return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
}
- public String getTreeUrlStr() {
- return _tree_url_str;
- }
-
public String getSpeciesTreeUrlStr() {
return _species_tree_url_str;
}
+ public String getTreeUrlStr() {
+ return _tree_url_str;
+ }
+
@Override
public void init() {
boolean has_exception = false;
TAXONOMY_EXTRACTION.NO );
if ( ( species_trees != null ) && ( species_trees.length > 0 ) ) {
AptxUtil.printAppletMessage( NAME, "successfully read species tree" );
- getMainFrameApplet().setSpeciesTree( species_trees[ 0 ] );
+ 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 {
+ getMainFrameApplet().setSpeciesTree( species_trees[ 0 ] );
+ }
+ }
+ else {
+ ForesterUtil.printErrorMessage( NAME, "failed to read species tree from " + getSpeciesTreeUrlStr() );
}
}
getMainFrameApplet().getMainPanel().getControlPanel().showWholeAll();
if ( default_sequence != null ) {
getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox()
.setSelectedItem( default_sequence );
- /* GUILHEM_END */
}
+ /* GUILHEM_END */
}
/**
_message_2 = message_2;
}
- private void setTreeUrlStr( final String url_string ) {
- _tree_url_str = url_string;
- }
-
private void setSpeciesTreeUrlStr( final String url_string ) {
_species_tree_url_str = url_string;
}
+
+ private void setTreeUrlStr( final String url_string ) {
+ _tree_url_str = url_string;
+ }
}
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.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() );
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 ),
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 );
+ }
+ 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 ] );
+ }
+ }
+ }
+ //
setVisible( false );
setMainPanel( new MainPanelApplets( getConfiguration(), this ) );
_jmenubar = new JMenuBar();
if ( !getConfiguration().isUseNativeUI() ) {
_jmenubar.setBackground( getConfiguration().getGuiMenuBackgroundColor() );
}
+ if ( getSpeciesTree() != null ) {
+ buildAnalysisMenu();
+ }
buildToolsMenu();
buildViewMenu();
buildFontSizeMenu();
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 );
+ }
+ 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 );
+ }
+ 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 );
+ 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;
}
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 -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\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() {
public final static boolean __SYNTH_LF = false; // TODO remove me
public final static boolean ALLOW_DDBJ_BLAST = false;
public final static String PRG_NAME = "Archaeopteryx";
- final static String VERSION = "0.9805+ A1ST";
- final static String PRG_DATE = "130306";
+ final static String VERSION = "0.9806 A1ST";
+ final static String PRG_DATE = "130308";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Verdana", "Tahoma",
"Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
import org.forester.archaeopteryx.tools.ProcessRunning;
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.NodeVisualization.NodeFill;
import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+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;
else if ( o == _exit_item ) {
close();
}
+ else if ( o == _gsdi_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDI();
+ }
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
+ }
else if ( o == _taxcolor_item ) {
taxColor();
}
JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
}
+ 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 );
+ 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 );
+ }
+ 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 );
+ 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 );
+ }
+ }
+
boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
JOptionPane.showMessageDialog( this,
}
}
+ 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() ) {
if ( !_configuration.isUseNativeUI() ) {
_jmenubar.setBackground( _configuration.getGuiMenuBackgroundColor() );
}
- //TODO if species tree...
- buildAnalysisMenu();
+ if ( _species_tree != null ) {
+ buildAnalysisMenu();
+ }
buildToolsMenu();
buildViewMenu();
buildFontSizeMenu();
System.gc();
}
+ @Override
+ public MainPanel getMainPanel() {
+ return _mainpanel;
+ }
+
void buildAnalysisMenu() {
_analysis_menu = MainFrame.createMenu( "Analysis", getConfiguration() );
_analysis_menu.add( _gsdi_item = new JMenuItem( "GSDI (Generalized Speciation Duplication Inference)" ) );
}
@Override
- public MainPanel getMainPanel() {
- return _mainpanel;
- }
-
- @Override
void readPhylogeniesFromURL() {
throw new NoSuchMethodError( "not implemented" );
}
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;
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"
}
}
+ private void setArrowCursor() {
+ try {
+ _mainpanel.getCurrentTreePanel().setArrowCursor();
+ }
+ catch ( final Exception ex ) {
+ // Do nothing.
+ }
+ }
+
private void setCurrentDir( final File current_dir ) {
_current_dir = current_dir;
}
public final class ForesterConstants {
- public final static String FORESTER_VERSION = "1.023";
- public final static String FORESTER_DATE = "130306";
+ public final static String FORESTER_VERSION = "1.024";
+ public final static String FORESTER_DATE = "130308";
public final static String PHYLO_XML_VERSION = "1.10";
public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org";
public final static String PHYLO_XML_XSD = "phyloxml.xsd";
git://source.jalview.org / jalview.git / commitdiff