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.sequence.Sequence;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
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 _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;
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 );
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 == _graphics_export_visible_only_cbmi ) {
updateOptions( getOptions() );
}
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 );
- gene_tree.clearHashIdToNodeMap();
- gene_tree.recalculateNumberOfExternalDescendants( true );
- _mainpanel.addPhylogenyInNewTab( 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 );
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
- if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
- JOptionPane.showMessageDialog( this,
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"
- + "Potential duplications: "
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDI successfully completed",
- JOptionPane.WARNING_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this,
- "Duplications: " + gsdi.getDuplicationsSum() + "\n"
- + "Potential duplications: "
- + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
- + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDI successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
- }
-
- void executeGSDIR() {
- if ( !isOKforSDI( false, false ) ) {
- return;
- }
- final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
- if ( ( p > 0 )
- && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
- JOptionPane.showMessageDialog( this,
- "Gene tree is not completely binary",
- "Cannot execute GSDI",
- JOptionPane.ERROR_MESSAGE );
- 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 Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
- 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 );
- final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
- if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
- JOptionPane.showMessageDialog( this,
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDIR successfully completed",
- JOptionPane.WARNING_MESSAGE );
- }
- else {
- JOptionPane.showMessageDialog( this,
- "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
- + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
- + "Stripped gene tree nodes: "
- + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
- + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
- + "Number of polytomies in species tree used: " + poly + "\n",
- "GSDIR successfully completed",
- JOptionPane.INFORMATION_MESSAGE );
- }
- }
-
void executeLineageInference() {
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || ( _mainpanel.getCurrentPhylogeny().isEmpty() ) ) {
return;
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 GSDI",
- 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 GSDI",
- 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 GSDI",
- JOptionPane.ERROR_MESSAGE );
- return false;
- }
- else {
- return true;
- }
- }
-
@Override
void readPhylogeniesFromURL() {
URL url = null;
_contentpane.repaint();
}
+ private void addExpressionValuesFromFile() {
+ if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Need to load evolutionary tree first",
+ "Can Not Read Expression Values",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ final File my_dir = getCurrentDir();
+ if ( my_dir != null ) {
+ _values_filechooser.setCurrentDirectory( my_dir );
+ }
+ final int result = _values_filechooser.showOpenDialog( _contentpane );
+ final File file = _values_filechooser.getSelectedFile();
+ if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
+ BasicTable<String> t = null;
+ try {
+ t = BasicTableParser.parse( file, "\t" );
+ if ( t.getNumberOfColumns() < 2 ) {
+ t = BasicTableParser.parse( file, "," );
+ }
+ if ( t.getNumberOfColumns() < 2 ) {
+ t = BasicTableParser.parse( file, " " );
+ }
+ }
+ catch ( final IOException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getMessage(),
+ "Could Not Read Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( t.getNumberOfColumns() < 2 ) {
+ JOptionPane.showMessageDialog( this,
+ "Table contains " + t.getNumberOfColumns() + " column(s)",
+ "Problem with Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( t.getNumberOfRows() < 1 ) {
+ JOptionPane.showMessageDialog( this,
+ "Table contains zero rows",
+ "Problem with Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
+ if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
+ JOptionPane.showMessageDialog( this,
+ "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
+ + phy.getNumberOfExternalNodes() + " external nodes",
+ "Warning",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ int not_found = 0;
+ for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ final String node_name = node.getName();
+ if ( !ForesterUtil.isEmpty( node_name ) ) {
+ int row = -1;
+ try {
+ row = t.findRow( node_name );
+ }
+ catch ( final IllegalArgumentException e ) {
+ JOptionPane
+ .showMessageDialog( this,
+ e.getMessage(),
+ "Error Mapping Node Identifiers to Expression Value Identifiers",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ if ( row < 0 ) {
+ if ( node.isExternal() ) {
+ not_found++;
+ }
+ continue;
+ }
+ final List<Double> l = new ArrayList<Double>();
+ for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
+ double d = -100;
+ try {
+ d = Double.parseDouble( t.getValueAsString( col, row ) );
+ }
+ catch ( final NumberFormatException e ) {
+ JOptionPane.showMessageDialog( this,
+ "Could not parse \"" + t.getValueAsString( col, row )
+ + "\" into a decimal value",
+ "Issue with Expression Value Table",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ stats.addValue( d );
+ l.add( d );
+ }
+ if ( !l.isEmpty() ) {
+ if ( node.getNodeData().getProperties() != null ) {
+ node.getNodeData().getProperties()
+ .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
+ }
+ node.getNodeData().setVector( l );
+ }
+ }
+ }
+ if ( not_found > 0 ) {
+ JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
+ + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
+ }
+ getCurrentTreePanel().setStatisticsForExpressionValues( stats );
+ }
+ }
+
private void addSequencesFromFile() {
if ( ( getCurrentTreePanel() == null ) || ( getCurrentTreePanel().getPhylogeny() == null ) ) {
JOptionPane.showMessageDialog( this,
}
}
- 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,
- "Need to load evolutionary tree first",
- "Can Not Read Expression Values",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
- final File my_dir = getCurrentDir();
- if ( my_dir != null ) {
- _values_filechooser.setCurrentDirectory( my_dir );
- }
- final int result = _values_filechooser.showOpenDialog( _contentpane );
- final File file = _values_filechooser.getSelectedFile();
- if ( ( file != null ) && ( file.length() > 0 ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
- BasicTable<String> t = null;
- try {
- t = BasicTableParser.parse( file, "\t" );
- if ( t.getNumberOfColumns() < 2 ) {
- t = BasicTableParser.parse( file, "," );
- }
- if ( t.getNumberOfColumns() < 2 ) {
- t = BasicTableParser.parse( file, " " );
- }
- }
- catch ( final IOException e ) {
- JOptionPane.showMessageDialog( this,
- e.getMessage(),
- "Could Not Read Expression Value Table",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( t.getNumberOfColumns() < 2 ) {
- JOptionPane.showMessageDialog( this,
- "Table contains " + t.getNumberOfColumns() + " column(s)",
- "Problem with Expression Value Table",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( t.getNumberOfRows() < 1 ) {
- JOptionPane.showMessageDialog( this,
- "Table contains zero rows",
- "Problem with Expression Value Table",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
- if ( t.getNumberOfRows() != phy.getNumberOfExternalNodes() ) {
- JOptionPane.showMessageDialog( this,
- "Table contains " + t.getNumberOfRows() + " rows, but tree contains "
- + phy.getNumberOfExternalNodes() + " external nodes",
- "Warning",
- JOptionPane.WARNING_MESSAGE );
- }
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- int not_found = 0;
- for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
- final PhylogenyNode node = iter.next();
- final String node_name = node.getName();
- if ( !ForesterUtil.isEmpty( node_name ) ) {
- int row = -1;
- try {
- row = t.findRow( node_name );
- }
- catch ( final IllegalArgumentException e ) {
- JOptionPane
- .showMessageDialog( this,
- e.getMessage(),
- "Error Mapping Node Identifiers to Expression Value Identifiers",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- if ( row < 0 ) {
- if ( node.isExternal() ) {
- not_found++;
- }
- continue;
- }
- final List<Double> l = new ArrayList<Double>();
- for( int col = 1; col < t.getNumberOfColumns(); ++col ) {
- double d = -100;
- try {
- d = Double.parseDouble( t.getValueAsString( col, row ) );
- }
- catch ( final NumberFormatException e ) {
- JOptionPane.showMessageDialog( this,
- "Could not parse \"" + t.getValueAsString( col, row )
- + "\" into a decimal value",
- "Issue with Expression Value Table",
- JOptionPane.ERROR_MESSAGE );
- return;
- }
- stats.addValue( d );
- l.add( d );
- }
- if ( !l.isEmpty() ) {
- if ( node.getNodeData().getProperties() != null ) {
- node.getNodeData().getProperties()
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
- }
- node.getNodeData().setVector( l );
- }
- }
- }
- if ( not_found > 0 ) {
- JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
- }
- getCurrentTreePanel().setStatisticsForExpressionValues( stats );
- }
- }
-
private void choosePdfWidth() {
final String s = ( String ) JOptionPane.showInputDialog( this,
"Please enter the default line width for PDF export.\n"
}
}
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;
}
git://source.jalview.org / jalview.git / blobdiff