import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
-import java.util.Map;
import java.util.Set;
import javax.swing.ButtonGroup;
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.SequenceWriter;
public final class MainFrameApplication extends MainFrame {
- private final static int FRAME_X_SIZE = 800;
- private final static int FRAME_Y_SIZE = 800;
+ private final static int FRAME_X_SIZE = 900;
+ private final static int FRAME_Y_SIZE = 900;
// Filters for the file-open dialog (classes defined in this file)
private static final long serialVersionUID = -799735726778865234L;
private static final boolean PREPROCESS_TREES = false;
// Application-only print menu items
private JMenuItem _collapse_below_threshold;
private JMenuItem _collapse_below_branch_length;
- private JMenuItem _collapse_by_taxonomic_rank;
private ButtonGroup _radio_group_1;
private ButtonGroup _radio_group_2;
// Others:
}
collapseBelowThreshold();
}
- else if ( o == _collapse_by_taxonomic_rank ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- collapseByTaxonomicRank();
- }
+
else if ( o == _collapse_below_branch_length ) {
if ( isSubtreeDisplayed() ) {
return;
l.add( d );
}
if ( !l.isEmpty() ) {
- if ( node.getNodeData().getProperties() != null ) {
- node.getNodeData().getProperties()
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
- }
+
node.getNodeData().setVector( l );
}
}
}
}
- private void collapse( final Phylogeny phy ) {
+ private void collapseBelowThreshold( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();
double min_support = Double.MAX_VALUE;
}
}
- private void collapseByTaxonomicRank() {
- if ( _mainpanel.getCurrentTreePanel() != null ) {
- final Map<String, Integer> present_ranks = AptxUtil.getRankCounts( _mainpanel.getCurrentTreePanel().getPhylogeny());
- final String[] ranks = AptxUtil.getAllPossibleRanks(present_ranks);
- String rank = ( String ) JOptionPane
- .showInputDialog( this,
- "What rank should the collapsing be based on",
- "Rank Selection",
- JOptionPane.QUESTION_MESSAGE,
- null,
- ranks,
- null );
- if ( !ForesterUtil.isEmpty( rank ) ) {
- if ( rank.indexOf( '(' ) > 0 ) {
- rank = rank.substring( 0, rank.indexOf( '(' ) ).trim();
- }
- _mainpanel.getCurrentTreePanel().collapseByTaxonomicRank( rank );
- }
- }
- }
-
private void collapseBelowBranchLengthThreshold() {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
}
if ( success && ( m >= 0.0 ) ) {
setMinNotCollapseConfidenceValue( m );
- collapse( phy );
+ collapseBelowThreshold( phy );
}
}
}
_mainpanel.getControlPanel().showWhole();
_mainpanel.getCurrentTreePanel().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
_mainpanel.getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- if ( getMainPanel().getMainFrame() == null ) {
- // Must be "E" applet version.
- ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
- .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- }
- else {
- getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
- }
+
+ getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+
activateSaveAllIfNeeded();
System.gc();
}
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
_options_jmenu
.add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
- _options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
_radio_group_1 = new ButtonGroup();
_radio_group_1.add( _ext_node_dependent_cladogram_rbmi );
- _radio_group_1.add( _uniform_cladograms_rbmi );
- _radio_group_1.add( _non_lined_up_cladograms_rbmi );
+ _radio_group_1.add( _non_lined_up_cladograms_rbmi );
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
_options_jmenu
.add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
_options_jmenu
.add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
+
+ _options_jmenu
+ .add( _collapsed_with_average_height_cbmi = new JCheckBoxMenuItem( "Proportional Height of Collapsed Subtrees" ) );
+
+
+ _options_jmenu
+ .add( _show_abbreviated_labels_for_collapsed_nodes_cbmi = new JCheckBoxMenuItem( "Add Abbreviated Labels to Collapsed Subtrees" ) );
+
+
+
_options_jmenu
.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
+
+
+
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
_options_jmenu
.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
customizeCheckBoxMenuItem( _abbreviate_scientific_names, getOptions().isAbbreviateScientificTaxonNames() );
customizeCheckBoxMenuItem( _search_case_senstive_cbmi, getOptions().isSearchCaseSensitive() );
customizeCheckBoxMenuItem( _show_scale_cbmi, getOptions().isShowScale() );
+ customizeCheckBoxMenuItem( _collapsed_with_average_height_cbmi, getOptions().isCollapsedWithAverageHeigh() );
+ customizeCheckBoxMenuItem( _show_abbreviated_labels_for_collapsed_nodes_cbmi, getOptions().isShowAbbreviatedLabelsForCollapsedNodes() );
+
customizeRadioButtonMenuItem( _non_lined_up_cladograms_rbmi,
getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP );
- customizeRadioButtonMenuItem( _uniform_cladograms_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );
customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,
- getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );
+ getOptions().getCladogramType() == CLADOGRAM_TYPE.LINED_UP );
customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );
customizeCheckBoxMenuItem( _label_direction_cbmi,
getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
_delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );
customizeJMenuItem( _delete_not_selected_nodes_item );
_tools_menu.addSeparator();
- _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
+ _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Single Taxonomy-Subtrees" ) );
customizeJMenuItem( _collapse_species_specific_subtrees );
- _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );
- _tools_menu.add( _collapse_by_taxonomic_rank = new JMenuItem( "Collapse By Taxonomic Rank" ) );
- customizeJMenuItem( _collapse_by_taxonomic_rank );
- _collapse_by_taxonomic_rank.setToolTipText( "To (reversibly) collapse subtrees by taxonomic rank" );
+ _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse subtrees associated with only one taxonomy (such as species specific subtrees)" );
_tools_menu
.add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
customizeJMenuItem( _collapse_below_threshold );
git://source.jalview.org / jalview.git / blobdiff