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
import org.forester.phylogeny.factories.PhylogenyFactory;\r
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
-import org.forester.sequence.Sequence;\r
+import org.forester.sequence.MolecularSequence;\r
import org.forester.util.BasicDescriptiveStatistics;\r
import org.forester.util.BasicTable;\r
import org.forester.util.BasicTableParser;\r
private final static SequencesFileFilter seqsfilter = new SequencesFileFilter();\r
private final static DefaultFilter defaultfilter = new DefaultFilter();\r
private static final long serialVersionUID = -799735726778865234L;\r
+ private static final boolean PREPROCESS_TREES = false;\r
private final JFileChooser _values_filechooser;\r
private final JFileChooser _sequences_filechooser;\r
private final JFileChooser _open_filechooser;\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
private PhylogeneticInferenceOptions _phylogenetic_inference_options = null;\r
private Msa _msa = null;\r
private File _msa_file = null;\r
- private List<Sequence> _seqs = null;\r
+ private List<MolecularSequence> _seqs = null;\r
private File _seqs_file = null;\r
JMenuItem _read_values_jmi;\r
JMenuItem _read_seqs_jmi;\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
return _msa_file;\r
}\r
\r
- public List<Sequence> getSeqs() {\r
+ public List<MolecularSequence> getSeqs() {\r
return _seqs;\r
}\r
\r
if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
setSeqsFile( null );\r
setSeqs( null );\r
- List<Sequence> seqs = null;\r
+ List<MolecularSequence> seqs = null;\r
try {\r
if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
seqs = FastaParser.parse( new FileInputStream( file ) );\r
- for( final Sequence seq : seqs ) {\r
+ for( final MolecularSequence seq : seqs ) {\r
System.out.println( SequenceWriter.toFasta( seq, 60 ) );\r
}\r
}\r
.createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );\r
setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );\r
setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );\r
- MainFrame.updateOptionsMenuDependingOnPhylogenyType( getMainPanel(),\r
- _show_scale_cbmi,\r
- _show_branch_length_values_cbmi,\r
- _non_lined_up_cladograms_rbmi,\r
- _uniform_cladograms_rbmi,\r
- _ext_node_dependent_cladogram_rbmi,\r
- _label_direction_cbmi );\r
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );\r
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );\r
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );\r
+ try {\r
+ getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();\r
+ getMainPanel().getControlPanel().setVisibilityOfX();\r
+ }\r
+ catch ( final Exception ignore ) {\r
+ // do nothing, not important.\r
+ }\r
}\r
} );\r
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );\r
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );\r
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );\r
_options_jmenu\r
- .add( _show_branch_length_values_cbmi = new JCheckBoxMenuItem( DISPLAY_BRANCH_LENGTH_VALUES_LABEL ) );\r
- _options_jmenu\r
.add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );\r
_options_jmenu\r
.add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );\r
+ _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );\r
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {\r
- _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( SHOW_DOMAIN_LABELS_LABEL ) );\r
+ _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );\r
+ _options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );\r
}\r
_options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );\r
_options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) );\r
getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP );\r
customizeRadioButtonMenuItem( _ext_node_dependent_cladogram_rbmi,\r
getOptions().getCladogramType() == CLADOGRAM_TYPE.EXT_NODE_SUM_DEP );\r
- customizeCheckBoxMenuItem( _show_branch_length_values_cbmi, getOptions().isShowBranchLengthValues() );\r
customizeCheckBoxMenuItem( _show_overview_cbmi, getOptions().isShowOverview() );\r
customizeCheckBoxMenuItem( _label_direction_cbmi,\r
getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );\r
.getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );\r
customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()\r
.getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );\r
+ customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );\r
+ customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );\r
_jmenubar.add( _options_jmenu );\r
}\r
\r
_tools_menu.addSeparator();\r
_tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );\r
_remove_visual_styles_item\r
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny." );\r
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );\r
customizeJMenuItem( _remove_visual_styles_item );\r
_tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );\r
- _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny." );\r
+ _remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );\r
customizeJMenuItem( _remove_branch_color_item );\r
_tools_menu.addSeparator();\r
_tools_menu.add( _annotate_item = new JMenuItem( "Annotate Sequences of Selected Nodes" ) );\r
_tools_menu.add( _midpoint_root_item = new JMenuItem( "Midpoint-Root" ) );\r
customizeJMenuItem( _midpoint_root_item );\r
_tools_menu.addSeparator();\r
- _tools_menu.add( _deleted_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );\r
- customizeJMenuItem( _deleted_selected_nodes_item );\r
- _tools_menu.add( _deleted_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );\r
- customizeJMenuItem( _deleted_not_selected_nodes_item );\r
+ _tools_menu.add( _delete_selected_nodes_item = new JMenuItem( "Delete Selected Nodes" ) );\r
+ _delete_selected_nodes_item.setToolTipText( "To delete all selected external nodes" );\r
+ customizeJMenuItem( _delete_selected_nodes_item );\r
+ _tools_menu.add( _delete_not_selected_nodes_item = new JMenuItem( "Retain Selected Nodes" ) );\r
+ _delete_not_selected_nodes_item.setToolTipText( "To delete all not selected external nodes" );\r
+ customizeJMenuItem( _delete_not_selected_nodes_item );\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
if ( ( phys != null ) && ( phys.length > 0 ) ) {\r
if ( nhx_or_nexus && getOptions().isInternalNumberAreConfidenceForNhParsing() ) {\r
for( final Phylogeny phy : phys ) {\r
- \r
PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );\r
}\r
}\r
_msa_file = msa_file;\r
}\r
\r
- void setSeqs( final List<Sequence> seqs ) {\r
+ void setSeqs( final List<MolecularSequence> seqs ) {\r
_seqs = seqs;\r
}\r
\r
}\r
final int result = _sequences_filechooser.showOpenDialog( _contentpane );\r
final File file = _sequences_filechooser.getSelectedFile();\r
- List<Sequence> seqs = null;\r
+ List<MolecularSequence> seqs = null;\r
if ( ( file != null ) && !file.isDirectory() && ( result == JFileChooser.APPROVE_OPTION ) ) {\r
try {\r
if ( FastaParser.isLikelyFasta( new FileInputStream( file ) ) ) {\r
}\r
}\r
if ( seqs != null ) {\r
- for( final Sequence seq : seqs ) {\r
+ for( final MolecularSequence seq : seqs ) {\r
System.out.println( seq.getIdentifier() );\r
}\r
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();\r
int total_counter = 0;\r
int attached_counter = 0;\r
- for( final Sequence seq : seqs ) {\r
+ for( final MolecularSequence seq : seqs ) {\r
++total_counter;\r
final String seq_name = seq.getIdentifier();\r
if ( !ForesterUtil.isEmpty( seq_name ) ) {\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
}\r
}\r
}\r
+ if ( PREPROCESS_TREES ) {\r
+ preProcessTreesUponReading( phys );\r
+ }\r
AptxUtil.addPhylogeniesToTabs( phys,\r
file.getName(),\r
file.getAbsolutePath(),\r
System.gc();\r
}\r
\r
+ private void preProcessTreesUponReading( final Phylogeny[] phys ) {\r
+ for( final Phylogeny phy : phys ) {\r
+ if ( ( phy != null ) && !phy.isEmpty() ) {\r
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {\r
+ final PhylogenyNode n = it.next();\r
+ if ( n.isExternal() ) {\r
+ if ( n.getNodeData().isHasSequence() ) {\r
+ final Sequence s = n.getNodeData().getSequence();\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
+ }\r
+ else if ( !ForesterUtil.isEmpty( n.getName() ) ) {\r
+ s.setGeneName( n.getName() );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
private void readSpeciesTreeFromFile() {\r
Phylogeny t = null;\r
boolean exception = false;\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