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.writers.PhylogenyWriter;
42 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
43 import org.forester.phylogeny.data.BranchData;
44 import org.forester.phylogeny.data.Confidence;
45 import org.forester.phylogeny.data.Identifier;
46 import org.forester.phylogeny.data.PhylogenyDataUtil;
47 import org.forester.phylogeny.data.Sequence;
48 import org.forester.phylogeny.data.SequenceRelation;
49 import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
50 import org.forester.phylogeny.iterators.ExternalForwardIterator;
51 import org.forester.phylogeny.iterators.LevelOrderTreeIterator;
52 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
53 import org.forester.phylogeny.iterators.PostorderTreeIterator;
54 import org.forester.phylogeny.iterators.PreorderTreeIterator;
55 import org.forester.util.FailedConditionCheckException;
56 import org.forester.util.ForesterUtil;
58 public class Phylogeny {
60 public final static boolean ALLOW_MULTIPLE_PARENTS_DEFAULT = false;
61 private PhylogenyNode _root;
62 private boolean _rooted;
63 private boolean _allow_multiple_parents;
66 private String _description;
67 private String _distance_unit;
68 private Confidence _confidence;
69 private Identifier _identifier;
70 private boolean _rerootable;
71 private HashMap<Long, PhylogenyNode> _id_to_node_map;
72 private List<PhylogenyNode> _external_nodes_set;
73 private Collection<Sequence> _sequenceRelationQueries;
74 private Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> _relevant_sequence_relation_types;
77 * Default Phylogeny constructor. Constructs an empty Phylogeny.
84 * Adds this Phylogeny to the list of child nodes of PhylogenyNode parent
85 * and sets the parent of this to parent.
88 * the PhylogenyNode to add
90 public void addAsChild( final PhylogenyNode parent ) {
92 throw new IllegalArgumentException( "Attempt to add an empty tree." );
95 throw new IllegalArgumentException( "Attempt to add an unrooted tree." );
97 parent.addAsChild( getRoot() );
98 externalNodesHaveChanged();
101 public void addAsSibling( final PhylogenyNode sibling ) {
103 throw new IllegalArgumentException( "Attempt to add an empty tree." );
106 throw new IllegalArgumentException( "Attempt to add an unrooted tree." );
108 final int sibling_index = sibling.getChildNodeIndex();
109 final PhylogenyNode new_node = new PhylogenyNode();
110 final PhylogenyNode sibling_parent = sibling.getParent();
111 new_node.setChild1( sibling );
112 new_node.setChild2( getRoot() );
113 new_node.setParent( sibling_parent );
114 sibling.setParent( new_node );
115 sibling_parent.setChildNode( sibling_index, new_node );
116 final double new_dist = sibling.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ? PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT
117 : sibling.getDistanceToParent() / 2;
118 new_node.setDistanceToParent( new_dist );
119 sibling.setDistanceToParent( new_dist );
120 externalNodesHaveChanged();
124 * This calculates the height of the subtree emanating at n for rooted,
125 * tree-shaped phylogenies
128 * the root-node of a subtree
129 * @return the height of the subtree emanating at n
131 public double calculateSubtreeHeight( final PhylogenyNode n ) {
132 if ( n.isExternal() || n.isCollapse() ) {
133 return ForesterUtil.isLargerOrEqualToZero( n.getDistanceToParent() );
136 double max = -Double.MAX_VALUE;
137 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
138 final double l = calculateSubtreeHeight( n.getChildNode( i ) );
143 return max + ForesterUtil.isLargerOrEqualToZero( n.getDistanceToParent() );
147 public void clearHashIdToNodeMap() {
148 setIdToNodeMap( null );
152 * Returns a deep copy of this Phylogeny.
154 * (The resulting Phylogeny has its references in the external nodes
155 * corrected, if they are lacking/obsolete in this.)
157 public Phylogeny copy() {
158 return copy( _root );
162 * Returns a deep copy of this Phylogeny.
164 * (The resulting Phylogeny has its references in the external nodes
165 * corrected, if they are lacking/obsolete in this.)
167 public Phylogeny copy( final PhylogenyNode source ) {
168 final Phylogeny tree = new Phylogeny();
173 tree._rooted = _rooted;
174 tree._name = new String( _name );
175 tree._description = new String( _description );
176 tree._type = new String( _type );
177 tree._rerootable = _rerootable;
178 tree._distance_unit = new String( _distance_unit );
179 if ( _confidence != null ) {
180 tree._confidence = ( Confidence ) _confidence.copy();
182 if ( _identifier != null ) {
183 tree._identifier = ( Identifier ) _identifier.copy();
185 tree.setAllowMultipleParents( isAllowMultipleParents() );
186 tree._root = PhylogenyMethods.copySubTree( source );
191 * Returns a shallow copy of this Phylogeny.
193 * (The resulting Phylogeny has its references in the external nodes
194 * corrected, if they are lacking/obsolete in this.)
196 public Phylogeny copyShallow() {
197 return copyShallow( _root );
200 public Phylogeny copyShallow( final PhylogenyNode source ) {
201 final Phylogeny tree = new Phylogeny();
206 tree._rooted = _rooted;
208 tree._description = _description;
210 tree._rerootable = _rerootable;
211 tree._distance_unit = _distance_unit;
212 tree._confidence = _confidence;
213 tree._identifier = _identifier;
214 tree.setAllowMultipleParents( isAllowMultipleParents() );
215 tree._root = PhylogenyMethods.copySubTreeShallow( source );
220 * Need to call clearHashIdToNodeMap() afterwards (not done automatically
221 * to allow client multiple deletions in linear time).
222 * Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this
223 * if tree is to be displayed.
225 * @param remove_us the parent node of the subtree to be deleted
227 public void deleteSubtree( final PhylogenyNode remove_us, final boolean collapse_resulting_node_with_one_desc ) {
228 if ( isEmpty() || ( remove_us.isRoot() && ( getNumberOfExternalNodes() != 1 ) ) ) {
231 if ( remove_us.isRoot() && ( getNumberOfExternalNodes() == 1 ) ) {
234 else if ( !collapse_resulting_node_with_one_desc ) {
235 remove_us.getParent().removeChildNode( remove_us );
238 final PhylogenyNode removed_node = remove_us;
239 final PhylogenyNode p = remove_us.getParent();
241 if ( p.getNumberOfDescendants() == 2 ) {
242 if ( removed_node.isFirstChildNode() ) {
243 setRoot( getRoot().getChildNode( 1 ) );
244 getRoot().setParent( null );
247 setRoot( getRoot().getChildNode( 0 ) );
248 getRoot().setParent( null );
252 p.removeChildNode( removed_node.getChildNodeIndex() );
256 final PhylogenyNode pp = removed_node.getParent().getParent();
257 if ( p.getNumberOfDescendants() == 2 ) {
258 final int pi = p.getChildNodeIndex();
259 if ( removed_node.isFirstChildNode() ) {
260 p.getChildNode( 1 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
261 .getDistanceToParent(), p.getChildNode( 1 ).getDistanceToParent() ) );
262 pp.setChildNode( pi, p.getChildNode( 1 ) );
265 p.getChildNode( 0 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
266 .getDistanceToParent(), p.getChildNode( 0 ).getDistanceToParent() ) );
267 pp.setChildNode( pi, p.getChildNode( 0 ) );
271 p.removeChildNode( removed_node.getChildNodeIndex() );
275 remove_us.removeConnections();
276 externalNodesHaveChanged();
279 public void externalNodesHaveChanged() {
280 _external_nodes_set = null;
283 public String[] getAllExternalNodeNames() {
288 final String[] names = new String[ getNumberOfExternalNodes() ];
289 for( final PhylogenyNodeIterator iter = iteratorExternalForward(); iter.hasNext(); ) {
290 names[ i++ ] = new String( iter.next().getName() );
295 public Confidence getConfidence() {
299 public String getDescription() {
303 public String getDistanceUnit() {
304 return _distance_unit;
309 * Warning. The order of the returned nodes is random
310 * -- and hence cannot be relied on.
312 * @return Unordered set of PhylogenyNode
314 public List<PhylogenyNode> getExternalNodes() {
315 if ( _external_nodes_set == null ) {
316 _external_nodes_set = new ArrayList<PhylogenyNode>();
317 for( final PhylogenyNodeIterator it = iteratorPostorder(); it.hasNext(); ) {
318 final PhylogenyNode n = it.next();
319 if ( n.isExternal() ) {
320 _external_nodes_set.add( n );
324 return _external_nodes_set;
328 * Returns the number of duplications of this Phylogeny (int). A return
329 * value of -1 indicates that the number of duplications is unknown.
331 // public int getNumberOfDuplications() {
332 // return _number_of_duplications;
333 // } // getNumberOfDuplications()
335 * Sets the number of duplications of this Phylogeny (int). A value of -1
336 * indicates that the number of duplications is unknown.
339 * set to true for clean NH format
341 // public void setNumberOfDuplications( int i ) {
343 // _number_of_duplications = -1;
346 // _number_of_duplications = i;
348 // } // setNumberOfDuplications( int )
350 * Returns the first external PhylogenyNode.
352 public PhylogenyNode getFirstExternalNode() {
354 throw new FailedConditionCheckException( "attempt to obtain first external node of empty phylogeney" );
356 PhylogenyNode node = getRoot();
357 while ( node.isInternal() ) {
358 node = node.getFirstChildNode();
364 * This calculates the height for rooted, tree-shaped phylogenies. The
365 * height is the longest distance from the root to an external node. Please
366 * note. Child nodes of collapsed nodes are ignored -- which is useful for
367 * display purposes but might be misleading for other applications.
369 * @return the height for rooted, tree-shaped phylogenies
371 public double getHeight() {
375 return calculateSubtreeHeight( getRoot() );
378 public Identifier getIdentifier() {
383 * Returns the name of this Phylogeny.
385 public String getName() {
390 * Finds the PhylogenyNode of this Phylogeny which has a matching ID number.
391 * @return PhylogenyNode with matching ID, null if not found
393 public PhylogenyNode getNode( final long id ) throws NoSuchElementException {
395 throw new NoSuchElementException( "attempt to get node in an empty phylogeny" );
397 if ( ( getIdToNodeMap() == null ) || getIdToNodeMap().isEmpty() ) {
400 return getIdToNodeMap().get( id );
404 * Returns a PhylogenyNode of this Phylogeny which has a matching name.
405 * Throws an Exception if seqname is not present in this or not unique.
408 * name (String) of PhylogenyNode to find
409 * @return PhylogenyNode with matchin name
411 public PhylogenyNode getNode( final String name ) {
415 final List<PhylogenyNode> nodes = getNodes( name );
416 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
417 throw new IllegalArgumentException( "node named \"" + name + "\" not found" );
419 if ( nodes.size() > 1 ) {
420 throw new IllegalArgumentException( "node named \"" + name + "\" not unique" );
422 return nodes.get( 0 );
426 * This is time-inefficient since it runs a iterator each time it is called.
429 public int getNodeCount() {
434 for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); it.next() ) {
441 * Returns a List with references to all Nodes of this Phylogeny which have
445 * name (String) of Nodes to find
446 * @return Vector of references to Nodes of this Phylogeny with matching
448 * @see #getNodesWithMatchingSpecies(String)
450 public List<PhylogenyNode> getNodes( final String name ) {
454 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
455 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
456 final PhylogenyNode n = iter.next();
457 if ( n.getName().equals( name ) ) {
464 public List<PhylogenyNode> getNodesViaSequenceName( final String seq_name ) {
468 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
469 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
470 final PhylogenyNode n = iter.next();
471 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getName().equals( seq_name ) ) {
478 public List<PhylogenyNode> getNodesViaSequenceSymbol( final String seq_name ) {
482 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
483 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
484 final PhylogenyNode n = iter.next();
485 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getSymbol().equals( seq_name ) ) {
492 public List<PhylogenyNode> getNodesViaGeneName( final String seq_name ) {
496 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
497 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
498 final PhylogenyNode n = iter.next();
499 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getGeneName().equals( seq_name ) ) {
506 public List<PhylogenyNode> getNodesViaTaxonomyCode( final String taxonomy_code ) {
510 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
511 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
512 final PhylogenyNode n = iter.next();
513 if ( n.getNodeData().isHasTaxonomy()
514 && n.getNodeData().getTaxonomy().getTaxonomyCode().equals( taxonomy_code ) ) {
522 * Returns a Vector with references to all Nodes of this Phylogeny which
523 * have a matching species name.
526 * species name (String) of Nodes to find
527 * @return Vector of references to Nodes of this Phylogeny with matching
529 * @see #getNodes(String)
531 public List<PhylogenyNode> getNodesWithMatchingSpecies( final String specname ) {
535 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
536 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
537 final PhylogenyNode n = iter.next();
538 if ( PhylogenyMethods.getSpecies( n ).equals( specname ) ) {
545 public PhylogenyNode getNodeViaSequenceName( final String seq_name ) {
549 final List<PhylogenyNode> nodes = getNodesViaSequenceName( seq_name );
550 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
551 throw new IllegalArgumentException( "node with sequence named [" + seq_name + "] not found" );
553 if ( nodes.size() > 1 ) {
554 throw new IllegalArgumentException( "node with sequence named [" + seq_name + "] not unique" );
556 return nodes.get( 0 );
559 public PhylogenyNode getNodeViaTaxonomyCode( final String taxonomy_code ) {
563 final List<PhylogenyNode> nodes = getNodesViaTaxonomyCode( taxonomy_code );
564 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
565 throw new IllegalArgumentException( "node with taxonomy code \"" + taxonomy_code + "\" not found" );
567 if ( nodes.size() > 1 ) {
568 throw new IllegalArgumentException( "node with taxonomy code \"" + taxonomy_code + "\" not unique" );
570 return nodes.get( 0 );
573 public int getNumberOfBranches() {
578 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); iter.next() ) {
587 public int getNumberOfInternalNodes() {
592 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
593 if ( iter.next().isInternal() ) {
604 * Returns the sum of external Nodes of this Phylogeny (int).
606 public int getNumberOfExternalNodes() {
610 return getExternalNodes().size();
614 * Returns all paralogs of the external PhylogenyNode n of this Phylogeny.
615 * paralog are returned as List of node references.
617 * PRECONDITION: This tree must be binary and rooted, and speciation -
618 * duplication need to be assigned for each of its internal Nodes.
620 * Returns null if this Phylogeny is empty or if n is internal.
622 * (Last modified: 11/22/00) Olivier CHABROL :
623 * olivier.chabrol@univ-provence.fr
626 * external PhylogenyNode whose orthologs are to be returned
627 * @return Vector of references to all orthologous Nodes of PhylogenyNode n
628 * of this Phylogeny, null if this Phylogeny is empty or if n is
631 public List<PhylogenyNode> getParalogousNodes( final PhylogenyNode n, final String[] taxonomyCodeRange ) {
632 PhylogenyNode node = n;
633 PhylogenyNode prev = null;
634 final List<PhylogenyNode> v = new ArrayList<PhylogenyNode>();
635 final Map<PhylogenyNode, List<String>> map = new HashMap<PhylogenyNode, List<String>>();
636 getTaxonomyMap( getRoot(), map );
637 if ( !node.isExternal() || isEmpty() ) {
640 final String searchNodeSpeciesId = PhylogenyMethods.getTaxonomyIdentifier( n );
641 if ( !node.isExternal() || isEmpty() ) {
644 List<String> taxIdList = null;
645 final List<String> taxonomyCodeRangeList = Arrays.asList( taxonomyCodeRange );
646 while ( !node.isRoot() ) {
648 node = node.getParent();
649 taxIdList = map.get( node );
650 if ( node.isDuplication() && isContains( taxIdList, taxonomyCodeRangeList ) ) {
651 if ( node.getChildNode1() == prev ) {
652 v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode2()
653 .getAllExternalDescendants() ) );
656 v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode1()
657 .getAllExternalDescendants() ) );
664 public Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> getRelevantSequenceRelationTypes() {
665 if ( _relevant_sequence_relation_types == null ) {
666 _relevant_sequence_relation_types = new Vector<SEQUENCE_RELATION_TYPE>();
668 return _relevant_sequence_relation_types;
672 * Returns the root PhylogenyNode of this Phylogeny.
674 public PhylogenyNode getRoot() {
678 public Collection<Sequence> getSequenceRelationQueries() {
679 return _sequenceRelationQueries;
682 public String getType() {
687 * Deletes this Phylogeny.
696 _id_to_node_map = null;
700 setAllowMultipleParents( Phylogeny.ALLOW_MULTIPLE_PARENTS_DEFAULT );
704 * Returns whether this is a completely binary tree (i.e. all internal nodes
708 public boolean isCompletelyBinary() {
712 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
713 final PhylogenyNode node = iter.next();
714 if ( node.isInternal() && ( node.getNumberOfDescendants() != 2 ) ) {
722 * Checks whether a Phylogeny object is deleted (or empty).
724 * @return true if the tree is deleted (or empty), false otherwise
726 public boolean isEmpty() {
727 return ( getRoot() == null );
730 public boolean isRerootable() {
735 * Returns true is this Phylogeny is rooted.
737 public boolean isRooted() {
741 public boolean isTree() {
745 public PhylogenyNodeIterator iteratorExternalForward() {
746 return new ExternalForwardIterator( this );
749 public PhylogenyNodeIterator iteratorLevelOrder() {
750 return new LevelOrderTreeIterator( this );
753 public PhylogenyNodeIterator iteratorPostorder() {
754 return new PostorderTreeIterator( this );
757 public PhylogenyNodeIterator iteratorPreorder() {
758 return new PreorderTreeIterator( this );
762 * Resets the ID numbers of the nodes of this Phylogeny in level order,
763 * starting with start_label (for the root). <br>
764 * WARNING. After this method has been called, node IDs are no longer
767 public void levelOrderReID() {
771 _id_to_node_map = null;
773 for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); ) {
774 final PhylogenyNode node = it.next();
775 if ( node.isRoot() ) {
776 node.setId( PhylogenyNode.getNodeCount() );
779 node.setId( node.getParent().getId() + 1 );
780 if ( node.getId() > max ) {
785 PhylogenyNode.setNodeCount( max + 1 );
789 * Prints descriptions of all external Nodes of this Phylogeny to
792 public void printExtNodes() {
796 for( final PhylogenyNodeIterator iter = iteratorExternalForward(); iter.hasNext(); ) {
797 System.out.println( iter.next() + "\n" );
802 * (Re)counts the number of children for each PhylogenyNode of this
803 * Phylogeny. As an example, this method needs to be called after a
804 * Phylogeny has been reRooted and it is to be displayed.
806 * @param consider_collapsed_nodes
807 * set to true to take into account collapsed nodes (collapsed
808 * nodes have 1 child).
810 public void recalculateNumberOfExternalDescendants( final boolean consider_collapsed_nodes ) {
814 for( final PhylogenyNodeIterator iter = iteratorPostorder(); iter.hasNext(); ) {
815 final PhylogenyNode node = iter.next();
816 if ( node.isExternal() || ( consider_collapsed_nodes && node.isCollapse() ) ) {
817 node.setSumExtNodes( 1 );
821 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
822 sum += node.getChildNode( i ).getNumberOfExternalNodes();
824 node.setSumExtNodes( sum );
830 * Places the root of this Phylogeny on the parent branch of the
831 * PhylogenyNode with a corresponding ID. The new root is always placed on
832 * the middle of the branch. If the resulting reRooted Phylogeny is to be
833 * used any further, in most cases the following methods have to be called
834 * on the resulting Phylogeny:
836 * <li>recalculateNumberOfExternalDescendants(boolean)
837 * <li>recalculateAndReset()
840 * ID (int) of PhylogenyNode of this Phylogeny
842 public void reRoot( final long id ) {
843 reRoot( getNode( id ) );
847 * Places the root of this Phylogeny on the parent branch PhylogenyNode n.
848 * The new root is always placed on the middle of the branch.
850 * If the resulting reRooted Phylogeny is to be used any further, in most
851 * cases the following three methods have to be called on the resulting
854 * <li>recalculateNumberOfExternalDescendants(boolean) <li>recalculateAndReset()
857 * (Last modified: 10/01/01)
860 * PhylogenyNode of this Phylogeny\
862 public void reRoot( final PhylogenyNode n ) {
866 public void reRoot( final PhylogenyNode n, final double distance_n_to_parent ) {
867 if ( isEmpty() || ( getNumberOfExternalNodes() < 2 ) ) {
874 else if ( n.getParent().isRoot() ) {
875 if ( ( n.getParent().getNumberOfDescendants() == 2 ) && ( distance_n_to_parent >= 0 ) ) {
876 final double d = n.getParent().getChildNode1().getDistanceToParent()
877 + n.getParent().getChildNode2().getDistanceToParent();
879 if ( n.getChildNodeIndex() == 0 ) {
880 other = n.getParent().getChildNode2();
883 other = n.getParent().getChildNode1();
885 n.setDistanceToParent( distance_n_to_parent );
886 final double dm = d - distance_n_to_parent;
888 other.setDistanceToParent( dm );
891 other.setDistanceToParent( 0 );
894 if ( n.getParent().getNumberOfDescendants() > 2 ) {
895 final int index = n.getChildNodeIndex();
896 final double dn = n.getDistanceToParent();
897 final PhylogenyNode prev_root = getRoot();
898 prev_root.getDescendants().remove( index );
899 final PhylogenyNode new_root = new PhylogenyNode();
900 new_root.setChildNode( 0, n );
901 new_root.setChildNode( 1, prev_root );
902 if ( n.getBranchDataDirectly() != null ) {
903 prev_root.setBranchData( ( BranchData ) n.getBranchDataDirectly().copy() );
906 if ( distance_n_to_parent >= 0 ) {
907 n.setDistanceToParent( distance_n_to_parent );
908 final double d = dn - distance_n_to_parent;
910 prev_root.setDistanceToParent( d );
913 prev_root.setDistanceToParent( 0 );
918 final double d = dn / 2.0;
919 n.setDistanceToParent( d );
920 prev_root.setDistanceToParent( d );
927 PhylogenyNode b = null;
928 PhylogenyNode c = null;
929 final PhylogenyNode new_root = new PhylogenyNode();
930 double distance1 = 0.0;
931 double distance2 = 0.0;
932 BranchData branch_data_1 = null;
933 BranchData branch_data_2 = null;
936 new_root.setChildNode( 0, a );
937 new_root.setChildNode( 1, b );
938 distance1 = c.getDistanceToParent();
939 if ( c.getBranchDataDirectly() != null ) {
940 branch_data_1 = ( BranchData ) c.getBranchDataDirectly().copy();
942 c.setDistanceToParent( b.getDistanceToParent() );
943 if ( b.getBranchDataDirectly() != null ) {
944 c.setBranchData( ( BranchData ) b.getBranchDataDirectly().copy() );
946 if ( a.getBranchDataDirectly() != null ) {
947 b.setBranchData( ( BranchData ) a.getBranchDataDirectly().copy() );
949 // New root is always placed in the middle of the branch:
950 if ( a.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
951 b.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
954 if ( distance_n_to_parent >= 0.0 ) {
955 final double diff = a.getDistanceToParent() - distance_n_to_parent;
956 a.setDistanceToParent( distance_n_to_parent );
957 b.setDistanceToParent( diff >= 0.0 ? diff : 0.0 );
960 final double d = a.getDistanceToParent() / 2.0;
961 a.setDistanceToParent( d );
962 b.setDistanceToParent( d );
965 b.setChildNodeOnly( a.getChildNodeIndex( b ), c );
966 // moving to the old root, swapping references:
967 while ( !c.isRoot() ) {
971 b.setChildNodeOnly( a.getChildNodeIndex( b ), c );
973 distance2 = c.getDistanceToParent();
974 branch_data_2 = c.getBranchDataDirectly();
975 c.setDistanceToParent( distance1 );
976 c.setBranchData( branch_data_1 );
977 distance1 = distance2;
978 branch_data_1 = branch_data_2;
980 // removing the old root:
981 if ( c.getNumberOfDescendants() == 2 ) {
982 final PhylogenyNode node = c.getChildNode( 1 - b.getChildNodeIndex( c ) );
984 if ( ( c.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT )
985 && ( node.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
986 node.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
989 node.setDistanceToParent( ( c.getDistanceToParent() >= 0.0 ? c.getDistanceToParent() : 0.0 )
990 + ( node.getDistanceToParent() >= 0.0 ? node.getDistanceToParent() : 0.0 ) );
992 if ( c.getBranchDataDirectly() != null ) {
993 node.setBranchData( ( BranchData ) c.getBranchDataDirectly().copy() );
995 for( int i = 0; i < b.getNumberOfDescendants(); ++i ) {
996 if ( b.getChildNode( i ) == c ) {
997 b.setChildNodeOnly( i, node );
1004 c.removeChildNode( b.getChildNodeIndex( c ) );
1006 setRoot( new_root );
1011 * Sets all Nodes of this Phylogeny to not-collapsed.
1013 * In most cases methods adjustNodeCount(false) and recalculateAndReset()
1014 * need to be called after this method has been called.
1016 public void setAllNodesToNotCollapse() {
1020 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1021 final PhylogenyNode node = iter.next();
1022 node.setCollapse( false );
1026 public void setConfidence( final Confidence confidence ) {
1027 _confidence = confidence;
1030 public void setDescription( final String description ) {
1031 _description = description;
1034 public void setDistanceUnit( final String _distance_unit ) {
1035 this._distance_unit = _distance_unit;
1038 public void setIdentifier( final Identifier identifier ) {
1039 _identifier = identifier;
1042 public void setIdToNodeMap( final HashMap<Long, PhylogenyNode> idhash ) {
1043 _id_to_node_map = idhash;
1047 * Sets the indicators of all Nodes of this Phylogeny to 0.
1049 public void setIndicatorsToZero() {
1053 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1054 iter.next().setIndicator( ( byte ) 0 );
1056 } // setIndicatorsToZero()
1059 * Sets the name of this Phylogeny to s.
1061 public void setName( final String s ) {
1065 public void setRelevantSequenceRelationTypes( final Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> types ) {
1066 _relevant_sequence_relation_types = types;
1069 public void setRerootable( final boolean rerootable ) {
1070 _rerootable = rerootable;
1073 public void setRoot( final PhylogenyNode n ) {
1078 * Sets whether this Phylogeny is rooted or not.
1080 public void setRooted( final boolean b ) {
1082 } // setRooted( boolean )
1084 public void setSequenceRelationQueries( final Collection<Sequence> sequencesByName ) {
1085 _sequenceRelationQueries = sequencesByName;
1088 public void setType( final String type ) {
1092 public String toNewHampshire() {
1093 return toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1096 public String toNewHampshire( final boolean simple_nh,
1097 final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
1099 return new PhylogenyWriter().toNewHampshire( this, simple_nh, true, nh_conversion_support_style )
1102 catch ( final IOException e ) {
1103 throw new Error( "this should not have happend: " + e.getMessage() );
1107 public String toNewHampshireX() {
1109 return new PhylogenyWriter().toNewHampshireX( this ).toString();
1111 catch ( final IOException e ) {
1112 throw new Error( "this should not have happend: " + e.getMessage() );
1116 public String toNexus() {
1117 return toNexus( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1120 public String toNexus( final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) {
1122 return new PhylogenyWriter().toNexus( this, svs ).toString();
1124 catch ( final IOException e ) {
1125 throw new Error( "this should not have happend: " + e.getMessage() );
1129 public String toPhyloXML( final int phyloxml_level ) {
1131 return new PhylogenyWriter().toPhyloXML( this, phyloxml_level ).toString();
1133 catch ( final IOException e ) {
1134 throw new Error( "this should not have happend: " + e.getMessage() );
1138 // ---------------------------------------------------------
1139 // Writing of Phylogeny to Strings
1140 // ---------------------------------------------------------
1142 * Converts this Phylogeny to a New Hampshire X (String) representation.
1144 * @return New Hampshire X (String) representation of this
1145 * @see #toNewHampshireX()
1148 public String toString() {
1149 return toNewHampshireX();
1153 * Removes the root PhylogenyNode this Phylogeny.
1155 public void unRoot() throws RuntimeException {
1157 throw new FailedConditionCheckException( "Attempt to unroot a phylogeny which is not tree-like." );
1162 setIndicatorsToZero();
1163 if ( !isRooted() || ( getNumberOfExternalNodes() <= 1 ) ) {
1170 private HashMap<Long, PhylogenyNode> getIdToNodeMap() {
1171 return _id_to_node_map;
1175 * Return Node by TaxonomyId Olivier CHABROL :
1176 * olivier.chabrol@univ-provence.fr
1179 * search taxonomy identifier
1181 * sublist node to search
1182 * @return List node with the same taxonomy identifier
1184 private List<PhylogenyNode> getNodeByTaxonomyID( final String taxonomyID, final List<PhylogenyNode> nodes ) {
1185 final List<PhylogenyNode> retour = new ArrayList<PhylogenyNode>();
1186 for( final PhylogenyNode node : nodes ) {
1187 if ( taxonomyID.equals( PhylogenyMethods.getTaxonomyIdentifier( node ) ) ) {
1195 * List all species contains in all leaf under a node Olivier CHABROL :
1196 * olivier.chabrol@univ-provence.fr
1199 * PhylogenyNode whose sub node species are returned
1200 * @return species contains in all leaf under the param node
1202 private List<String> getSubNodeTaxonomy( final PhylogenyNode node ) {
1203 final List<String> taxonomyList = new ArrayList<String>();
1204 final List<PhylogenyNode> childs = node.getAllExternalDescendants();
1205 String speciesId = null;
1206 for( final PhylogenyNode phylogenyNode : childs ) {
1207 // taxId = new Long(phylogenyNode.getTaxonomyID());
1208 speciesId = PhylogenyMethods.getTaxonomyIdentifier( phylogenyNode );
1209 if ( !taxonomyList.contains( speciesId ) ) {
1210 taxonomyList.add( speciesId );
1213 return taxonomyList;
1217 * Create a map [<PhylogenyNode, List<String>], the list contains the
1218 * species contains in all leaf under phylogeny node Olivier CHABROL :
1219 * olivier.chabrol@univ-provence.fr
1222 * the tree root node
1226 private void getTaxonomyMap( final PhylogenyNode node, final Map<PhylogenyNode, List<String>> map ) {
1228 if ( node.isExternal() ) {
1231 map.put( node, getSubNodeTaxonomy( node ) );
1232 getTaxonomyMap( node.getChildNode1(), map );
1233 getTaxonomyMap( node.getChildNode2(), map );
1236 private boolean isAllowMultipleParents() {
1237 return _allow_multiple_parents;
1241 * Util method to check if all element of a list is contains in the
1242 * rangeList. Olivier CHABROL : olivier.chabrol@univ-provence.fr
1247 * the range list to compare
1248 * @return <code>true</code> if all param list element are contains in param
1249 * rangeList, <code>false</code> otherwise.
1251 private boolean isContains( final List<String> list, final List<String> rangeList ) {
1252 if ( list.size() > rangeList.size() ) {
1256 for( final Iterator<String> iterator = list.iterator(); iterator.hasNext(); ) {
1257 l = iterator.next();
1258 if ( !rangeList.contains( l ) ) {
1266 * Hashes the ID number of each PhylogenyNode of this Phylogeny to its
1267 * corresponding PhylogenyNode, in order to make method getNode( id ) run in
1268 * constant time. Important: The user is responsible for calling this method
1269 * (again) after this Phylogeny has been changed/created/renumbered.
1271 private void reHashIdToNodeMap() {
1275 setIdToNodeMap( new HashMap<Long, PhylogenyNode>() );
1276 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1277 final PhylogenyNode node = iter.next();
1278 getIdToNodeMap().put( node.getId(), node );
1282 private void setAllowMultipleParents( final boolean allow_multiple_parents ) {
1283 _allow_multiple_parents = allow_multiple_parents;