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;
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;
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;
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" ) );
gene_tree.setAllNodesToNotCollapse();
gene_tree.recalculateNumberOfExternalDescendants( false );
GSDI gsdi = null;
- final Phylogeny species_tree = _species_tree.copy();
+ final Phylogeny species_tree = getSpeciesTree().copy();
try {
- gsdi = new GSDI( gene_tree, species_tree, false, true, true );
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
}
catch ( final SDIException e ) {
JOptionPane.showMessageDialog( this,
gene_tree.setAllNodesToNotCollapse();
gene_tree.recalculateNumberOfExternalDescendants( false );
GSDIR gsdir = null;
- final Phylogeny species_tree = _species_tree.copy();
+ final Phylogeny species_tree = getSpeciesTree().copy();
try {
- gsdir = new GSDIR( gene_tree, species_tree, true, true );
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
}
catch ( final SDIException e ) {
JOptionPane.showMessageDialog( this,
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();
return _jmenubar;
}
+ final Phylogeny getSpeciesTree() {
+ return _species_tree;
+ }
+
void help() {
final StringBuilder sb = new StringBuilder();
sb.append( "Display options\n" );
if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
return false;
}
- else if ( ( _species_tree == null ) || _species_tree.isEmpty() ) {
+ 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 && !_species_tree.isCompletelyBinary() ) {
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
JOptionPane.showMessageDialog( this,
"Species tree is not completely binary",
"Cannot execute GSDI",
}
}
+ final void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
+
void setTypeMenuToAllUnselected() {
_convex_type_cbmi.setSelected( false );
_curved_type_cbmi.setSelected( false );