( final File current_dir ) { - _current_dir = current_dir; + private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) { + _min_not_collapse_bl = min_not_collapse_bl; } private void setMinNotCollapseConfidenceValue( final double min_not_collapse ) { _min_not_collapse = min_not_collapse; } - private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) { - _min_not_collapse_bl = min_not_collapse_bl; + void setMsa( final Msa msa ) { + _msa = msa; + } + + void setMsaFile( final File msa_file ) { + _msa_file = msa_file; } private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) { _phylogenetic_inference_options = phylogenetic_inference_options; } + void setSeqs( final List seqs ) { + _seqs = seqs; + } + + void setSeqsFile( final File seqs_file ) { + _seqs_file = seqs_file; + } + private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) { nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() ); nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() ); @@ -2510,470 +2253,5 @@ public final class MainFrameApplication extends MainFrame { nhx.setAllowErrorsInDistanceToParent( getOptions().isAllowErrorsInDistanceToParent() ); } - private void writeAllToFile() { - if ( ( getMainPanel().getTabbedPane() == null ) || ( getMainPanel().getTabbedPane().getTabCount() < 1 ) ) { - return; - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _save_filechooser.setCurrentDirectory( my_dir ); - } - _save_filechooser.setSelectedFile( new File( "" ) ); - final int result = _save_filechooser.showSaveDialog( _contentpane ); - final File file = _save_filechooser.getSelectedFile(); - setCurrentDir( _save_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( file.exists() ) { - final int i = JOptionPane.showConfirmDialog( this, - file + " already exists. Overwrite?", - "Warning", - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.WARNING_MESSAGE ); - if ( i != JOptionPane.OK_OPTION ) { - return; - } - else { - try { - file.delete(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - "Failed to delete: " + file, - "Error", - JOptionPane.WARNING_MESSAGE ); - } - } - } - final int count = getMainPanel().getTabbedPane().getTabCount(); - final List trees = new ArrayList(); - for( int i = 0; i < count; ++i ) { - final Phylogeny phy = getMainPanel().getPhylogeny( i ); - if ( ForesterUtil.isEmpty( phy.getName() ) - && !ForesterUtil.isEmpty( getMainPanel().getTabbedPane().getTitleAt( i ) ) ) { - phy.setName( getMainPanel().getTabbedPane().getTitleAt( i ) ); - } - trees.add( phy ); - getMainPanel().getTreePanels().get( i ).setEdited( false ); - } - final PhylogenyWriter writer = new PhylogenyWriter(); - try { - writer.toPhyloXML( file, trees, 0, ForesterUtil.LINE_SEPARATOR ); - } - catch ( final IOException e ) { - JOptionPane.showMessageDialog( this, - "Failed to write to: " + file, - "Error", - JOptionPane.WARNING_MESSAGE ); - } - } - } - - private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) { - try { - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toNewHampshire( t, true, getOptions().getNhConversionSupportValueStyle(), file ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringSaveAs( e ); - } - return exception; - } - - private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) { - try { - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringSaveAs( e ); - } - return exception; - } - - private boolean writeAsPhyloXml( final Phylogeny t, boolean exception, final File file ) { - try { - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toPhyloXML( file, t, 0 ); - } - catch ( final Exception e ) { - exception = true; - exceptionOccuredDuringSaveAs( e ); - } - return exception; - } - - private void writeToFile( final Phylogeny t ) { - if ( t == null ) { - return; - } - String initial_filename = null; - if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { - try { - initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().getCanonicalPath(); - } - catch ( final IOException e ) { - initial_filename = null; - } - } - if ( !ForesterUtil.isEmpty( initial_filename ) ) { - _save_filechooser.setSelectedFile( new File( initial_filename ) ); - } - else { - _save_filechooser.setSelectedFile( new File( "" ) ); - } - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _save_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _save_filechooser.showSaveDialog( _contentpane ); - final File file = _save_filechooser.getSelectedFile(); - setCurrentDir( _save_filechooser.getCurrentDirectory() ); - boolean exception = false; - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( file.exists() ) { - final int i = JOptionPane.showConfirmDialog( this, - file + " already exists.\nOverwrite?", - "Overwrite?", - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.QUESTION_MESSAGE ); - if ( i != JOptionPane.OK_OPTION ) { - return; - } - else { - final File to = new File( file.getAbsoluteFile().toString() + Constants.BACKUP_FILE_SUFFIX ); - try { - ForesterUtil.copyFile( file, to ); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - "Failed to create backup copy " + to, - "Failed to Create Backup Copy", - JOptionPane.WARNING_MESSAGE ); - } - try { - file.delete(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - "Failed to delete: " + file, - "Failed to Delete", - JOptionPane.WARNING_MESSAGE ); - } - } - } - if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) { - exception = writeAsNewHampshire( t, exception, file ); - } - else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) { - exception = writeAsPhyloXml( t, exception, file ); - } - else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nexusfilter ) { - exception = writeAsNexus( t, exception, file ); - } - // "*.*": - else { - final String file_name = file.getName().trim().toLowerCase(); - if ( file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) - || file_name.endsWith( ".tree" ) ) { - exception = writeAsNewHampshire( t, exception, file ); - } - else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) { - exception = writeAsNexus( t, exception, file ); - } - // XML is default: - else { - exception = writeAsPhyloXml( t, exception, file ); - } - } - if ( !exception ) { - getMainPanel().setTitleOfSelectedTab( file.getName() ); - getMainPanel().getCurrentTreePanel().setTreeFile( file ); - getMainPanel().getCurrentTreePanel().setEdited( false ); - } - } - } - - private void writeToGraphicsFile( final Phylogeny t, final GraphicsExportType type ) { - if ( ( t == null ) || t.isEmpty() ) { - return; - } - String initial_filename = ""; - if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { - initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString(); - } - if ( initial_filename.indexOf( '.' ) > 0 ) { - initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); - } - initial_filename = initial_filename + "." + type; - _writetographics_filechooser.setSelectedFile( new File( initial_filename ) ); - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _writetographics_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _writetographics_filechooser.showSaveDialog( _contentpane ); - File file = _writetographics_filechooser.getSelectedFile(); - setCurrentDir( _writetographics_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( !file.toString().toLowerCase().endsWith( type.toString() ) ) { - file = new File( file.toString() + "." + type ); - } - if ( file.exists() ) { - final int i = JOptionPane.showConfirmDialog( this, - file + " already exists. Overwrite?", - "Warning", - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.WARNING_MESSAGE ); - if ( i != JOptionPane.OK_OPTION ) { - return; - } - else { - try { - file.delete(); - } - catch ( final Exception e ) { - JOptionPane.showMessageDialog( this, - "Failed to delete: " + file, - "Error", - JOptionPane.WARNING_MESSAGE ); - } - } - } - writePhylogenyToGraphicsFile( file.toString(), type ); - } - } - - private void writeToPdf( final Phylogeny t ) { - if ( ( t == null ) || t.isEmpty() ) { - return; - } - String initial_filename = ""; - if ( getMainPanel().getCurrentTreePanel().getTreeFile() != null ) { - initial_filename = getMainPanel().getCurrentTreePanel().getTreeFile().toString(); - } - if ( initial_filename.indexOf( '.' ) > 0 ) { - initial_filename = initial_filename.substring( 0, initial_filename.lastIndexOf( '.' ) ); - } - initial_filename = initial_filename + ".pdf"; - _writetopdf_filechooser.setSelectedFile( new File( initial_filename ) ); - final File my_dir = getCurrentDir(); - if ( my_dir != null ) { - _writetopdf_filechooser.setCurrentDirectory( my_dir ); - } - final int result = _writetopdf_filechooser.showSaveDialog( _contentpane ); - File file = _writetopdf_filechooser.getSelectedFile(); - setCurrentDir( _writetopdf_filechooser.getCurrentDirectory() ); - if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) { - if ( !file.toString().toLowerCase().endsWith( ".pdf" ) ) { - file = new File( file.toString() + ".pdf" ); - } - if ( file.exists() ) { - final int i = JOptionPane.showConfirmDialog( this, - file + " already exists. Overwrite?", - "WARNING", - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.WARNING_MESSAGE ); - if ( i != JOptionPane.OK_OPTION ) { - return; - } - } - printPhylogenyToPdf( file.toString() ); - } - } - - public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) { - return new MainFrameApplication( phys, config ); - } - - public static MainFrame createInstance( final Phylogeny[] phys, - final Configuration config, - final String title, - final File current_dir ) { - return new MainFrameApplication( phys, config, title, current_dir ); - } - - static MainFrame createInstance( final Phylogeny[] phys, final Configuration config, final String title ) { - return new MainFrameApplication( phys, config, title ); - } - - static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) { - return new MainFrameApplication( phys, config_file_name, title ); - } - - static void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) { - mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", " - + o.getPrintSizeY() + ")" ); - } - - static void setTextForPdfLineWidthChooserMenuItem( final JMenuItem mi, final Options o ) { - mi.setText( "Enter Default Line Width for PDF Export... (current: " + o.getPrintLineWidth() + ")" ); - } - - static void warnIfNotPhyloXmlValidation( final Configuration c ) { - if ( !c.isValidatePhyloXmlAgainstSchema() ) { - JOptionPane - .showMessageDialog( null, - ForesterUtil - .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]", - 80 ), - "Warning", - JOptionPane.WARNING_MESSAGE ); - } - } + } // MainFrameApplication. - -class DefaultFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) - || file_name.endsWith( ".nwk" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".ph" ) - || file_name.endsWith( ".tr" ) || file_name.endsWith( ".dnd" ) || file_name.endsWith( ".tree" ) - || file_name.endsWith( ".nhx" ) || file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) - || file_name.endsWith( "phylo.xml" ) || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".nexus" ) - || file_name.endsWith( ".nx" ) || file_name.endsWith( ".nex" ) || file_name.endsWith( ".tre" ) - || file_name.endsWith( ".zip" ) || file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) - || file_name.endsWith( ".con" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "All supported files (*.xml, *.phyloxml, *phylo.xml, *.nhx, *.nh, *.newick, *.nex, *.nexus, *.phy, *.tre, *.tree, *.tol, ...)"; - } -} - -class GraphicsFileFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".jpg" ) || file_name.endsWith( ".jpeg" ) || file_name.endsWith( ".png" ) - || file_name.endsWith( ".gif" ) || file_name.endsWith( ".bmp" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "Image files (*.jpg, *.jpeg, *.png, *.gif, *.bmp)"; - } -} - -class MsaFileFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".msa" ) || file_name.endsWith( ".aln" ) || file_name.endsWith( ".fasta" ) - || file_name.endsWith( ".fas" ) || file_name.endsWith( ".fa" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "Multiple sequence alignment files (*.msa, *.aln, *.fasta, *.fa, *.fas)"; - } -} - -class NexusFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) || file_name.endsWith( ".nx" ) - || file_name.endsWith( ".tre" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "Nexus files (*.nex, *.nexus, *.nx, *.tre)"; - } -} // NexusFilter - -class NHFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".nh" ) || file_name.endsWith( ".newick" ) || file_name.endsWith( ".phy" ) - || file_name.endsWith( ".tr" ) || file_name.endsWith( ".tree" ) || file_name.endsWith( ".dnd" ) - || file_name.endsWith( ".ph" ) || file_name.endsWith( ".phb" ) || file_name.endsWith( ".nwk" ) - || f.isDirectory(); - } - - @Override - public String getDescription() { - return "New Hampshire - Newick files (*.nh, *.newick, *.phy, *.tree, *.dnd, *.tr, *.ph, *.phb, *.nwk)"; - } -} // NHFilter - -class NHXFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".nhx" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "NHX files (*.nhx) [deprecated]"; - } -} - -class PdfFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - return f.getName().trim().toLowerCase().endsWith( ".pdf" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "PDF files (*.pdf)"; - } -} // PdfFilter - -class SequencesFileFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".fasta" ) || file_name.endsWith( ".fa" ) || file_name.endsWith( ".fas" ) - || file_name.endsWith( ".seqs" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "Sequences files (*.fasta, *.fa, *.fas, *.seqs )"; - } -} - -class TolFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return ( file_name.endsWith( ".tol" ) || file_name.endsWith( ".tolxml" ) || file_name.endsWith( ".zip" ) || f - .isDirectory() ) && ( !file_name.endsWith( ".xml.zip" ) ); - } - - @Override - public String getDescription() { - return "Tree of Life files (*.tol, *.tolxml)"; - } -} // TolFilter - -class XMLFilter extends FileFilter { - - @Override - public boolean accept( final File f ) { - final String file_name = f.getName().trim().toLowerCase(); - return file_name.endsWith( ".xml" ) || file_name.endsWith( ".phyloxml" ) || file_name.endsWith( "phylo.xml" ) - || file_name.endsWith( ".pxml" ) || file_name.endsWith( ".zip" ) || f.isDirectory(); - } - - @Override - public String getDescription() { - return "phyloXML files (*.xml, *.phyloxml, *phylo.xml, *.pxml, *.zip)"; - } -} // XMLFilter