import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
+import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import javax.swing.filechooser.FileFilter;
import javax.swing.plaf.synth.SynthLookAndFeel;
+import org.forester.analysis.TaxonomyDataManager;
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
-import org.forester.archaeopteryx.Util.GraphicsExportType;
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.archaeopteryx.tools.PhylogeneticInferrer;
import org.forester.archaeopteryx.tools.SequenceDataRetriver;
-import org.forester.archaeopteryx.tools.TaxonomyDataObtainer;
import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
import org.forester.archaeopteryx.webservices.WebservicesManager;
import org.forester.io.parsers.FastaParser;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.io.writers.SequenceWriter;
import org.forester.msa.Msa;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
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.SDI;
import org.forester.sdi.SDIR;
-import org.forester.sdi.SDIse;
import org.forester.sequence.Sequence;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
import org.forester.util.BasicTableParser;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
-import org.forester.util.ForesterUtil.PhylogenyNodeField;
-import org.forester.util.ForesterUtil.TAXONOMY_EXTRACTION;
import org.forester.util.WindowsUtils;
class DefaultFilter extends FileFilter {
// Analysis menu
private JMenu _analysis_menu;
private JMenuItem _load_species_tree_item;
- private JMenuItem _sdi_item;
private JMenuItem _gsdi_item;
private JMenuItem _root_min_dups_item;
private JMenuItem _root_min_cost_l_item;
JMenuItem _read_values_jmi;
private MainFrameApplication( final Phylogeny[] phys, final Configuration config, final String title ) {
+ this( phys, config, title, null );
+ }
+
+ private MainFrameApplication( final Phylogeny[] phys,
+ final Configuration config,
+ final String title,
+ final File current_dir ) {
+ super();
_configuration = config;
if ( _configuration == null ) {
throw new IllegalArgumentException( "configuration is null" );
//UIManager.setLookAndFeel( "com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel" );
}
catch ( final UnsupportedLookAndFeelException e ) {
- Util.dieWithSystemError( "unsupported look and feel: " + e.toString() );
+ AptxUtil.dieWithSystemError( "unsupported look and feel: " + e.toString() );
}
catch ( final ClassNotFoundException e ) {
- Util.dieWithSystemError( "class not found exception: " + e.toString() );
+ AptxUtil.dieWithSystemError( "class not found exception: " + e.toString() );
}
catch ( final InstantiationException e ) {
- Util.dieWithSystemError( "instantiation exception: " + e.toString() );
+ AptxUtil.dieWithSystemError( "instantiation exception: " + e.toString() );
}
catch ( final IllegalAccessException e ) {
- Util.dieWithSystemError( "illegal access exception: " + e.toString() );
+ AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
}
catch ( final Exception e ) {
- Util.dieWithSystemError( e.toString() );
+ AptxUtil.dieWithSystemError( e.toString() );
+ }
+ if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
+ setCurrentDir( current_dir );
}
// hide until everything is ready
setVisible( false );
setOptions( Options.createInstance( _configuration ) );
+ setInferenceManager( InferenceManager.createInstance( _configuration ) );
setPhylogeneticInferenceOptions( PhylogeneticInferenceOptions.createInstance( _configuration ) );
- _textframe = null;
+ // _textframe = null; #~~~~
_species_tree = null;
// set title
setTitle( Constants.PRG_NAME + " " + Constants.VERSION + " (" + Constants.PRG_DATE + ")" );
// addKeyListener( this );
setVisible( true );
if ( ( phys != null ) && ( phys.length > 0 ) ) {
- Util.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
+ AptxUtil.addPhylogeniesToTabs( phys, title, null, _configuration, _mainpanel );
validate();
getMainPanel().getControlPanel().showWholeAll();
getMainPanel().getControlPanel().showWhole();
System.gc();
}
+ private MainFrameApplication( final Phylogeny[] phys, final Configuration config ) {
+ _configuration = config;
+ if ( _configuration == null ) {
+ throw new IllegalArgumentException( "configuration is null" );
+ }
+ setVisible( false );
+ setOptions( Options.createInstance( _configuration ) );
+ _mainpanel = new MainPanel( _configuration, this );
+ _open_filechooser = null;
+ _open_filechooser_for_species_tree = null;
+ _save_filechooser = null;
+ _writetopdf_filechooser = null;
+ _writetographics_filechooser = null;
+ _msa_filechooser = null;
+ _seqs_filechooser = null;
+ _values_filechooser = null;
+ _jmenubar = new JMenuBar();
+ buildFileMenu();
+ buildTypeMenu();
+ _contentpane = getContentPane();
+ _contentpane.setLayout( new BorderLayout() );
+ _contentpane.add( _mainpanel, BorderLayout.CENTER );
+ // App is this big
+ setSize( MainFrameApplication.FRAME_X_SIZE, MainFrameApplication.FRAME_Y_SIZE );
+ // The window listener
+ setDefaultCloseOperation( WindowConstants.DO_NOTHING_ON_CLOSE );
+ addWindowListener( new WindowAdapter() {
+
+ @Override
+ public void windowClosing( final WindowEvent e ) {
+ exit();
+ }
+ } );
+ // setVisible( true );
+ if ( ( phys != null ) && ( phys.length > 0 ) ) {
+ AptxUtil.addPhylogeniesToTabs( phys, "", null, _configuration, _mainpanel );
+ validate();
+ getMainPanel().getControlPanel().showWholeAll();
+ getMainPanel().getControlPanel().showWhole();
+ }
+ //activateSaveAllIfNeeded();
+ // ...and its children
+ _contentpane.repaint();
+ }
+
private MainFrameApplication( final Phylogeny[] phys, final String config_file, final String title ) {
// Reads the config file (false, false => not url, not applet):
- this( phys, new Configuration( config_file, false, false ), title );
+ this( phys, new Configuration( config_file, false, false, true ), title );
}
@Override
else if ( o == _load_species_tree_item ) {
readSpeciesTreeFromFile();
}
- else if ( o == _sdi_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- executeSDI();
- }
else if ( o == _lineage_inference ) {
if ( isSubtreeDisplayed() ) {
JOptionPane.showMessageDialog( this,
_contentpane.repaint();
}
catch ( final Exception ex ) {
- Util.unexpectedException( ex );
+ AptxUtil.unexpectedException( ex );
}
catch ( final Error err ) {
- Util.unexpectedError( err );
+ AptxUtil.unexpectedError( err );
}
}
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
- _analysis_menu.add( _sdi_item = new JMenuItem( "SDI (Speciation Duplication Inference)" ) );
- if ( !Constants.__RELEASE && !Constants.__SNAPSHOT_RELEASE ) {
- _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
- }
+ _analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
_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( _load_species_tree_item = new JMenuItem( "Load Species Tree..." ) );
- customizeJMenuItem( _sdi_item );
customizeJMenuItem( _gsdi_item );
customizeJMenuItem( _root_min_dups_item );
customizeJMenuItem( _root_min_cost_l_item );
}
void buildPhylogeneticInferenceMenu() {
+ final InferenceManager im = getInferenceManager();
_inference_menu = MainFrame.createMenu( "Inference", getConfiguration() );
- _inference_menu
- .add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment...(EXPERIMENTAL - DO NOT USE!!) " ) );
+ _inference_menu.add( _inference_from_msa_item = new JMenuItem( "From Multiple Sequence Alignment..." ) );
customizeJMenuItem( _inference_from_msa_item );
_inference_from_msa_item.setToolTipText( "Basic phylogenetic inference from MSA" );
- _inference_menu
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences...(EXPERIMENTAL - DO NOT USE!!) " ) );
- customizeJMenuItem( _inference_from_seqs_item );
- _inference_from_seqs_item.setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
+ if ( im.canDoMsa() ) {
+ _inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
+ customizeJMenuItem( _inference_from_seqs_item );
+ _inference_from_seqs_item
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
+ }
+ else {
+ _inference_menu
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
+ customizeJMenuItem( _inference_from_seqs_item );
+ _inference_from_seqs_item.setEnabled( false );
+ }
_jmenubar.add( _inference_menu );
}
_save_all_item.setEnabled( false );
_file_jmenu.addSeparator();
_file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
- if ( Util.canWriteFormat( "tif" ) || Util.canWriteFormat( "tiff" ) || Util.canWriteFormat( "TIF" ) ) {
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
_file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
}
_file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
_file_jmenu.add( _write_to_jpg_item = new JMenuItem( "Export to JPG file..." ) );
- if ( Util.canWriteFormat( "gif" ) ) {
+ if ( AptxUtil.canWriteFormat( "gif" ) ) {
_file_jmenu.add( _write_to_gif_item = new JMenuItem( "Export to GIF file..." ) );
}
- if ( Util.canWriteFormat( "bmp" ) ) {
+ if ( AptxUtil.canWriteFormat( "bmp" ) ) {
_file_jmenu.add( _write_to_bmp_item = new JMenuItem( "Export to BMP file..." ) );
}
_file_jmenu.addSeparator();
_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_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( _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( _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_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_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 ) );
_options_jmenu.add( _print_size_mi = new JMenuItem( "" ) );
_options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
_options_jmenu.addSeparator();
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Input:" ), getConfiguration() ) );
_options_jmenu
- .add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Parsing:" ), getConfiguration() ) );
- _options_jmenu
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Numbers Are Confidence Values" ) );
+ .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
_options_jmenu
.add( _extract_pfam_style_tax_codes_cbmi = new JCheckBoxMenuItem( "Extract Taxonomy Codes from Pfam-style Labels" ) );
+ _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Output:" ), getConfiguration() ) );
+ _options_jmenu
+ .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
+ _use_brackets_for_conf_in_nh_export_cbmi
+ .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
+ _options_jmenu
+ .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
customizeJMenuItem( _choose_font_mi );
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _switch_colors_mi );
customizeCheckBoxMenuItem( _print_using_actual_size_cbmi, getOptions().isPrintUsingActualSize() );
customizeCheckBoxMenuItem( _graphics_export_using_actual_size_cbmi, getOptions()
.isGraphicsExportUsingActualSize() );
+ customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
+ customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+ customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
_jmenubar.add( _options_jmenu );
}
_tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
customizeJMenuItem( _collapse_species_specific_subtrees );
_tools_menu
- .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold" ) );
+ .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
customizeJMenuItem( _collapse_below_threshold );
_collapse_below_threshold
- .setToolTipText( "To permanently collapse branches without at least one support value above a given threshold" );
+ .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( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
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_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
+ _tools_menu.add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
- _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
+ _obtain_uniprot_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" ) );
}
if ( to_be_removed.size() > 0 ) {
phy.externalNodesHaveChanged();
- phy.hashIDs();
+ 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()
gene_tree.setAllNodesToNotCollapse();
gene_tree.recalculateNumberOfExternalDescendants( false );
GSDI gsdi = null;
- int duplications = -1;
try {
- gsdi = new GSDI( gene_tree, _species_tree.copy(), true );
- duplications = gsdi.getDuplicationsSum();
+ gsdi = new GSDI( gene_tree, _species_tree.copy(), false, true, true );
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this, e.toString(), "Error during GSDI", JOptionPane.ERROR_MESSAGE );
}
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( gsdi.getSpeciesTree(), getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
_mainpanel.getCurrentTreePanel().setEdited( true );
- JOptionPane.showMessageDialog( this,
- "Number of duplications: " + duplications,
- "GSDI successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
+ JOptionPane.showMessageDialog( this, "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: " + gsdi.getSpeciationOrDuplicationEventsSum() + "\n" + "Speciations: "
+ + gsdi.getSpeciationsSum(), "GSDI successfully completed", JOptionPane.INFORMATION_MESSAGE );
}
void executeFunctionAnalysis() {
}
}
- void executeSDI() {
- if ( !isOKforSDI( true, true ) ) {
- return;
- }
- if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not rooted",
- "Cannot execute SDI",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
- gene_tree.setAllNodesToNotCollapse();
- gene_tree.recalculateNumberOfExternalDescendants( false );
- SDI sdi = null;
- int duplications = -1;
- try {
- sdi = new SDIse( gene_tree, _species_tree.copy() );
- duplications = sdi.getDuplicationsSum();
- }
- catch ( final Exception e ) {
- JOptionPane.showMessageDialog( this, e.toString(), "Error during SDI", JOptionPane.ERROR_MESSAGE );
- }
- gene_tree.setRerootable( false );
- _mainpanel.getCurrentTreePanel().setTree( gene_tree );
- getControlPanel().setShowEvents( true );
- showWhole();
- _mainpanel.getCurrentTreePanel().setEdited( true );
- JOptionPane.showMessageDialog( this,
- "Number of duplications: " + duplications,
- "SDI successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
-
void executeSDIR( final boolean minimize_cost ) {
if ( !isOKforSDI( true, true ) ) {
return;
}
void exit() {
- removeTextFrame();
+ removeAllTextFrames();
_mainpanel.terminate();
_contentpane.removeAll();
setVisible( false );
System.exit( 0 );
}
- private void extractTaxCodeFromNodeNames() {
+ public void end() {
+ _mainpanel.terminate();
+ _contentpane.removeAll();
+ setVisible( false );
+ dispose();
+ }
+
+ private void extractTaxCodeFromNodeNames() throws PhyloXmlDataFormatException {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
final PhylogenyNode n = it.next();
final String name = n.getName().trim();
if ( !ForesterUtil.isEmpty( name ) ) {
- final String code = ForesterUtil.extractTaxonomyCodeFromNodeName( name,
- false,
- TAXONOMY_EXTRACTION.YES );
+ final String code = ParserUtils
+ .extractTaxonomyCodeFromNodeName( name, PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
if ( !ForesterUtil.isEmpty( code ) ) {
PhylogenyMethods.setTaxonomyCode( n, code );
}
private File getCurrentDir() {
if ( ( _current_dir == null ) || !_current_dir.canRead() ) {
- if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) > -1 ) {
+ if ( ForesterUtil.isWindowns() ) {
try {
_current_dir = new File( WindowsUtils.getCurrentUserDesktopPath() );
}
return false;
}
- private void moveNodeNamesToSeqNames() {
+ private void moveNodeNamesToSeqNames() throws PhyloXmlDataFormatException {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- ForesterUtil.transferNodeNameToField( phy, PhylogenyNodeField.SEQUENCE_NAME );
+ PhylogenyMethods
+ .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
}
}
}
- private void moveNodeNamesToTaxSn() {
+ private void moveNodeNamesToTaxSn() throws PhyloXmlDataFormatException {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- ForesterUtil.transferNodeNameToField( phy, PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME );
+ PhylogenyMethods.transferNodeNameToField( phy,
+ PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+ false );
}
}
}
phy.setRoot( node );
phy.setRooted( true );
phys[ 0 ] = phy;
- Util.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
+ AptxUtil.addPhylogeniesToTabs( phys, "", "", getConfiguration(), getMainPanel() );
_mainpanel.getControlPanel().showWhole();
_mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
_mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
- _mainpanel.getCurrentTreePanel(),
- phy.copy() );
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ false,
+ true );
new Thread( t ).start();
}
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
- _mainpanel.getCurrentTreePanel(),
- phy.copy(),
- true );
+ final TaxonomyDataManager t = new TaxonomyDataManager( this,
+ _mainpanel.getCurrentTreePanel(),
+ phy.copy(),
+ true,
+ true );
new Thread( t ).start();
}
}
try {
final NHXParser nhx = new NHXParser();
setSpecialOptionsForNhxParser( nhx );
- phys = ForesterUtil.readPhylogenies( nhx, file );
+ phys = PhylogenyMethods.readPhylogenies( nhx, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
try {
final PhyloXmlParser xml_parser = createPhyloXmlParser();
- phys = ForesterUtil.readPhylogenies( xml_parser, file );
+ phys = PhylogenyMethods.readPhylogenies( xml_parser, file );
}
catch ( final Exception e ) {
exception = true;
}
else if ( _open_filechooser.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
- phys = ForesterUtil.readPhylogenies( new TolParser(), file );
+ phys = PhylogenyMethods.readPhylogenies( new TolParser(), file );
}
catch ( final Exception e ) {
exception = true;
try {
final NexusPhylogeniesParser nex = new NexusPhylogeniesParser();
setSpecialOptionsForNexParser( nex );
- phys = ForesterUtil.readPhylogenies( nex, file );
+ phys = PhylogenyMethods.readPhylogenies( nex, file );
nhx_or_nexus = true;
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final PhylogenyParser parser = ForesterUtil
+ final PhylogenyParser parser = ParserUtils
.createParserDependingOnFileType( file, getConfiguration()
.isValidatePhyloXmlAgainstSchema() );
if ( parser instanceof NexusPhylogeniesParser ) {
else if ( parser instanceof PhyloXmlParser ) {
warnIfNotPhyloXmlValidation( getConfiguration() );
}
- phys = ForesterUtil.readPhylogenies( parser, file );
+ phys = PhylogenyMethods.readPhylogenies( parser, file );
}
catch ( final Exception e ) {
exception = true;
if ( nhx_or_nexus ) {
for( final Phylogeny phy : phys ) {
if ( getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
- ForesterUtil.transferInternalNodeNamesToConfidence( phy );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
if ( PhylogenyMethods.getMinimumDescendentsPerInternalNodes( phy ) == 1 ) {
one_desc = true;
}
}
}
- Util.addPhylogeniesToTabs( phys,
- file.getName(),
- file.getAbsolutePath(),
- getConfiguration(),
- getMainPanel() );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ file.getName(),
+ file.getAbsolutePath(),
+ getConfiguration(),
+ getMainPanel() );
_mainpanel.getControlPanel().showWhole();
if ( nhx_or_nexus && one_desc ) {
JOptionPane
setMsa( null );
Msa msa = null;
try {
- if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {
- msa = FastaParser.parseMsa( new FileInputStream( file ) );
- System.out.println( msa.toString() );
+ final InputStream is = new FileInputStream( file );
+ if ( FastaParser.isLikelyFasta( file ) ) {
+ msa = FastaParser.parseMsa( is );
}
else {
- msa = GeneralMsaParser.parse( new FileInputStream( file ) );
+ msa = GeneralMsaParser.parse( is );
}
}
catch ( final MsaFormatException e ) {
parser = new TolParser();
}
else {
- parser = ForesterUtil.createParserDependingOnUrlContents( url, getConfiguration()
+ parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
.isValidatePhyloXmlAgainstSchema() );
}
if ( parser instanceof NexusPhylogeniesParser ) {
if ( ( phys != null ) && ( phys.length > 0 ) ) {
if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {
for( final Phylogeny phy : phys ) {
- ForesterUtil.transferInternalNodeNamesToConfidence( phy );
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
}
- Util.addPhylogeniesToTabs( phys,
- new File( url.getFile() ).getName(),
- new File( url.getFile() ).toString(),
- getConfiguration(),
- getMainPanel() );
+ AptxUtil.addPhylogeniesToTabs( phys,
+ new File( url.getFile() ).getName(),
+ new File( url.getFile() ).toString(),
+ getConfiguration(),
+ getMainPanel() );
_mainpanel.getControlPanel().showWhole();
}
}
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.xmlfilter ) {
try {
- final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
}
else if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrameApplication.tolfilter ) {
try {
- final Phylogeny[] trees = ForesterUtil.readPhylogenies( new TolParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new TolParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final Phylogeny[] trees = ForesterUtil.readPhylogenies( new PhyloXmlParser(), file );
+ final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( new PhyloXmlParser(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
private void setSpecialOptionsForNhxParser( final NHXParser nhx ) {
nhx.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() );
- ForesterUtil.TAXONOMY_EXTRACTION te = ForesterUtil.TAXONOMY_EXTRACTION.NO;
+ PhylogenyMethods.TAXONOMY_EXTRACTION te = PhylogenyMethods.TAXONOMY_EXTRACTION.NO;
if ( getOptions().isExtractPfamTaxonomyCodesInNhParsing() ) {
- te = ForesterUtil.TAXONOMY_EXTRACTION.YES;
+ te = PhylogenyMethods.TAXONOMY_EXTRACTION.YES;
}
nhx.setTaxonomyExtraction( te );
}
private boolean writeAsNewHampshire( final Phylogeny t, boolean exception, final File file ) {
try {
final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toNewHampshire( t, false, true, file );
+ writer.toNewHampshire( t, false, true, getOptions().getNhConversionSupportValueStyle(), file );
}
catch ( final Exception e ) {
exception = true;
private boolean writeAsNexus( final Phylogeny t, boolean exception, final File file ) {
try {
final PhylogenyWriter writer = new PhylogenyWriter();
- writer.toNexus( file, t );
+ writer.toNexus( file, t, getOptions().getNhConversionSupportValueStyle() );
}
catch ( final Exception e ) {
exception = true;
return exception;
}
- private void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
+ void writePhylogenyToGraphicsFile( final String file_name, final GraphicsExportType type ) {
_mainpanel.getCurrentTreePanel().setParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
_mainpanel.getCurrentTreePanel().getHeight(),
true );
String file_written_to = "";
boolean error = false;
try {
- file_written_to = Util.writePhylogenyToGraphicsFile( file_name,
- _mainpanel.getCurrentTreePanel().getWidth(),
- _mainpanel.getCurrentTreePanel().getHeight(),
- _mainpanel.getCurrentTreePanel(),
- _mainpanel.getControlPanel(),
- type,
- getOptions() );
+ 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;
return new MainFrameApplication( phys, config, title );
}
+ public static MainFrameApplication createInstance( final Phylogeny[] phys, final Configuration config ) {
+ return new MainFrameApplication( phys, config );
+ }
+
static MainFrame createInstance( final Phylogeny[] phys, final String config_file_name, final String title ) {
return new MainFrameApplication( phys, config_file_name, 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 void setTextForGraphicsSizeChooserMenuItem( final JMenuItem mi, final Options o ) {
mi.setText( "Enter Default Size for Graphics Export... (current: " + o.getPrintSizeX() + ", "
+ o.getPrintSizeY() + ")" );
git://source.jalview.org / jalview.git / blobdiff