import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
-import org.forester.archaeopteryx.tools.GoAnnotation;
import org.forester.archaeopteryx.tools.InferenceManager;
import org.forester.archaeopteryx.tools.PhyloInferenceDialog;
import org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.sdi.GSDI;
-import org.forester.sdi.GSDIR;
-import org.forester.sdi.SDIException;
-import org.forester.sdi.SDIR;
import org.forester.sequence.Sequence;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
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;
private final JFileChooser _writetographics_filechooser;
- // Analysis menu
- private JMenu _analysis_menu;
- private JMenuItem _load_species_tree_item;
- private JMenuItem _gsdi_item;
- private JMenuItem _gsdir_item;
- private JMenuItem _root_min_dups_item;
- private JMenuItem _root_min_cost_l_item;
- private JMenuItem _lineage_inference;
- private JMenuItem _function_analysis;
// Application-only print menu items
private JMenuItem _print_item;
private JMenuItem _write_to_pdf_item;
private JMenuItem _write_to_tif_item;
private JMenuItem _write_to_png_item;
private JMenuItem _write_to_bmp_item;
- private Phylogeny _species_tree;
private File _current_dir;
private ButtonGroup _radio_group_1;
private ButtonGroup _radio_group_2;
private File _msa_file = null;
private List<Sequence> _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;
_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();
setInferenceManager( InferenceManager.createInstance( _configuration ) );
setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
// _textframe = null; #~~~~
- _species_tree = null;
// set title
setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
_mainpanel = new MainPanel( _configuration, this );
_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() ) {
@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() );
}
}
} );
}
executeLineageInference();
}
- else if ( o == _function_analysis ) {
- executeFunctionAnalysis();
- }
else if ( o == _obtain_detailed_taxonomic_information_jmi ) {
if ( isSubtreeDisplayed() ) {
return;
}
addExpressionValuesFromFile();
}
+ else if ( o == _read_seqs_jmi ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ addSequencesFromFile();
+ }
else if ( o == _move_node_names_to_tax_sn_jmi ) {
moveNodeNamesToTaxSn();
}
else if ( o == _extract_tax_code_from_node_names_jmi ) {
extractTaxDataFromNodeNames();
}
- else if ( o == _gsdi_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- executeGSDI();
- }
- else if ( o == _gsdir_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- executeGSDIR();
- }
- else if ( o == _root_min_dups_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- executeSDIR( false );
- }
- else if ( o == _root_min_cost_l_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- executeSDIR( true );
- }
else if ( o == _graphics_export_visible_only_cbmi ) {
updateOptions( getOptions() );
}
}
collapseBelowThreshold();
}
- else if ( ( o == _extract_taxonomy_pfam_rbmi ) || ( o == _extract_taxonomy_yes_rbmi ) ) {
+ else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )
+ || ( o == _extract_taxonomy_agressive_rbmi ) ) {
if ( _replace_underscores_cbmi != null ) {
_replace_underscores_cbmi.setSelected( false );
}
updateOptions( getOptions() );
}
+ else if ( o == _extract_taxonomy_no_rbmi ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _inference_from_msa_item ) {
executePhyleneticInference( false );
}
}
}
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",
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",
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",
return;
}
catch ( final Exception e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
e.printStackTrace();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
}
}
- 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 );
}
}
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",
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",
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",
return;
}
catch ( final Exception e ) {
- try {
- _mainpanel.getCurrentTreePanel().setArrowCursor();
- }
- catch ( final Exception ex ) {
- // Do nothing.
- }
+ setArrowCursor();
e.printStackTrace();
JOptionPane.showMessageDialog( this,
e.getLocalizedMessage(),
// return;
// }
System.gc();
- setSeqsFile( _seqs_filechooser.getSelectedFile() );
+ setSeqsFile( _seqs_pi_filechooser.getSelectedFile() );
setSeqs( seqs );
}
}
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
_analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
- _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (re-rooting)" ) );
- _analysis_menu.addSeparator();
- _analysis_menu.add( _root_min_dups_item = new JMenuItem( "Root by Minimizing Duplications | Height (SDI)" ) );
- _analysis_menu.add( _root_min_cost_l_item = new JMenuItem( "Root by Minimizing Cost L | Height (SDI)" ) );
- _analysis_menu.addSeparator();
+ _analysis_menu.add( _gsdir_item = new JMenuItem( "GSDIR (GSDI with re-rooting)" ) );
_analysis_menu.add( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
customizeJMenuItem( _gsdi_item );
customizeJMenuItem( _gsdir_item );
- customizeJMenuItem( _root_min_dups_item );
- customizeJMenuItem( _root_min_cost_l_item );
customizeJMenuItem( _load_species_tree_item );
_analysis_menu.addSeparator();
_analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
_radio_group_1.add( _uniform_cladograms_rbmi );
_radio_group_1.add( _non_lined_up_cladograms_rbmi );
+ ///////
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );
+ _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 ) );
+ if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
+ }
+ _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_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( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) );
_options_jmenu
.add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) );
- _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
- _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
- _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
- _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
- _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
_options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) );
_color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP );
_options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) );
+ _options_jmenu.add( _label_direction_cbmi = new JCheckBoxMenuItem( LABEL_DIRECTION_LABEL ) );
+ _label_direction_cbmi.setToolTipText( LABEL_DIRECTION_TIP );
_options_jmenu.add( _screen_antialias_cbmi = new JCheckBoxMenuItem( SCREEN_ANTIALIAS_LABEL ) );
_options_jmenu.add( _background_gradient_cbmi = new JCheckBoxMenuItem( BG_GRAD_LABEL ) );
- if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );
- }
+ _options_jmenu.add( _cycle_node_shape_mi = new JMenuItem( MainFrame.CYCLE_NODE_SHAPE_LABEL ) );
+ _options_jmenu.add( _cycle_node_fill_mi = new JMenuItem( MainFrame.CYCLE_NODE_FILL_LABEL ) );
+ _options_jmenu.add( _choose_node_size_mi = new JMenuItem( MainFrame.CHOOSE_NODE_SIZE_LABEL ) );
_options_jmenu.add( _choose_minimal_confidence_mi = new JMenuItem( "" ) );
_options_jmenu.add( _overview_placment_mi = new JMenuItem( "" ) );
_options_jmenu.add( _switch_colors_mi = new JMenuItem( "" ) );
_options_jmenu.add( _choose_font_mi = new JMenuItem( "" ) );
+ ///////
_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( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
_options_jmenu
- .add( _extract_taxonomy_pfam_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Pfam-style Node Names" ) );
- _extract_taxonomy_pfam_rbmi
- .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE/134-298\"" );
+ .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
_options_jmenu
- .add( _extract_taxonomy_yes_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes from Node Names" ) );
- _extract_taxonomy_yes_rbmi
- .setToolTipText( "To extract 5-letter taxonomy codes from node names in the form of \"BCL2_MOUSE\" or \"BCL2_MOUSE B-cell lymphoma 2...\"" );
+ .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
+ _options_jmenu
+ .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
+ _extract_taxonomy_pfam_strict_rbmi
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
+ _extract_taxonomy_pfam_relaxed_rbmi
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
+ _extract_taxonomy_agressive_rbmi
+ .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
_radio_group_2 = new ButtonGroup();
_radio_group_2.add( _extract_taxonomy_no_rbmi );
- _radio_group_2.add( _extract_taxonomy_pfam_rbmi );
- _radio_group_2.add( _extract_taxonomy_yes_rbmi );
+ _radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
+ _radio_group_2.add( _extract_taxonomy_pfam_relaxed_rbmi );
+ _radio_group_2.add( _extract_taxonomy_agressive_rbmi );
//
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
_options_jmenu
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 );
customizeJMenuItem( _choose_node_size_mi );
customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
+ customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
customizeCheckBoxMenuItem( _show_domain_labels, getOptions().isShowDomainLabels() );
+ customizeCheckBoxMenuItem( _show_annotation_ref_source, getOptions().isShowAnnotationRefSource() );
customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
.isInternalNumberAreConfidenceForNhParsing() );
customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
- customizeRadioButtonMenuItem( _extract_taxonomy_yes_rbmi,
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.YES );
- customizeRadioButtonMenuItem( _extract_taxonomy_pfam_rbmi,
- getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ customizeRadioButtonMenuItem( _extract_taxonomy_pfam_relaxed_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
+ getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
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.addSeparator();
+ _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
+ customizeJMenuItem( _obtain_seq_information_jmi );
+ _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu
.add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
_obtain_detailed_taxonomic_information_deleting_jmi
.setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
- _tools_menu.add( _obtain_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
- customizeJMenuItem( _obtain_seq_information_jmi );
- _obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu.addSeparator();
- if ( !Constants.__RELEASE ) {
- _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );
- customizeJMenuItem( _function_analysis );
- _function_analysis
- .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 );
}
exit();
}
- void executeFunctionAnalysis() {
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
- return;
- }
- final GoAnnotation a = new GoAnnotation( this,
- _mainpanel.getCurrentTreePanel(),
- _mainpanel.getCurrentPhylogeny() );
- new Thread( a ).start();
- }
-
- void executeGSDI() {
- if ( !isOKforSDI( false, true ) ) {
- return;
- }
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not rooted.",
- "Cannot execute GSDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
- gene_tree.setAllNodesToNotCollapse();
- gene_tree.recalculateNumberOfExternalDescendants( false );
- GSDI gsdi = null;
- final Phylogeny species_tree = _species_tree.copy();
- try {
- gsdi = new GSDI( gene_tree, species_tree, false, true, true );
- }
- catch ( final SDIException e ) {
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Error during GSDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final Exception e ) {
- AptxUtil.unexpectedException( e );
- return;
- }
- gene_tree.setRerootable( false );
- _mainpanel.getCurrentTreePanel().setTree( gene_tree );
- _mainpanel.getCurrentPhylogeny().clearHashIdToNodeMap();
- _mainpanel.getCurrentPhylogeny().recalculateNumberOfExternalDescendants( true );
- _mainpanel.getCurrentTreePanel().resetNodeIdToDistToLeafMap();
- _mainpanel.getCurrentTreePanel().setEdited( true );
- getControlPanel().setShowEvents( true );
- showWhole();
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
- showWhole();
- _mainpanel.getTabbedPane().setSelectedIndex( selected );
- showWhole();
- _mainpanel.getCurrentTreePanel().setEdited( true );
- JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
- + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
- + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
- }
-
- void executeGSDIR() {
- if ( !isOKforSDI( false, true ) ) {
- return;
- }
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
- gene_tree.setAllNodesToNotCollapse();
- gene_tree.recalculateNumberOfExternalDescendants( false );
- GSDIR gsdir = null;
- final Phylogeny species_tree = _species_tree.copy();
- try {
- gsdir = new GSDIR( gene_tree, species_tree, true, true );
- }
- catch ( final SDIException e ) {
- JOptionPane.showMessageDialog( this,
- e.getLocalizedMessage(),
- "Error during GSDIR",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- catch ( final Exception e ) {
- AptxUtil.unexpectedException( e );
- return;
- }
- final List<Phylogeny> assigned_trees = gsdir.getMinDuplicationsSumGeneTrees();
- final List<Integer> shortests = GSDIR.getIndexesOfShortestTree( assigned_trees );
- final Phylogeny result_gene_tree = assigned_trees.get( shortests.get( 0 ) );
- result_gene_tree.setRerootable( false );
- result_gene_tree.clearHashIdToNodeMap();
- result_gene_tree.recalculateNumberOfExternalDescendants( true );
- _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
- getControlPanel().setShowEvents( true );
- showWhole();
- final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
- _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
- showWhole();
- _mainpanel.getTabbedPane().setSelectedIndex( selected );
- showWhole();
- _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 successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
-
void executeLineageInference() {
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
return;
new Thread( inferrer ).start();
}
- void executeSDIR( final boolean minimize_cost ) {
- if ( !isOKforSDI( true, true ) ) {
- return;
- }
- Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
- final SDIR sdiunrooted = new SDIR();
- gene_tree.setAllNodesToNotCollapse();
- gene_tree.recalculateNumberOfExternalDescendants( false );
- try {
- gene_tree = sdiunrooted.infer( gene_tree, _species_tree, minimize_cost, // minimize cost
- !minimize_cost, // minimize sum of dups
- true, // minimize height
- true, // return tree(s)
- 1 )[ 0 ]; // # of trees to return
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this, e.toString(), "Error during SDIR", JOptionPane.ERROR_MESSAGE );
- return;
- }
- final int duplications = sdiunrooted.getMinimalDuplications();
- gene_tree.setRerootable( false );
- _mainpanel.getCurrentTreePanel().setTree( gene_tree );
- getControlPanel().setShowEvents( true );
- showWhole();
- _mainpanel.getCurrentTreePanel().setEdited( true );
- JOptionPane.showMessageDialog( this,
- "Number of duplications: " + duplications,
- "SDIR successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
-
void exit() {
removeAllTextFrames();
_mainpanel.terminate();
System.exit( 0 );
}
- boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
- if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
- return false;
- }
- else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
- JOptionPane.showMessageDialog( this,
- "No species tree loaded",
- "Cannot execute SDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else if ( species_tree_has_to_binary && !_species_tree.isCompletelyBinary() ) {
- JOptionPane.showMessageDialog( this,
- "Species tree is not completely binary",
- "Cannot execute SDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not completely binary",
- "Cannot execute SDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else {
- return true;
- }
- }
-
@Override
void readPhylogeniesFromURL() {
URL url = null;
}
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 {
if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
BasicTable<String> t = null;
try {
- t = BasicTableParser.parse( file, "\t" );
+ t = BasicTableParser.parse( file, '\t' );
if ( t.getNumberOfColumns() < 2 ) {
- t = BasicTableParser.parse( file, "," );
+ t = BasicTableParser.parse( file, ',' );
}
if ( t.getNumberOfColumns() < 2 ) {
- t = BasicTableParser.parse( file, " " );
+ t = BasicTableParser.parse( file, ' ' );
}
}
catch ( final IOException e ) {
}
}
+ 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<Sequence> 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<PhylogenyNode> 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 );
+ }
+ }
+ }
+
private void choosePdfWidth() {
final String s = ( String ) JOptionPane.showInputDialog( this,
"Please enter the default line width for PDF export.\n"
}
}
if ( xml_parser == null ) {
- xml_parser = new PhyloXmlParser();
+ xml_parser = PhyloXmlParser.createPhyloXmlParser();
}
return xml_parser;
}
final PhylogenyNode n = it.next();
final String name = n.getName().trim();
if ( !ForesterUtil.isEmpty( name ) ) {
- final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.YES );
+ final String nt = ParserUtils.extractTaxonomyDataFromNodeName( n,
+ TAXONOMY_EXTRACTION.AGGRESSIVE );
if ( !ForesterUtil.isEmpty( nt ) ) {
if ( counter < 15 ) {
sb.append( name + ": " + nt + "\n" );
private File getCurrentDir() {
if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
- if ( ForesterUtil.isWindowns() ) {
+ if ( ForesterUtil.isWindows() ) {
try {
_current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
}
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();
}
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();
}
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
+ .createPhyloXmlParserXsdValidating(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
+ .createPhyloXmlParserXsdValidating(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
}
}
if ( !exception && ( t != null ) ) {
- _species_tree = t;
+ setSpeciesTree( t );
JOptionPane.showMessageDialog( this,
"Species tree successfully loaded",
"Species tree loaded",
}
}
+ private void setArrowCursor() {
+ try {
+ _mainpanel.getCurrentTreePanel().setArrowCursor();
+ }
+ catch ( final Exception ex ) {
+ // Do nothing.
+ }
+ }
+
private void setCurrentDir( final File current_dir ) {
_current_dir = current_dir;
}
final int count = getMainPanel().getTabbedPane().getTabCount();
final List<Phylogeny> trees = new ArrayList<Phylogeny>();
for( int i = 0; i < count; ++i ) {
- trees.add( getMainPanel().getPhylogeny( 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();
git://source.jalview.org / jalview.git / blobdiff