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=2ccf1eb18fe0b885eb88ea4a532b67532aac55ae;hpb=baa7e9117411d330ce57667fdc4a60086ef0951e;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 2ccf1eb..e2f4737 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -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(); @@ -268,7 +270,6 @@ public final class MainFrameApplication extends MainFrame { catch ( final IllegalAccessException e ) { AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() ); } - if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) { setCurrentDir( current_dir ); } @@ -303,7 +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() ); @@ -319,16 +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() ) { @@ -392,11 +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() ); } } } ); @@ -501,6 +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(); } @@ -508,7 +518,7 @@ public final class MainFrameApplication extends MainFrame { moveNodeNamesToSeqNames(); } else if ( o == _extract_tax_code_from_node_names_jmi ) { - extractTaxCodeFromNodeNames(); + extractTaxDataFromNodeNames(); } else if ( o == _gsdi_item ) { if ( isSubtreeDisplayed() ) { @@ -646,12 +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", @@ -659,12 +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", @@ -672,12 +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", @@ -685,12 +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(), @@ -725,18 +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 ); @@ -753,12 +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", @@ -766,12 +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", @@ -779,12 +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", @@ -792,12 +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(), @@ -827,7 +797,7 @@ public final class MainFrameApplication extends MainFrame { // return; // } System.gc(); - setSeqsFile( _seqs_filechooser.getSelectedFile() ); + setSeqsFile( _seqs_pi_filechooser.getSelectedFile() ); setSeqs( seqs ); } } @@ -964,7 +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 ) ); @@ -1035,7 +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 ); @@ -1131,17 +1107,17 @@ public final class MainFrameApplication extends MainFrame { .setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" ); _tools_menu.addSeparator(); _tools_menu + .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) ); + customizeJMenuItem( _extract_tax_code_from_node_names_jmi ); + _extract_tax_code_from_node_names_jmi + .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" ); + _tools_menu .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) ); customizeJMenuItem( _move_node_names_to_tax_sn_jmi ); _move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" ); _tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) ); customizeJMenuItem( _move_node_names_to_seq_names_jmi ); _move_node_names_to_seq_names_jmi.setToolTipText( "To interpret node names as sequence (protein, gene) names" ); - _tools_menu - .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Codes from Node Names" ) ); - customizeJMenuItem( _extract_tax_code_from_node_names_jmi ); - _extract_tax_code_from_node_names_jmi - .setToolTipText( "To extract taxonomic codes (mnemonics) from nodes names in the form of 'xyz_ECOLI'" ); _tools_menu.addSeparator(); _tools_menu .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) ); @@ -1164,9 +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 ); } @@ -1266,9 +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 ); @@ -1283,10 +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 ); } @@ -1477,9 +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 { @@ -1513,6 +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, @@ -1872,22 +2013,64 @@ public final class MainFrameApplication extends MainFrame { } } - private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException { + private void extractTaxDataFromNodeNames() throws PhyloXmlDataFormatException { + final StringBuilder sb = new StringBuilder(); + final StringBuilder sb_failed = new StringBuilder(); + int counter = 0; + int counter_failed = 0; if ( getCurrentTreePanel() != null ) { final Phylogeny phy = getCurrentTreePanel().getPhylogeny(); if ( ( phy != null ) && !phy.isEmpty() ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); + final PhylogenyNodeIterator it = phy.iteratorExternalForward(); while ( it.hasNext() ) { final PhylogenyNode n = it.next(); final String name = n.getName().trim(); if ( !ForesterUtil.isEmpty( name ) ) { - final String code = ParserUtils - .extractTaxonomyCodeFromNodeName( name, NHXParser.TAXONOMY_EXTRACTION.YES ); - if ( !ForesterUtil.isEmpty( code ) ) { - PhylogenyMethods.setTaxonomyCode( n, code ); + final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.YES ); + if ( !ForesterUtil.isEmpty( nt ) ) { + if ( counter < 15 ) { + sb.append( name + ": " + nt + "\n" ); + } + else if ( counter == 15 ) { + sb.append( "...\n" ); + } + counter++; + } + else { + if ( counter_failed < 15 ) { + sb_failed.append( name + "\n" ); + } + else if ( counter_failed == 15 ) { + sb_failed.append( "...\n" ); + } + counter_failed++; } } } + if ( counter > 0 ) { + String failed = ""; + String all = "all "; + if ( counter_failed > 0 ) { + all = ""; + failed = "\nCould not extract taxonomic data for " + counter_failed + + " named external nodes:\n" + sb_failed; + } + JOptionPane.showMessageDialog( this, + "Extracted taxonomic data from " + all + counter + + " named external nodes:\n" + sb.toString() + failed, + "Taxonomic Data Extraction Completed", + counter_failed > 0 ? JOptionPane.WARNING_MESSAGE + : JOptionPane.INFORMATION_MESSAGE ); + } + else { + JOptionPane + .showMessageDialog( this, + "Could not extract any taxonomic data.\nMaybe node names are empty\n" + + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n" + + "or nodes already have taxonomic data?\n", + "No Taxonomic Data Extracted", + JOptionPane.ERROR_MESSAGE ); + } } } } @@ -2029,9 +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(); } @@ -2059,9 +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(); } @@ -2433,18 +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(); @@ -2519,9 +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 ); } @@ -2535,9 +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 ); } @@ -2775,7 +2940,7 @@ class NHXFilter extends FileFilter { @Override public String getDescription() { - return "NHX files (*.nhx)"; + return "NHX files (*.nhx) [deprecated]"; } }