2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
11 // This library is free software; you can redistribute it and/or
12 // modify it under the terms of the GNU Lesser General Public
13 // License as published by the Free Software Foundation; either
14 // version 2.1 of the License, or (at your option) any later version.
16 // This library is distributed in the hope that it will be useful,
17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 // Lesser General Public License for more details.
21 // You should have received a copy of the GNU Lesser General Public
22 // License along with this library; if not, write to the Free Software
23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 // Contact: phylosoft @ gmail . com
26 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
28 package org.forester.phylogeny;
30 import java.io.IOException;
31 import java.util.ArrayList;
32 import java.util.Arrays;
33 import java.util.Collection;
34 import java.util.HashMap;
35 import java.util.Iterator;
36 import java.util.List;
38 import java.util.NoSuchElementException;
39 import java.util.Vector;
41 import org.forester.io.parsers.nhx.NHXParser;
42 import org.forester.io.writers.PhylogenyWriter;
43 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
44 import org.forester.phylogeny.data.BranchData;
45 import org.forester.phylogeny.data.Confidence;
46 import org.forester.phylogeny.data.Identifier;
47 import org.forester.phylogeny.data.PhylogenyDataUtil;
48 import org.forester.phylogeny.data.Sequence;
49 import org.forester.phylogeny.data.SequenceRelation;
50 import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
51 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
52 import org.forester.phylogeny.factories.PhylogenyFactory;
53 import org.forester.phylogeny.iterators.ExternalForwardIterator;
54 import org.forester.phylogeny.iterators.LevelOrderTreeIterator;
55 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
56 import org.forester.phylogeny.iterators.PostorderTreeIterator;
57 import org.forester.phylogeny.iterators.PreorderTreeIterator;
58 import org.forester.util.FailedConditionCheckException;
59 import org.forester.util.ForesterUtil;
61 public class Phylogeny {
63 public final static boolean ALLOW_MULTIPLE_PARENTS_DEFAULT = false;
64 private PhylogenyNode _root;
65 private boolean _rooted;
66 private boolean _allow_multiple_parents;
69 private String _description;
70 private String _distance_unit;
71 private Confidence _confidence;
72 private Identifier _identifier;
73 private boolean _rerootable;
74 private HashMap<Long, PhylogenyNode> _id_to_node_map;
75 private List<PhylogenyNode> _external_nodes_set;
76 private Collection<Sequence> _sequenceRelationQueries;
77 private Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> _relevant_sequence_relation_types;
80 * Default Phylogeny constructor. Constructs an empty Phylogeny.
87 * Adds this Phylogeny to the list of child nodes of PhylogenyNode parent
88 * and sets the parent of this to parent.
91 * the PhylogenyNode to add
93 public void addAsChild( final PhylogenyNode parent ) {
95 throw new IllegalArgumentException( "Attempt to add an empty tree." );
98 throw new IllegalArgumentException( "Attempt to add an unrooted tree." );
100 parent.addAsChild( getRoot() );
101 externalNodesHaveChanged();
104 public void addAsSibling( final PhylogenyNode sibling ) {
106 throw new IllegalArgumentException( "Attempt to add an empty tree." );
109 throw new IllegalArgumentException( "Attempt to add an unrooted tree." );
111 final int sibling_index = sibling.getChildNodeIndex();
112 final PhylogenyNode new_node = new PhylogenyNode();
113 final PhylogenyNode sibling_parent = sibling.getParent();
114 new_node.setChild1( sibling );
115 new_node.setChild2( getRoot() );
116 new_node.setParent( sibling_parent );
117 sibling.setParent( new_node );
118 sibling_parent.setChildNode( sibling_index, new_node );
119 final double new_dist = sibling.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ? PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT
120 : sibling.getDistanceToParent() / 2;
121 new_node.setDistanceToParent( new_dist );
122 sibling.setDistanceToParent( new_dist );
123 externalNodesHaveChanged();
127 * This calculates the height of the subtree emanating at n for rooted,
128 * tree-shaped phylogenies
131 * the root-node of a subtree
132 * @return the height of the subtree emanating at n
134 public double calculateSubtreeHeight( final PhylogenyNode n, final boolean take_collapse_into_account ) {
135 if ( n.isExternal() || ( take_collapse_into_account && n.isCollapse() ) ) {
136 return n.getDistanceToParent() > 0 ? n.getDistanceToParent() : 0;
139 double max = -Double.MAX_VALUE;
140 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
141 final double l = calculateSubtreeHeight( n.getChildNode( i ), take_collapse_into_account );
146 return max + ( n.getDistanceToParent() > 0 ? n.getDistanceToParent() : 0) ;
150 public void clearHashIdToNodeMap() {
151 setIdToNodeMap( null );
155 * Returns a deep copy of this Phylogeny.
157 * (The resulting Phylogeny has its references in the external nodes
158 * corrected, if they are lacking/obsolete in this.)
160 public Phylogeny copy() {
161 return copy( _root );
165 * Returns a deep copy of this Phylogeny.
167 * (The resulting Phylogeny has its references in the external nodes
168 * corrected, if they are lacking/obsolete in this.)
170 public Phylogeny copy( final PhylogenyNode source ) {
171 final Phylogeny tree = new Phylogeny();
176 tree._rooted = _rooted;
177 tree._name = new String( _name );
178 tree._description = new String( _description );
179 tree._type = new String( _type );
180 tree._rerootable = _rerootable;
181 tree._distance_unit = new String( _distance_unit );
182 if ( _confidence != null ) {
183 tree._confidence = ( Confidence ) _confidence.copy();
185 if ( _identifier != null ) {
186 tree._identifier = ( Identifier ) _identifier.copy();
188 tree.setAllowMultipleParents( isAllowMultipleParents() );
189 tree._root = PhylogenyMethods.copySubTree( source );
194 * Returns a shallow copy of this Phylogeny.
196 * (The resulting Phylogeny has its references in the external nodes
197 * corrected, if they are lacking/obsolete in this.)
199 public Phylogeny copyShallow() {
200 return copyShallow( _root );
203 public Phylogeny copyShallow( final PhylogenyNode source ) {
204 final Phylogeny tree = new Phylogeny();
209 tree._rooted = _rooted;
211 tree._description = _description;
213 tree._rerootable = _rerootable;
214 tree._distance_unit = _distance_unit;
215 tree._confidence = _confidence;
216 tree._identifier = _identifier;
217 tree.setAllowMultipleParents( isAllowMultipleParents() );
218 tree._root = PhylogenyMethods.copySubTreeShallow( source );
223 * Need to call clearHashIdToNodeMap() afterwards (not done automatically
224 * to allow client multiple deletions in linear time).
225 * Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this
226 * if tree is to be displayed.
228 * @param remove_us the parent node of the subtree to be deleted
230 public void deleteSubtree( final PhylogenyNode remove_us, final boolean collapse_resulting_node_with_one_desc ) {
231 if ( isEmpty() || ( remove_us.isRoot() && ( getNumberOfExternalNodes() != 1 ) ) ) {
234 if ( remove_us.isRoot() && ( getNumberOfExternalNodes() == 1 ) ) {
237 else if ( !collapse_resulting_node_with_one_desc ) {
238 remove_us.getParent().removeChildNode( remove_us );
241 final PhylogenyNode removed_node = remove_us;
242 final PhylogenyNode p = remove_us.getParent();
244 if ( p.getNumberOfDescendants() == 2 ) {
245 if ( removed_node.isFirstChildNode() ) {
246 setRoot( getRoot().getChildNode( 1 ) );
247 getRoot().setParent( null );
250 setRoot( getRoot().getChildNode( 0 ) );
251 getRoot().setParent( null );
255 p.removeChildNode( removed_node.getChildNodeIndex() );
259 final PhylogenyNode pp = removed_node.getParent().getParent();
260 if ( p.getNumberOfDescendants() == 2 ) {
261 final int pi = p.getChildNodeIndex();
262 if ( removed_node.isFirstChildNode() ) {
263 p.getChildNode( 1 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
264 .getDistanceToParent(), p.getChildNode( 1 ).getDistanceToParent() ) );
265 pp.setChildNode( pi, p.getChildNode( 1 ) );
268 p.getChildNode( 0 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
269 .getDistanceToParent(), p.getChildNode( 0 ).getDistanceToParent() ) );
270 pp.setChildNode( pi, p.getChildNode( 0 ) );
274 p.removeChildNode( removed_node.getChildNodeIndex() );
278 remove_us.removeConnections();
279 externalNodesHaveChanged();
282 public void externalNodesHaveChanged() {
283 _external_nodes_set = null;
286 public String[] getAllExternalNodeNames() {
291 final String[] names = new String[ getNumberOfExternalNodes() ];
292 for( final PhylogenyNodeIterator iter = iteratorExternalForward(); iter.hasNext(); ) {
293 names[ i++ ] = new String( iter.next().getName() );
298 public Confidence getConfidence() {
302 public String getDescription() {
306 public String getDistanceUnit() {
307 return _distance_unit;
310 public final static Phylogeny createInstanceFromNhxString( final String nhx ) throws IOException {
311 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
312 return factory.create( nhx, new NHXParser() )[ 0 ];
317 * Warning. The order of the returned nodes is random
318 * -- and hence cannot be relied on.
320 * @return Unordered set of PhylogenyNode
322 public List<PhylogenyNode> getExternalNodes() {
323 if ( _external_nodes_set == null ) {
324 _external_nodes_set = new ArrayList<PhylogenyNode>();
325 for( final PhylogenyNodeIterator it = iteratorPostorder(); it.hasNext(); ) {
326 final PhylogenyNode n = it.next();
327 if ( n.isExternal() ) {
328 _external_nodes_set.add( n );
332 return _external_nodes_set;
336 * Returns the number of duplications of this Phylogeny (int). A return
337 * value of -1 indicates that the number of duplications is unknown.
339 // public int getNumberOfDuplications() {
340 // return _number_of_duplications;
341 // } // getNumberOfDuplications()
343 * Sets the number of duplications of this Phylogeny (int). A value of -1
344 * indicates that the number of duplications is unknown.
347 * set to true for clean NH format
349 // public void setNumberOfDuplications( int i ) {
351 // _number_of_duplications = -1;
354 // _number_of_duplications = i;
356 // } // setNumberOfDuplications( int )
358 * Returns the first external PhylogenyNode.
360 public PhylogenyNode getFirstExternalNode() {
362 throw new FailedConditionCheckException( "attempt to obtain first external node of empty phylogeney" );
364 PhylogenyNode node = getRoot();
365 while ( node.isInternal() ) {
366 node = node.getFirstChildNode();
372 * This calculates the height for rooted, tree-shaped phylogenies. The
373 * height is the longest distance from the root to an external node.
375 * @return the height for rooted, tree-shaped phylogenies
377 public double calculateHeight(final boolean take_collapse_into_account) {
381 return calculateSubtreeHeight( getRoot(), take_collapse_into_account );
384 public Identifier getIdentifier() {
389 * Returns the name of this Phylogeny.
391 public String getName() {
396 * Finds the PhylogenyNode of this Phylogeny which has a matching ID number.
397 * @return PhylogenyNode with matching ID, null if not found
399 public PhylogenyNode getNode( final long id ) throws NoSuchElementException {
401 throw new NoSuchElementException( "attempt to get node in an empty phylogeny" );
403 if ( ( getIdToNodeMap() == null ) || getIdToNodeMap().isEmpty() ) {
406 return getIdToNodeMap().get( id );
410 * Returns a PhylogenyNode of this Phylogeny which has a matching name.
411 * Throws an Exception if seqname is not present in this or not unique.
414 * name (String) of PhylogenyNode to find
415 * @return PhylogenyNode with matchin name
417 public PhylogenyNode getNode( final String name ) {
421 final List<PhylogenyNode> nodes = getNodes( name );
422 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
423 throw new IllegalArgumentException( "node named \"" + name + "\" not found" );
425 if ( nodes.size() > 1 ) {
426 throw new IllegalArgumentException( "node named \"" + name + "\" not unique" );
428 return nodes.get( 0 );
432 * This is time-inefficient since it runs a iterator each time it is called.
435 public int getNodeCount() {
440 for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); it.next() ) {
447 * Returns a List with references to all Nodes of this Phylogeny which have
451 * name (String) of Nodes to find
452 * @return Vector of references to Nodes of this Phylogeny with matching
454 * @see #getNodesWithMatchingSpecies(String)
456 public List<PhylogenyNode> getNodes( final String name ) {
460 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
461 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
462 final PhylogenyNode n = iter.next();
463 if ( n.getName().equals( name ) ) {
470 public List<PhylogenyNode> getNodesViaSequenceName( final String seq_name ) {
474 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
475 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
476 final PhylogenyNode n = iter.next();
477 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getName().equals( seq_name ) ) {
484 public List<PhylogenyNode> getNodesViaSequenceSymbol( final String seq_name ) {
488 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
489 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
490 final PhylogenyNode n = iter.next();
491 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getSymbol().equals( seq_name ) ) {
498 public List<PhylogenyNode> getNodesViaGeneName( final String seq_name ) {
502 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
503 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
504 final PhylogenyNode n = iter.next();
505 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getGeneName().equals( seq_name ) ) {
512 public List<PhylogenyNode> getNodesViaTaxonomyCode( final String taxonomy_code ) {
516 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
517 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
518 final PhylogenyNode n = iter.next();
519 if ( n.getNodeData().isHasTaxonomy()
520 && n.getNodeData().getTaxonomy().getTaxonomyCode().equals( taxonomy_code ) ) {
528 * Returns a Vector with references to all Nodes of this Phylogeny which
529 * have a matching species name.
532 * species name (String) of Nodes to find
533 * @return Vector of references to Nodes of this Phylogeny with matching
535 * @see #getNodes(String)
537 public List<PhylogenyNode> getNodesWithMatchingSpecies( final String specname ) {
541 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
542 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
543 final PhylogenyNode n = iter.next();
544 if ( PhylogenyMethods.getSpecies( n ).equals( specname ) ) {
551 public PhylogenyNode getNodeViaSequenceName( final String seq_name ) {
555 final List<PhylogenyNode> nodes = getNodesViaSequenceName( seq_name );
556 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
557 throw new IllegalArgumentException( "node with sequence named [" + seq_name + "] not found" );
559 if ( nodes.size() > 1 ) {
560 throw new IllegalArgumentException( "node with sequence named [" + seq_name + "] not unique" );
562 return nodes.get( 0 );
565 public PhylogenyNode getNodeViaTaxonomyCode( final String taxonomy_code ) {
569 final List<PhylogenyNode> nodes = getNodesViaTaxonomyCode( taxonomy_code );
570 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
571 throw new IllegalArgumentException( "node with taxonomy code \"" + taxonomy_code + "\" not found" );
573 if ( nodes.size() > 1 ) {
574 throw new IllegalArgumentException( "node with taxonomy code \"" + taxonomy_code + "\" not unique" );
576 return nodes.get( 0 );
579 public int getNumberOfBranches() {
584 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); iter.next() ) {
593 public int getNumberOfInternalNodes() {
598 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
599 if ( iter.next().isInternal() ) {
610 * Returns the sum of external Nodes of this Phylogeny (int).
612 public int getNumberOfExternalNodes() {
616 return getExternalNodes().size();
620 * Returns all paralogs of the external PhylogenyNode n of this Phylogeny.
621 * paralog are returned as List of node references.
623 * PRECONDITION: This tree must be binary and rooted, and speciation -
624 * duplication need to be assigned for each of its internal Nodes.
626 * Returns null if this Phylogeny is empty or if n is internal.
628 * (Last modified: 11/22/00) Olivier CHABROL :
629 * olivier.chabrol@univ-provence.fr
632 * external PhylogenyNode whose orthologs are to be returned
633 * @return Vector of references to all orthologous Nodes of PhylogenyNode n
634 * of this Phylogeny, null if this Phylogeny is empty or if n is
637 public List<PhylogenyNode> getParalogousNodes( final PhylogenyNode n, final String[] taxonomyCodeRange ) {
638 PhylogenyNode node = n;
639 PhylogenyNode prev = null;
640 final List<PhylogenyNode> v = new ArrayList<PhylogenyNode>();
641 final Map<PhylogenyNode, List<String>> map = new HashMap<PhylogenyNode, List<String>>();
642 getTaxonomyMap( getRoot(), map );
643 if ( !node.isExternal() || isEmpty() ) {
646 final String searchNodeSpeciesId = PhylogenyMethods.getTaxonomyIdentifier( n );
647 if ( !node.isExternal() || isEmpty() ) {
650 List<String> taxIdList = null;
651 final List<String> taxonomyCodeRangeList = Arrays.asList( taxonomyCodeRange );
652 while ( !node.isRoot() ) {
654 node = node.getParent();
655 taxIdList = map.get( node );
656 if ( node.isDuplication() && isContains( taxIdList, taxonomyCodeRangeList ) ) {
657 if ( node.getChildNode1() == prev ) {
658 v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode2()
659 .getAllExternalDescendants() ) );
662 v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode1()
663 .getAllExternalDescendants() ) );
670 public Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> getRelevantSequenceRelationTypes() {
671 if ( _relevant_sequence_relation_types == null ) {
672 _relevant_sequence_relation_types = new Vector<SEQUENCE_RELATION_TYPE>();
674 return _relevant_sequence_relation_types;
678 * Returns the root PhylogenyNode of this Phylogeny.
680 public PhylogenyNode getRoot() {
684 public Collection<Sequence> getSequenceRelationQueries() {
685 return _sequenceRelationQueries;
688 public String getType() {
693 * Deletes this Phylogeny.
702 _id_to_node_map = null;
706 setAllowMultipleParents( Phylogeny.ALLOW_MULTIPLE_PARENTS_DEFAULT );
710 * Returns whether this is a completely binary tree (i.e. all internal nodes
714 public boolean isCompletelyBinary() {
718 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
719 final PhylogenyNode node = iter.next();
720 if ( node.isInternal() && ( node.getNumberOfDescendants() != 2 ) ) {
728 * Checks whether a Phylogeny object is deleted (or empty).
730 * @return true if the tree is deleted (or empty), false otherwise
732 public boolean isEmpty() {
733 return ( getRoot() == null );
736 public boolean isRerootable() {
741 * Returns true is this Phylogeny is rooted.
743 public boolean isRooted() {
747 public boolean isTree() {
751 public PhylogenyNodeIterator iteratorExternalForward() {
752 return new ExternalForwardIterator( this );
755 public PhylogenyNodeIterator iteratorLevelOrder() {
756 return new LevelOrderTreeIterator( this );
759 public PhylogenyNodeIterator iteratorPostorder() {
760 return new PostorderTreeIterator( this );
763 public PhylogenyNodeIterator iteratorPreorder() {
764 return new PreorderTreeIterator( this );
768 * Resets the ID numbers of the nodes of this Phylogeny in level order,
769 * starting with start_label (for the root). <br>
770 * WARNING. After this method has been called, node IDs are no longer
773 public void levelOrderReID() {
777 _id_to_node_map = null;
779 for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); ) {
780 final PhylogenyNode node = it.next();
781 if ( node.isRoot() ) {
782 node.setId( PhylogenyNode.getNodeCount() );
785 node.setId( node.getParent().getId() + 1 );
786 if ( node.getId() > max ) {
791 PhylogenyNode.setNodeCount( max + 1 );
795 * Prints descriptions of all external Nodes of this Phylogeny to
798 public void printExtNodes() {
802 for( final PhylogenyNodeIterator iter = iteratorExternalForward(); iter.hasNext(); ) {
803 System.out.println( iter.next() + "\n" );
808 * (Re)counts the number of children for each PhylogenyNode of this
809 * Phylogeny. As an example, this method needs to be called after a
810 * Phylogeny has been reRooted and it is to be displayed.
812 * @param consider_collapsed_nodes
813 * set to true to take into account collapsed nodes (collapsed
814 * nodes have 1 child).
816 public void recalculateNumberOfExternalDescendants( final boolean consider_collapsed_nodes ) {
820 for( final PhylogenyNodeIterator iter = iteratorPostorder(); iter.hasNext(); ) {
821 final PhylogenyNode node = iter.next();
822 if ( node.isExternal() || ( consider_collapsed_nodes && node.isCollapse() ) ) {
823 node.setSumExtNodes( 1 );
827 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
828 sum += node.getChildNode( i ).getNumberOfExternalNodes();
830 node.setSumExtNodes( sum );
836 * Places the root of this Phylogeny on the parent branch of the
837 * PhylogenyNode with a corresponding ID. The new root is always placed on
838 * the middle of the branch. If the resulting reRooted Phylogeny is to be
839 * used any further, in most cases the following methods have to be called
840 * on the resulting Phylogeny:
842 * <li>recalculateNumberOfExternalDescendants(boolean)
843 * <li>recalculateAndReset()
846 * ID (int) of PhylogenyNode of this Phylogeny
848 public void reRoot( final long id ) {
849 reRoot( getNode( id ) );
853 * Places the root of this Phylogeny on the parent branch PhylogenyNode n.
854 * The new root is always placed on the middle of the branch.
856 * If the resulting reRooted Phylogeny is to be used any further, in most
857 * cases the following three methods have to be called on the resulting
860 * <li>recalculateNumberOfExternalDescendants(boolean) <li>recalculateAndReset()
863 * (Last modified: 10/01/01)
866 * PhylogenyNode of this Phylogeny\
868 public void reRoot( final PhylogenyNode n ) {
872 public void reRoot( final PhylogenyNode n, final double distance_n_to_parent ) {
873 if ( isEmpty() || ( getNumberOfExternalNodes() < 2 ) ) {
880 else if ( n.getParent().isRoot() ) {
881 if ( ( n.getParent().getNumberOfDescendants() == 2 ) && ( distance_n_to_parent >= 0 ) ) {
882 final double d = n.getParent().getChildNode1().getDistanceToParent()
883 + n.getParent().getChildNode2().getDistanceToParent();
885 if ( n.getChildNodeIndex() == 0 ) {
886 other = n.getParent().getChildNode2();
889 other = n.getParent().getChildNode1();
891 n.setDistanceToParent( distance_n_to_parent );
892 final double dm = d - distance_n_to_parent;
894 other.setDistanceToParent( dm );
897 other.setDistanceToParent( 0 );
900 if ( n.getParent().getNumberOfDescendants() > 2 ) {
901 final int index = n.getChildNodeIndex();
902 final double dn = n.getDistanceToParent();
903 final PhylogenyNode prev_root = getRoot();
904 prev_root.getDescendants().remove( index );
905 final PhylogenyNode new_root = new PhylogenyNode();
906 new_root.setChildNode( 0, n );
907 new_root.setChildNode( 1, prev_root );
908 if ( n.getBranchDataDirectly() != null ) {
909 prev_root.setBranchData( ( BranchData ) n.getBranchDataDirectly().copy() );
912 if ( distance_n_to_parent >= 0 ) {
913 n.setDistanceToParent( distance_n_to_parent );
914 final double d = dn - distance_n_to_parent;
916 prev_root.setDistanceToParent( d );
919 prev_root.setDistanceToParent( 0 );
924 final double d = dn / 2.0;
925 n.setDistanceToParent( d );
926 prev_root.setDistanceToParent( d );
933 PhylogenyNode b = null;
934 PhylogenyNode c = null;
935 final PhylogenyNode new_root = new PhylogenyNode();
936 double distance1 = 0.0;
937 double distance2 = 0.0;
938 BranchData branch_data_1 = null;
939 BranchData branch_data_2 = null;
942 new_root.setChildNode( 0, a );
943 new_root.setChildNode( 1, b );
944 distance1 = c.getDistanceToParent();
945 if ( c.getBranchDataDirectly() != null ) {
946 branch_data_1 = ( BranchData ) c.getBranchDataDirectly().copy();
948 c.setDistanceToParent( b.getDistanceToParent() );
949 if ( b.getBranchDataDirectly() != null ) {
950 c.setBranchData( ( BranchData ) b.getBranchDataDirectly().copy() );
952 if ( a.getBranchDataDirectly() != null ) {
953 b.setBranchData( ( BranchData ) a.getBranchDataDirectly().copy() );
955 // New root is always placed in the middle of the branch:
956 if ( a.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
957 b.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
960 if ( distance_n_to_parent >= 0.0 ) {
961 final double diff = a.getDistanceToParent() - distance_n_to_parent;
962 a.setDistanceToParent( distance_n_to_parent );
963 b.setDistanceToParent( diff >= 0.0 ? diff : 0.0 );
966 final double d = a.getDistanceToParent() / 2.0;
967 a.setDistanceToParent( d );
968 b.setDistanceToParent( d );
971 b.setChildNodeOnly( a.getChildNodeIndex( b ), c );
972 // moving to the old root, swapping references:
973 while ( !c.isRoot() ) {
977 b.setChildNodeOnly( a.getChildNodeIndex( b ), c );
979 distance2 = c.getDistanceToParent();
980 branch_data_2 = c.getBranchDataDirectly();
981 c.setDistanceToParent( distance1 );
982 c.setBranchData( branch_data_1 );
983 distance1 = distance2;
984 branch_data_1 = branch_data_2;
986 // removing the old root:
987 if ( c.getNumberOfDescendants() == 2 ) {
988 final PhylogenyNode node = c.getChildNode( 1 - b.getChildNodeIndex( c ) );
990 if ( ( c.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT )
991 && ( node.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
992 node.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
995 node.setDistanceToParent( ( c.getDistanceToParent() >= 0.0 ? c.getDistanceToParent() : 0.0 )
996 + ( node.getDistanceToParent() >= 0.0 ? node.getDistanceToParent() : 0.0 ) );
998 if ( c.getBranchDataDirectly() != null ) {
999 node.setBranchData( ( BranchData ) c.getBranchDataDirectly().copy() );
1001 for( int i = 0; i < b.getNumberOfDescendants(); ++i ) {
1002 if ( b.getChildNode( i ) == c ) {
1003 b.setChildNodeOnly( i, node );
1010 c.removeChildNode( b.getChildNodeIndex( c ) );
1012 setRoot( new_root );
1017 * Sets all Nodes of this Phylogeny to not-collapsed.
1019 * In most cases methods adjustNodeCount(false) and recalculateAndReset()
1020 * need to be called after this method has been called.
1022 public void setAllNodesToNotCollapse() {
1026 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1027 final PhylogenyNode node = iter.next();
1028 node.setCollapse( false );
1032 public void setConfidence( final Confidence confidence ) {
1033 _confidence = confidence;
1036 public void setDescription( final String description ) {
1037 _description = description;
1040 public void setDistanceUnit( final String _distance_unit ) {
1041 this._distance_unit = _distance_unit;
1044 public void setIdentifier( final Identifier identifier ) {
1045 _identifier = identifier;
1048 public void setIdToNodeMap( final HashMap<Long, PhylogenyNode> idhash ) {
1049 _id_to_node_map = idhash;
1053 * Sets the indicators of all Nodes of this Phylogeny to 0.
1055 public void setIndicatorsToZero() {
1059 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1060 iter.next().setIndicator( ( byte ) 0 );
1062 } // setIndicatorsToZero()
1065 * Sets the name of this Phylogeny to s.
1067 public void setName( final String s ) {
1071 public void setRelevantSequenceRelationTypes( final Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> types ) {
1072 _relevant_sequence_relation_types = types;
1075 public void setRerootable( final boolean rerootable ) {
1076 _rerootable = rerootable;
1079 public void setRoot( final PhylogenyNode n ) {
1084 * Sets whether this Phylogeny is rooted or not.
1086 public void setRooted( final boolean b ) {
1088 } // setRooted( boolean )
1090 public void setSequenceRelationQueries( final Collection<Sequence> sequencesByName ) {
1091 _sequenceRelationQueries = sequencesByName;
1094 public void setType( final String type ) {
1098 public String toNewHampshire() {
1099 return toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1102 public String toNewHampshire( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
1104 return new PhylogenyWriter().toNewHampshire( this, true, nh_conversion_support_style ).toString();
1106 catch ( final IOException e ) {
1107 throw new Error( "this should not have happend: " + e.getMessage() );
1111 public String toNewHampshireX() {
1113 return new PhylogenyWriter().toNewHampshireX( this ).toString();
1115 catch ( final IOException e ) {
1116 throw new Error( "this should not have happend: " + e.getMessage() );
1120 public String toNexus() {
1121 return toNexus( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1124 public String toNexus( final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) {
1126 return new PhylogenyWriter().toNexus( this, svs ).toString();
1128 catch ( final IOException e ) {
1129 throw new Error( "this should not have happend: " + e.getMessage() );
1133 public String toPhyloXML( final int phyloxml_level ) {
1135 return new PhylogenyWriter().toPhyloXML( this, phyloxml_level ).toString();
1137 catch ( final IOException e ) {
1138 throw new Error( "this should not have happend: " + e.getMessage() );
1142 // ---------------------------------------------------------
1143 // Writing of Phylogeny to Strings
1144 // ---------------------------------------------------------
1146 * Converts this Phylogeny to a New Hampshire X (String) representation.
1148 * @return New Hampshire X (String) representation of this
1149 * @see #toNewHampshireX()
1152 public String toString() {
1153 return toNewHampshireX();
1157 * Removes the root PhylogenyNode this Phylogeny.
1159 public void unRoot() throws RuntimeException {
1161 throw new FailedConditionCheckException( "Attempt to unroot a phylogeny which is not tree-like." );
1166 setIndicatorsToZero();
1167 if ( !isRooted() || ( getNumberOfExternalNodes() <= 1 ) ) {
1174 private HashMap<Long, PhylogenyNode> getIdToNodeMap() {
1175 return _id_to_node_map;
1179 * Return Node by TaxonomyId Olivier CHABROL :
1180 * olivier.chabrol@univ-provence.fr
1183 * search taxonomy identifier
1185 * sublist node to search
1186 * @return List node with the same taxonomy identifier
1188 private List<PhylogenyNode> getNodeByTaxonomyID( final String taxonomyID, final List<PhylogenyNode> nodes ) {
1189 final List<PhylogenyNode> retour = new ArrayList<PhylogenyNode>();
1190 for( final PhylogenyNode node : nodes ) {
1191 if ( taxonomyID.equals( PhylogenyMethods.getTaxonomyIdentifier( node ) ) ) {
1199 * List all species contains in all leaf under a node Olivier CHABROL :
1200 * olivier.chabrol@univ-provence.fr
1203 * PhylogenyNode whose sub node species are returned
1204 * @return species contains in all leaf under the param node
1206 private List<String> getSubNodeTaxonomy( final PhylogenyNode node ) {
1207 final List<String> taxonomyList = new ArrayList<String>();
1208 final List<PhylogenyNode> childs = node.getAllExternalDescendants();
1209 String speciesId = null;
1210 for( final PhylogenyNode phylogenyNode : childs ) {
1211 // taxId = new Long(phylogenyNode.getTaxonomyID());
1212 speciesId = PhylogenyMethods.getTaxonomyIdentifier( phylogenyNode );
1213 if ( !taxonomyList.contains( speciesId ) ) {
1214 taxonomyList.add( speciesId );
1217 return taxonomyList;
1221 * Create a map [<PhylogenyNode, List<String>], the list contains the
1222 * species contains in all leaf under phylogeny node Olivier CHABROL :
1223 * olivier.chabrol@univ-provence.fr
1226 * the tree root node
1230 private void getTaxonomyMap( final PhylogenyNode node, final Map<PhylogenyNode, List<String>> map ) {
1232 if ( node.isExternal() ) {
1235 map.put( node, getSubNodeTaxonomy( node ) );
1236 getTaxonomyMap( node.getChildNode1(), map );
1237 getTaxonomyMap( node.getChildNode2(), map );
1240 private boolean isAllowMultipleParents() {
1241 return _allow_multiple_parents;
1245 * Util method to check if all element of a list is contains in the
1246 * rangeList. Olivier CHABROL : olivier.chabrol@univ-provence.fr
1251 * the range list to compare
1252 * @return <code>true</code> if all param list element are contains in param
1253 * rangeList, <code>false</code> otherwise.
1255 private boolean isContains( final List<String> list, final List<String> rangeList ) {
1256 if ( list.size() > rangeList.size() ) {
1260 for( final Iterator<String> iterator = list.iterator(); iterator.hasNext(); ) {
1261 l = iterator.next();
1262 if ( !rangeList.contains( l ) ) {
1270 * Hashes the ID number of each PhylogenyNode of this Phylogeny to its
1271 * corresponding PhylogenyNode, in order to make method getNode( id ) run in
1272 * constant time. Important: The user is responsible for calling this method
1273 * (again) after this Phylogeny has been changed/created/renumbered.
1275 private void reHashIdToNodeMap() {
1279 setIdToNodeMap( new HashMap<Long, PhylogenyNode>() );
1280 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1281 final PhylogenyNode node = iter.next();
1282 getIdToNodeMap().put( node.getId(), node );
1286 private void setAllowMultipleParents( final boolean allow_multiple_parents ) {
1287 _allow_multiple_parents = allow_multiple_parents;