X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FMainFrameApplication.java;h=e2f47379672135ab125ac1a1f4294de9b961f4cc;hb=a29d5642b2f9a3db526f35ca5971c08700963503;hp=ca14a87a3364b7216ac8b74e1f724895d01589c4;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index ca14a87..e2f4737 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -129,9 +129,10 @@ public final class MainFrameApplication extends MainFrame { private final static DefaultFilter defaultfilter = new DefaultFilter(); private static final long serialVersionUID = -799735726778865234L; private final JFileChooser _values_filechooser; + private final JFileChooser _sequences_filechooser; private final JFileChooser _open_filechooser; private final JFileChooser _msa_filechooser; - private final JFileChooser _seqs_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; @@ -169,8 +170,8 @@ public final class MainFrameApplication extends MainFrame { private File _msa_file = null; private List _seqs = null; private File _seqs_file = null; - // expression values menu: JMenuItem _read_values_jmi; + JMenuItem _read_seqs_jmi; private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) { _configuration = config; @@ -186,8 +187,9 @@ public final class MainFrameApplication extends MainFrame { _writetopdf_filechooser = null; _writetographics_filechooser = null; _msa_filechooser = null; - _seqs_filechooser = null; + _seqs_pi_filechooser = null; _values_filechooser = null; + _sequences_filechooser = null; _jmenubar = new JMenuBar(); buildFileMenu(); buildTypeMenu(); @@ -302,7 +304,6 @@ public final class MainFrameApplication extends MainFrame { _save_filechooser.setCurrentDirectory( new File( "." ) ); _save_filechooser.setMultiSelectionEnabled( false ); _save_filechooser.setFileFilter( MainFrameApplication.xmlfilter ); - _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhxfilter ); _save_filechooser.addChoosableFileFilter( MainFrameApplication.nhfilter ); _save_filechooser.addChoosableFileFilter( MainFrameApplication.nexusfilter ); _save_filechooser.addChoosableFileFilter( _save_filechooser.getAcceptAllFileFilter() ); @@ -318,16 +319,20 @@ public final class MainFrameApplication extends MainFrame { _msa_filechooser.addChoosableFileFilter( _msa_filechooser.getAcceptAllFileFilter() ); _msa_filechooser.addChoosableFileFilter( MainFrameApplication.msafilter ); // Seqs: - _seqs_filechooser = new JFileChooser(); - _seqs_filechooser.setName( "Read Sequences File" ); - _seqs_filechooser.setCurrentDirectory( new File( "." ) ); - _seqs_filechooser.setMultiSelectionEnabled( false ); - _seqs_filechooser.addChoosableFileFilter( _seqs_filechooser.getAcceptAllFileFilter() ); - _seqs_filechooser.addChoosableFileFilter( MainFrameApplication.seqsfilter ); + _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 ); // Expression _values_filechooser = new JFileChooser(); _values_filechooser.setCurrentDirectory( new File( "." ) ); _values_filechooser.setMultiSelectionEnabled( false ); + // Sequences + _sequences_filechooser = new JFileChooser(); + _sequences_filechooser.setCurrentDirectory( new File( "." ) ); + _sequences_filechooser.setMultiSelectionEnabled( false ); // build the menu bar _jmenubar = new JMenuBar(); if ( !_configuration.isUseNativeUI() ) { @@ -391,11 +396,11 @@ public final class MainFrameApplication extends MainFrame { @Override public void componentResized( final ComponentEvent e ) { if ( _mainpanel.getCurrentTreePanel() != null ) { - _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel() - .getWidth(), - _mainpanel.getCurrentTreePanel() - .getHeight(), - false ); + _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel() + .getWidth(), + _mainpanel.getCurrentTreePanel() + .getHeight(), + getOptions().isAllowFontSizeChange() ); } } } ); @@ -500,6 +505,12 @@ public final class MainFrameApplication extends MainFrame { } addExpressionValuesFromFile(); } + else if ( o == _read_seqs_jmi ) { + if ( isSubtreeDisplayed() ) { + return; + } + addSequencesFromFile(); + } else if ( o == _move_node_names_to_tax_sn_jmi ) { moveNodeNamesToTaxSn(); } @@ -645,12 +656,7 @@ public final class MainFrameApplication extends MainFrame { } } catch ( final MsaFormatException e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } + setArrowCursor(); JOptionPane.showMessageDialog( this, e.getLocalizedMessage(), "Multiple sequence alignment format error", @@ -658,12 +664,7 @@ public final class MainFrameApplication extends MainFrame { return; } catch ( final IOException e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } + setArrowCursor(); JOptionPane.showMessageDialog( this, e.getLocalizedMessage(), "Failed to read multiple sequence alignment", @@ -671,12 +672,7 @@ public final class MainFrameApplication extends MainFrame { return; } catch ( final IllegalArgumentException e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } + setArrowCursor(); JOptionPane.showMessageDialog( this, e.getLocalizedMessage(), "Unexpected error during reading of multiple sequence alignment", @@ -684,12 +680,7 @@ public final class MainFrameApplication extends MainFrame { return; } catch ( final Exception e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } + setArrowCursor(); e.printStackTrace(); JOptionPane.showMessageDialog( this, e.getLocalizedMessage(), @@ -724,18 +715,18 @@ public final class MainFrameApplication extends MainFrame { } } - public void readSeqsFromFile() { + public void readSeqsFromFileforPI() { // Set an initial directory if none set yet final File my_dir = getCurrentDir(); - _seqs_filechooser.setMultiSelectionEnabled( false ); + _seqs_pi_filechooser.setMultiSelectionEnabled( false ); // Open file-open dialog and set current directory if ( my_dir != null ) { - _seqs_filechooser.setCurrentDirectory( my_dir ); + _seqs_pi_filechooser.setCurrentDirectory( my_dir ); } - final int result = _seqs_filechooser.showOpenDialog( _contentpane ); + final int result = _seqs_pi_filechooser.showOpenDialog( _contentpane ); // All done: get the seqs - final File file = _seqs_filechooser.getSelectedFile(); - setCurrentDir( _seqs_filechooser.getCurrentDirectory() ); + 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 ); @@ -752,12 +743,7 @@ public final class MainFrameApplication extends MainFrame { } } catch ( final MsaFormatException e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } + setArrowCursor(); JOptionPane.showMessageDialog( this, e.getLocalizedMessage(), "Multiple sequence file format error", @@ -765,12 +751,7 @@ public final class MainFrameApplication extends MainFrame { return; } catch ( final IOException e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } + setArrowCursor(); JOptionPane.showMessageDialog( this, e.getLocalizedMessage(), "Failed to read multiple sequence file", @@ -778,12 +759,7 @@ public final class MainFrameApplication extends MainFrame { return; } catch ( final IllegalArgumentException e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } + setArrowCursor(); JOptionPane.showMessageDialog( this, e.getLocalizedMessage(), "Unexpected error during reading of multiple sequence file", @@ -791,12 +767,7 @@ public final class MainFrameApplication extends MainFrame { return; } catch ( final Exception e ) { - try { - _mainpanel.getCurrentTreePanel().setArrowCursor(); - } - catch ( final Exception ex ) { - // Do nothing. - } + setArrowCursor(); e.printStackTrace(); JOptionPane.showMessageDialog( this, e.getLocalizedMessage(), @@ -826,7 +797,7 @@ public final class MainFrameApplication extends MainFrame { // return; // } System.gc(); - setSeqsFile( _seqs_filechooser.getSelectedFile() ); + setSeqsFile( _seqs_pi_filechooser.getSelectedFile() ); setSeqs( seqs ); } } @@ -963,7 +934,10 @@ public final class MainFrameApplication extends MainFrame { _options_jmenu .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) ); - _options_jmenu.add( _show_default_node_shapes_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL ) ); + _options_jmenu + .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) ); + _options_jmenu + .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) ); _options_jmenu .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) ); _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) ); @@ -1034,7 +1008,10 @@ public final class MainFrameApplication extends MainFrame { customizeJMenuItem( _print_size_mi ); customizeJMenuItem( _choose_pdf_width_mi ); customizeJMenuItem( _overview_placment_mi ); - customizeCheckBoxMenuItem( _show_default_node_shapes_cbmi, getOptions().isShowDefaultNodeShapes() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() + .isShowDefaultNodeShapesExternal() ); + customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() + .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); @@ -1163,9 +1140,14 @@ public final class MainFrameApplication extends MainFrame { .setToolTipText( "To add UniProtKB annotations for sequences with appropriate identifiers" ); _tools_menu.addSeparator(); } - _tools_menu.add( _read_values_jmi = new JMenuItem( "Read Vector/Expression Values" ) ); + _tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) ); customizeJMenuItem( _read_values_jmi ); - _read_values_jmi.setToolTipText( "To add vector (e.g. gene expression) values (beta)" ); + _read_values_jmi.setToolTipText( "To attach vector (e.g. gene expression) values to tree nodes (beta)" ); + _jmenubar.add( _tools_menu ); + _tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) ); + customizeJMenuItem( _read_seqs_jmi ); + _read_seqs_jmi + .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" ); _jmenubar.add( _tools_menu ); } @@ -1265,9 +1247,7 @@ public final class MainFrameApplication extends MainFrame { AptxUtil.unexpectedException( e ); return; } - final List assigned_trees = gsdir.getMinDuplicationsSumGeneTrees(); - final List shortests = GSDIR.getIndexesOfShortestTree( assigned_trees ); - final Phylogeny result_gene_tree = assigned_trees.get( shortests.get( 0 ) ); + final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree(); result_gene_tree.setRerootable( false ); result_gene_tree.clearHashIdToNodeMap(); result_gene_tree.recalculateNumberOfExternalDescendants( true ); @@ -1282,10 +1262,7 @@ public final class MainFrameApplication extends MainFrame { _mainpanel.getCurrentTreePanel().setEdited( true ); JOptionPane.showMessageDialog( this, "Duplications (min): " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: " - + gsdir.getSpeciationsSum() + "\n" - + "Number of root positions minimizing duplications sum: " - + gsdir.getMinDuplicationsSumGeneTrees().size() + "\n" - + "Number of shortest trees: " + shortests.size(), + + gsdir.getSpeciationsSum(), "GSDIR successfully completed", JOptionPane.INFORMATION_MESSAGE ); } @@ -1476,9 +1453,9 @@ public final class MainFrameApplication extends MainFrame { } void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) { - _mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), - _mainpanel.getCurrentTreePanel().getHeight(), - true ); + _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(), + _mainpanel.getCurrentTreePanel().getHeight(), + true ); String file_written_to = ""; boolean error = false; try { @@ -1512,6 +1489,171 @@ public final class MainFrameApplication extends MainFrame { _contentpane.repaint(); } + 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 Sequence seq : seqs ) { + System.out.println( seq.getIdentifier() ); + } + final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); + int total_counter = 0; + int attached_counter = 0; + for( final Sequence 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.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 ); + } + } + } + + private void setArrowCursor() { + try { + _mainpanel.getCurrentTreePanel().setArrowCursor(); + } + catch ( final Exception ex ) { + // Do nothing. + } + } + private void addExpressionValuesFromFile() { if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) { JOptionPane.showMessageDialog( this, @@ -2070,9 +2212,9 @@ public final class MainFrameApplication extends MainFrame { return; } if ( !getOptions().isPrintUsingActualSize() ) { - getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX() - 80, - getOptions().getPrintSizeY() - 140, - true ); + getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX() - 80, + getOptions().getPrintSizeY() - 140, + true ); getCurrentTreePanel().resetPreferredSize(); getCurrentTreePanel().repaint(); } @@ -2100,9 +2242,9 @@ public final class MainFrameApplication extends MainFrame { private void printPhylogenyToPdf( final String file_name ) { if ( !getOptions().isPrintUsingActualSize() ) { - getCurrentTreePanel().setParametersForPainting( getOptions().getPrintSizeX(), - getOptions().getPrintSizeY(), - true ); + getCurrentTreePanel().calcParametersForPainting( getOptions().getPrintSizeX(), + getOptions().getPrintSizeY(), + true ); getCurrentTreePanel().resetPreferredSize(); getCurrentTreePanel().repaint(); } @@ -2474,18 +2616,6 @@ public final class MainFrameApplication extends MainFrame { return exception; } - private boolean writeAsNHX( final Phylogeny t, boolean exception, final File file ) { - try { - final PhylogenyWriter writer = new PhylogenyWriter(); - writer.toNewHampshireX( t, file ); - } - 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(); @@ -2560,9 +2690,6 @@ public final class MainFrameApplication extends MainFrame { if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhfilter ) { exception = writeAsNewHampshire( t, exception, file ); } - else if ( _save_filechooser.getFileFilter() == MainFrameApplication.nhxfilter ) { - exception = writeAsNHX( t, exception, file ); - } else if ( _save_filechooser.getFileFilter() == MainFrameApplication.xmlfilter ) { exception = writeAsPhyloXml( t, exception, file ); } @@ -2576,9 +2703,6 @@ public final class MainFrameApplication extends MainFrame { || file_name.endsWith( ".tree" ) ) { exception = writeAsNewHampshire( t, exception, file ); } - else if ( file_name.endsWith( ".nhx" ) ) { - exception = writeAsNHX( t, exception, file ); - } else if ( file_name.endsWith( ".nex" ) || file_name.endsWith( ".nexus" ) ) { exception = writeAsNexus( t, exception, file ); } @@ -2816,7 +2940,7 @@ class NHXFilter extends FileFilter { @Override public String getDescription() { - return "NHX files (*.nhx)"; + return "NHX files (*.nhx) [deprecated]"; } }