import org.forester.phylogeny.PhylogenyNode;\r
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;\r
import org.forester.phylogeny.data.Confidence;\r
+import org.forester.phylogeny.data.PhylogenyDataUtil;\r
import org.forester.phylogeny.data.Sequence;\r
import org.forester.phylogeny.data.Taxonomy;\r
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;\r
private JMenuItem _write_to_tif_item;\r
private JMenuItem _write_to_png_item;\r
private JMenuItem _write_to_bmp_item;\r
+ private JMenuItem _collapse_below_threshold;\r
+ private JMenuItem _collapse_below_branch_length;\r
private File _current_dir;\r
private ButtonGroup _radio_group_1;\r
private ButtonGroup _radio_group_2;\r
// Others:\r
double _min_not_collapse = Constants.MIN_NOT_COLLAPSE_DEFAULT;\r
+ double _min_not_collapse_bl = 0.001;\r
// Phylogeny Inference menu\r
private JMenu _inference_menu;\r
private JMenuItem _inference_from_msa_item;\r
}\r
collapseBelowThreshold();\r
}\r
+ else if ( o == _collapse_below_branch_length ) {\r
+ if ( isSubtreeDisplayed() ) {\r
+ return;\r
+ }\r
+ collapseBelowBranchLengthThreshold();\r
+ }\r
else if ( ( o == _extract_taxonomy_pfam_strict_rbmi ) || ( o == _extract_taxonomy_pfam_relaxed_rbmi )\r
|| ( o == _extract_taxonomy_agressive_rbmi ) ) {\r
if ( _replace_underscores_cbmi != null ) {\r
_tools_menu.addSeparator();\r
_tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );\r
customizeJMenuItem( _collapse_species_specific_subtrees );\r
+ _collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );\r
_tools_menu\r
.add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );\r
customizeJMenuItem( _collapse_below_threshold );\r
_collapse_below_threshold\r
- .setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );\r
+ .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );\r
+ //\r
+ _tools_menu\r
+ .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );\r
+ customizeJMenuItem( _collapse_below_branch_length );\r
+ _collapse_below_branch_length\r
+ .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );\r
+ //\r
_tools_menu.addSeparator();\r
_tools_menu\r
.add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );\r
}\r
}\r
\r
- private void collapse( final Phylogeny phy, final double m ) {\r
+ private void collapseBl( final Phylogeny phy ) {\r
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
+ final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
+ double min_bl = Double.MAX_VALUE;\r
+ boolean bl_present = false;\r
+ while ( it.hasNext() ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( !n.isExternal() && !n.isRoot() ) {\r
+ final double bl = n.getDistanceToParent();\r
+ if ( bl != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {\r
+ bl_present = true;\r
+ if ( bl < getMinNotCollapseBlValue() ) {\r
+ to_be_removed.add( n );\r
+ }\r
+ if ( bl < min_bl ) {\r
+ min_bl = bl;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if ( bl_present ) {\r
+ for( final PhylogenyNode node : to_be_removed ) {\r
+ PhylogenyMethods.removeNode( node, phy );\r
+ }\r
+ if ( to_be_removed.size() > 0 ) {\r
+ phy.externalNodesHaveChanged();\r
+ phy.clearHashIdToNodeMap();\r
+ phy.recalculateNumberOfExternalDescendants( true );\r
+ getCurrentTreePanel().resetNodeIdToDistToLeafMap();\r
+ getCurrentTreePanel().updateSetOfCollapsedExternalNodes();\r
+ getCurrentTreePanel().calculateLongestExtNodeInfo();\r
+ getCurrentTreePanel().setNodeInPreorderToNull();\r
+ getCurrentTreePanel().recalculateMaxDistanceToRoot();\r
+ getCurrentTreePanel().resetPreferredSize();\r
+ getCurrentTreePanel().setEdited( true );\r
+ getCurrentTreePanel().repaint();\r
+ repaint();\r
+ }\r
+ if ( to_be_removed.size() > 0 ) {\r
+ JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()\r
+ + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "\r
+ + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No branch collapsed,\nminimum branch length is " + min_bl,\r
+ "No branch collapsed",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ }\r
+ else {\r
+ JOptionPane.showMessageDialog( this,\r
+ "No branch collapsed because no branch length values present",\r
+ "No branch length values present",\r
+ JOptionPane.INFORMATION_MESSAGE );\r
+ }\r
+ }\r
+\r
+ private void collapse( final Phylogeny phy ) {\r
final PhylogenyNodeIterator it = phy.iteratorPostorder();\r
final List<PhylogenyNode> to_be_removed = new ArrayList<PhylogenyNode>();\r
double min_support = Double.MAX_VALUE;\r
}\r
if ( success && ( m >= 0.0 ) ) {\r
setMinNotCollapseConfidenceValue( m );\r
- collapse( phy, m );\r
+ collapse( phy );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ private void collapseBelowBranchLengthThreshold() {\r
+ if ( getCurrentTreePanel() != null ) {\r
+ final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ final String s = ( String ) JOptionPane\r
+ .showInputDialog( this,\r
+ "Please enter the minimum branch length value\n",\r
+ "Minimal Branch Length Value",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null,\r
+ null,\r
+ getMinNotCollapseBlValue() );\r
+ if ( !ForesterUtil.isEmpty( s ) ) {\r
+ boolean success = true;\r
+ double m = 0.0;\r
+ final String m_str = s.trim();\r
+ if ( !ForesterUtil.isEmpty( m_str ) ) {\r
+ try {\r
+ m = Double.parseDouble( m_str );\r
+ }\r
+ catch ( final Exception ex ) {\r
+ success = false;\r
+ }\r
+ }\r
+ else {\r
+ success = false;\r
+ }\r
+ if ( success && ( m >= 0.0 ) ) {\r
+ setMinNotCollapseBlValue( m );\r
+ collapseBl( phy );\r
}\r
}\r
}\r
return _min_not_collapse;\r
}\r
\r
+ private double getMinNotCollapseBlValue() {\r
+ return _min_not_collapse_bl;\r
+ }\r
+\r
private PhylogeneticInferenceOptions getPhylogeneticInferenceOptions() {\r
if ( _phylogenetic_inference_options == null ) {\r
_phylogenetic_inference_options = new PhylogeneticInferenceOptions();\r
if ( n.isExternal() ) {\r
if ( n.getNodeData().isHasSequence() ) {\r
final Sequence s = n.getNodeData().getSequence();\r
- if ( ForesterUtil.isEmpty( s.getGeneName() ) ) {\r
+ if ( ForesterUtil.isEmpty( s.getGeneName() ) || s.getGeneName().startsWith( "LOC" ) ) {\r
if ( ( s.getAccession() != null )\r
&& !ForesterUtil.isEmpty( s.getAccession().getValue() ) ) {\r
s.setGeneName( s.getAccession().getValue() );\r
_min_not_collapse = min_not_collapse;\r
}\r
\r
+ private void setMinNotCollapseBlValue( final double min_not_collapse_bl ) {\r
+ _min_not_collapse_bl = min_not_collapse_bl;\r
+ }\r
+\r
private void setPhylogeneticInferenceOptions( final PhylogeneticInferenceOptions phylogenetic_inference_options ) {\r
_phylogenetic_inference_options = phylogenetic_inference_options;\r
}\r
git://source.jalview.org / jalview.git / blobdiff