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.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
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;
static final String FONT_SIZE_MENU_LABEL = "Font Size";
static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
static final String SHOW_DOMAIN_LABELS_LABEL = "Show Domain Labels";
+ static final String SHOW_ANN_REF_SOURCE_LABEL = "Show Seq Annotation Ref Sources";
static final String COLOR_LABELS_TIP = "To use parent branch colors for node labels as well, need to turn off taxonomy dependent colorization and turn on branch colorization for this to become apparent";
static final String ABBREV_SN_LABEL = "Abbreviate Scientific Taxonomic Names";
static final String TAXONOMY_COLORIZE_NODE_SHAPES_LABEL = "Colorize Node Shapes According to Taxonomy";
static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
+ static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Show Basic Tree Information";
JMenuBar _jmenubar;
JMenu _file_jmenu;
JMenu _tools_menu;
JMenuItem _gsdi_item;
JMenuItem _gsdir_item;
JMenuItem _lineage_inference;
- JMenuItem _function_analysis;
// file menu:
JMenuItem _open_item;
JMenuItem _open_url_item;
JCheckBoxMenuItem _show_scale_cbmi; //TODO fix me
JCheckBoxMenuItem _show_overview_cbmi;
JCheckBoxMenuItem _show_domain_labels;
+ JCheckBoxMenuItem _show_annotation_ref_source;
JCheckBoxMenuItem _abbreviate_scientific_names;
JCheckBoxMenuItem _color_labels_same_as_parent_branch;
JMenuItem _overview_placment_mi;
// _ parsing
JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
- JRadioButtonMenuItem _extract_taxonomy_yes_rbmi;
- JRadioButtonMenuItem _extract_taxonomy_pfam_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
JCheckBoxMenuItem _replace_underscores_cbmi;
JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
Configuration _configuration;
JMenuItem _remove_branch_color_item;
Options _options;
- Phylogeny _species_tree;
+ private Phylogeny _species_tree;
InferenceManager _inference_manager;
final ProcessPool _process_pool;
private String _previous_node_annotation_ref;
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();
}
else if ( o == _show_domain_labels ) {
updateOptions( getOptions() );
}
+ else if ( o == _show_annotation_ref_source ) {
+ updateOptions( getOptions() );
+ }
else if ( o == _abbreviate_scientific_names ) {
updateOptions( getOptions() );
}
void buildViewMenu() {
_view_jmenu = createMenu( "View", getConfiguration() );
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
_view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
_view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
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 = getSpeciesTree().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 = getSpeciesTree().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 );
+ }
+ }
+
boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
JOptionPane.showMessageDialog( this,
return _jmenubar;
}
+ final Phylogeny getSpeciesTree() {
+ return _species_tree;
+ }
+
void help() {
final StringBuilder sb = new StringBuilder();
sb.append( "Display options\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 ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
+ JOptionPane.showMessageDialog( this,
+ "No species tree loaded",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( species_tree_has_to_binary && !getSpeciesTree().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() ) {
}
}
+ final void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
+
void setTypeMenuToAllUnselected() {
_convex_type_cbmi.setSelected( false );
_curved_type_cbmi.setSelected( false );
options.setBackgroundColorGradient( ( _background_gradient_cbmi != null )
&& _background_gradient_cbmi.isSelected() );
options.setShowDomainLabels( ( _show_domain_labels != null ) && _show_domain_labels.isSelected() );
+ options.setShowAnnotationRefSource( ( _show_annotation_ref_source != null )
+ && _show_annotation_ref_source.isSelected() );
options.setAbbreviateScientificTaxonNames( ( _abbreviate_scientific_names != null )
&& _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _print_black_and_white_cbmi.isSelected() );
options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
&& _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
- if ( ( _extract_taxonomy_yes_rbmi != null ) && _extract_taxonomy_yes_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.AGRESSIVE );
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ }
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
}
- else if ( ( _extract_taxonomy_pfam_rbmi != null ) && _extract_taxonomy_pfam_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
}
else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
- options.setTaxonomyExtractio( TAXONOMY_EXTRACTION.NO );
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
}
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
&& _replace_underscores_cbmi.isSelected() );