import java.net.URL;
import java.util.LinkedList;
import java.util.List;
-import java.util.Map;
import java.util.NoSuchElementException;
import javax.swing.ButtonGroup;
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.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.data.SequenceRelation;
+import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
private final static String NAME = "ArchaeopteryxE";
private static final long serialVersionUID = -1220055577935759443L;
private Configuration _configuration;
- private MainPanelApplets _main_panel;
+ private MainPanelApplets _mainpanel;
private JMenuBar _jmenubar;
private JMenu _options_jmenu;
private JMenu _font_size_menu;
private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi;
private JCheckBoxMenuItem _show_confidence_stddev_cbmi;
private final LinkedList<TextFrame> _textframes = new LinkedList<TextFrame>();
+ private JMenu _analysis_menu;
+ private JMenuItem _gsdi_item;
+ private JMenuItem _gsdir_item;
+ private Phylogeny _species_tree;
- // private String _ext_node_data_buffer = "";
- // private int _ext_node_data_buffer_change_counter = 0;
@Override
public void actionPerformed( final ActionEvent e ) {
final Object o = e.getSource();
if ( o == _midpoint_root_item ) {
getMainPanel().getCurrentTreePanel().midpointRoot();
}
+ else if ( o == _gsdi_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDI();
+ }
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
+ }
else if ( o == _taxcolor_item ) {
getMainPanel().getCurrentTreePanel().taxColor();
}
}
else if ( o == _non_lined_up_cladograms_rbmi ) {
updateOptions( getOptions() );
- _main_panel.getControlPanel().showWhole();
+ _mainpanel.getControlPanel().showWhole();
}
else if ( o == _uniform_cladograms_rbmi ) {
updateOptions( getOptions() );
- _main_panel.getControlPanel().showWhole();
+ _mainpanel.getControlPanel().showWhole();
}
else if ( o == _ext_node_dependent_cladogram_rbmi ) {
updateOptions( getOptions() );
- _main_panel.getControlPanel().showWhole();
+ _mainpanel.getControlPanel().showWhole();
}
else if ( o == _search_case_senstive_cbmi ) {
updateOptions( getOptions() );
MainFrame.about();
}
else if ( o == _help_item ) {
- help( getConfiguration().getWebLinks() );
+ help();
}
else if ( o == _website_item ) {
try {
final ByteArrayOutputStream baos = new ByteArrayOutputStream();
try {
AptxUtil.writePhylogenyToGraphicsByteArrayOutputStream( baos,
- _main_panel.getWidth(),
- _main_panel.getHeight(),
+ _mainpanel.getWidth(),
+ _mainpanel.getHeight(),
getCurrentTreePanel(),
getCurrentTreePanel().getControlPanel(),
GraphicsExportType.valueOf( format ),
setupUI();
URL phys_url = null;
Phylogeny[] phys = null;
- final String phys_url_string = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
- AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + phys_url_string );
+ final String tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD );
+ AptxUtil.printAppletMessage( NAME, "URL for phylogenies is " + tree_url_str );
// Get URL to tree file
- if ( phys_url_string != null ) {
+ if ( tree_url_str != null ) {
try {
- phys_url = new URL( phys_url_string );
+ phys_url = new URL( tree_url_str );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( NAME, "error: " + e );
e.printStackTrace();
- JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + phys_url_string
+ JOptionPane.showMessageDialog( this, NAME + ": Could not create URL from: \"" + tree_url_str
+ "\"\nException: " + e, "Failed to create URL", JOptionPane.ERROR_MESSAGE );
}
}
getConfiguration().isValidatePhyloXmlAgainstSchema(),
getConfiguration().isReplaceUnderscoresInNhParsing(),
getConfiguration().isInternalNumberAreConfidenceForNhParsing(),
- getConfiguration().getTaxonomyExtraction() );
+ getConfiguration().getTaxonomyExtraction(),
+ getConfiguration().isMidpointReroot() );
}
catch ( final Exception e ) {
ForesterUtil.printErrorMessage( NAME, e.toString() );
else {
AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + phys_url );
}
+ //
+ final String species_tree_url_str = getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD );
+ if ( !ForesterUtil.isEmpty( species_tree_url_str ) ) {
+ AptxUtil.printAppletMessage( NAME, "URL of species tree to load: \"" + species_tree_url_str + "\"" );
+ Phylogeny[] species_trees = null;
+ try {
+ final URL species_tree_url = new URL( species_tree_url_str );
+ species_trees = AptxUtil.readPhylogeniesFromUrl( species_tree_url,
+ configuration.isValidatePhyloXmlAgainstSchema(),
+ configuration.isReplaceUnderscoresInNhParsing(),
+ false,
+ TAXONOMY_EXTRACTION.NO,
+ false );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.printErrorMessage( NAME, "could not read species tree from [" + species_tree_url_str
+ + "]" );
+ JOptionPane.showMessageDialog( this, NAME + ": could not read species tree from ["
+ + species_tree_url_str + "]", "Failed to read species tree", JOptionPane.ERROR_MESSAGE );
+ }
+ if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
+ AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
+ if ( species_trees[ 0 ].isEmpty() ) {
+ ForesterUtil.printErrorMessage( NAME, "species tree is empty" );
+ }
+ else if ( !species_trees[ 0 ].isRooted() ) {
+ ForesterUtil.printErrorMessage( NAME, "species tree is not rooted" );
+ }
+ else {
+ setSpeciesTree( species_trees[ 0 ] );
+ AptxUtil.printAppletMessage( NAME, "species tree OK" );
+ }
+ }
+ }
+ //
setVisible( false );
setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
_jmenubar = new JMenuBar();
if ( !getConfiguration().isUseNativeUI() ) {
_jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
}
+ if ( getSpeciesTree() != null ) {
+ buildAnalysisMenu();
+ }
buildToolsMenu();
buildViewMenu();
buildFontSizeMenu();
}
else {
AptxUtil.printAppletMessage( NAME, "not using tabbed display" );
+ if ( getSpeciesTree() != null ) {
+ AptxUtil.printAppletMessage( NAME,
+ "Warning: gsdi (gene duplication inference) only available tabbed display" );
+ }
AptxUtil.addPhylogenyToPanel( phys, getConfiguration(), getMainPanel() );
}
validate();
final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
if ( default_sequence != null ) {
getCurrentTreePanel().getControlPanel().getSequenceRelationBox().setSelectedItem( default_sequence );
- /* GUILHEM_END */
}
+ /* GUILHEM_END */
setVisible( true );
}
AptxUtil.printAppletMessage( NAME, "started" );
}
+ 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 (GSDI with re-rooting)" ) );
+ customizeJMenuItem( _gsdi_item );
+ customizeJMenuItem( _gsdir_item );
+ // _analysis_menu.addSeparator();
+ // _analysis_menu.add( _lineage_inference = new JMenuItem( INFER_ANCESTOR_TAXONOMIES ) );
+ // customizeJMenuItem( _lineage_inference );
+ // _lineage_inference.setToolTipText( "Inference of ancestor taxonomies/lineages" );
+ _jmenubar.add( _analysis_menu );
+ }
+
void buildFontSizeMenu() {
_font_size_menu = MainFrame.createMenu( MainFrame.FONT_SIZE_MENU_LABEL, getConfiguration() );
_font_size_menu.add( _super_tiny_fonts_mi = new JMenuItem( "Super tiny fonts" ) );
}
}
+ 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, 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 );
+ getMainPanel().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, 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 );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().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 );
+ }
+ }
+
Configuration getConfiguration() {
return _configuration;
}
return _options;
}
- void help( final Map<String, WebLink> weblinks ) {
+ void help() {
final StringBuilder sb = new StringBuilder();
sb.append( "Display options\n" );
sb.append( "-------------------\n" );
sb.append( "------------------------\n" );
sb.append( "Order Subtrees -- order the tree by branch length\n" );
sb.append( "Uncollapse All -- uncollapse any and all collapsed branches\n\n" );
- sb.append( "Memory problems (Java heap space error)\n" );
- sb.append( "---------------------------------------\n" );
- sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
- sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
- sb.append( "the '-Xmx' Java command line option. For example:\n" );
- sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
- if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
- sb.append( "Active web links\n" );
- sb.append( "--------------------\n" );
- for( final String key : weblinks.keySet() ) {
- sb.append( " " + weblinks.get( key ).toString() + "\n" );
- }
- }
- sb.append( "\n" );
sb.append( "phyloXML\n" );
sb.append( "-------------------\n" );
sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
}
}
+ 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;
+ }
+ }
+
+ boolean isSubtreeDisplayed() {
+ if ( getCurrentTreePanel() != null ) {
+ if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
+ JOptionPane
+ .showMessageDialog( this,
+ "This operation can only be performed on a complete tree, not on the currently displayed sub-tree only.",
+ "Operation can not be exectuted on a sub-tree",
+ JOptionPane.WARNING_MESSAGE );
+ return true;
+ }
+ }
+ return false;
+ }
+
void removeAllTextFrames() {
for( final TextFrame tf : _textframes ) {
if ( tf != null ) {
}
}
+ void showWhole() {
+ _mainpanel.getControlPanel().showWhole();
+ }
+
void switchColors() {
final TreeColorSet colorset = getMainPanel().getCurrentTreePanel().getTreeColorSet();
final ColorSchemeChooser csc = new ColorSchemeChooser( getMainPanel(), colorset );
}
private MainPanel getMainPanel() {
- return _main_panel;
+ return _mainpanel;
+ }
+
+ private Phylogeny getSpeciesTree() {
+ return _species_tree;
}
private boolean isScreenAntialias() {
}
private void setMainPanel( final MainPanelApplets main_panel ) {
- _main_panel = main_panel;
+ _mainpanel = main_panel;
+ }
+
+ private void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
}
private void setupUI() {
git://source.jalview.org / jalview.git / blobdiff