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: www.phylosoft.org/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<Integer, 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 );
164 * Returns a deep copy of this Phylogeny.
166 * (The resulting Phylogeny has its references in the external nodes
167 * corrected, if they are lacking/obsolete in this.)
169 public Phylogeny copy( final PhylogenyNode source ) {
170 final Phylogeny tree = new Phylogeny();
175 tree._rooted = _rooted;
176 tree._name = new String( _name );
177 tree._description = new String( _description );
178 tree._type = new String( _type );
179 tree._rerootable = _rerootable;
180 tree._distance_unit = new String( _distance_unit );
181 if ( _confidence != null ) {
182 tree._confidence = ( Confidence ) _confidence.copy();
184 if ( _identifier != null ) {
185 tree._identifier = ( Identifier ) _identifier.copy();
187 tree.setAllowMultipleParents( isAllowMultipleParents() );
188 tree._root = PhylogenyMethods.copySubTree( source );
193 * Returns a shallow copy of this Phylogeny.
195 * (The resulting Phylogeny has its references in the external nodes
196 * corrected, if they are lacking/obsolete in this.)
198 public Phylogeny copyShallow() {
199 return copyShallow( _root );
202 public Phylogeny copyShallow( final PhylogenyNode source ) {
203 final Phylogeny tree = new Phylogeny();
208 tree._rooted = _rooted;
210 tree._description = _description;
212 tree._rerootable = _rerootable;
213 tree._distance_unit = _distance_unit;
214 tree._confidence = _confidence;
215 tree._identifier = _identifier;
216 tree.setAllowMultipleParents( isAllowMultipleParents() );
217 tree._root = PhylogenyMethods.copySubTreeShallow( source );
222 * Need to call clearHashIdToNodeMap() afterwards (not done automatically
223 * to allow client multiple deletions in linear time).
224 * Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this
225 * if tree is to be displayed.
227 * @param remove_us the parent node of the subtree to be deleted
229 public void deleteSubtree( final PhylogenyNode remove_us, final boolean collapse_resulting_node_with_one_desc ) {
230 if ( isEmpty() || ( remove_us.isRoot() && ( getNumberOfExternalNodes() != 1 ) ) ) {
233 if ( remove_us.isRoot() && ( getNumberOfExternalNodes() == 1 ) ) {
236 else if ( !collapse_resulting_node_with_one_desc ) {
237 remove_us.getParent().removeChildNode( remove_us );
240 final PhylogenyNode removed_node = remove_us;
241 final PhylogenyNode p = remove_us.getParent();
243 if ( p.getNumberOfDescendants() == 2 ) {
244 if ( removed_node.isFirstChildNode() ) {
245 setRoot( getRoot().getChildNode( 1 ) );
246 getRoot().setParent( null );
249 setRoot( getRoot().getChildNode( 0 ) );
250 getRoot().setParent( null );
254 p.removeChildNode( removed_node.getChildNodeIndex() );
258 final PhylogenyNode pp = removed_node.getParent().getParent();
259 if ( p.getNumberOfDescendants() == 2 ) {
260 final int pi = p.getChildNodeIndex();
261 if ( removed_node.isFirstChildNode() ) {
262 p.getChildNode( 1 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
263 .getDistanceToParent(), p.getChildNode( 1 ).getDistanceToParent() ) );
264 pp.setChildNode( pi, p.getChildNode( 1 ) );
267 p.getChildNode( 0 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
268 .getDistanceToParent(), p.getChildNode( 0 ).getDistanceToParent() ) );
269 pp.setChildNode( pi, p.getChildNode( 0 ) );
273 p.removeChildNode( removed_node.getChildNodeIndex() );
277 remove_us.removeConnections();
278 externalNodesHaveChanged();
281 public void externalNodesHaveChanged() {
282 _external_nodes_set = null;
285 public String[] getAllExternalNodeNames() {
290 final String[] names = new String[ getNumberOfExternalNodes() ];
291 for( final PhylogenyNodeIterator iter = iteratorExternalForward(); iter.hasNext(); ) {
292 names[ i++ ] = new String( iter.next().getName() );
297 public Confidence getConfidence() {
301 public String getDescription() {
305 public String getDistanceUnit() {
306 return _distance_unit;
311 * Warning. The order of the returned nodes is random
312 * -- and hence cannot be relied on.
314 * @return Unordered set of PhylogenyNode
316 public List<PhylogenyNode> getExternalNodes() {
317 if ( _external_nodes_set == null ) {
318 _external_nodes_set = new ArrayList<PhylogenyNode>();
319 for( final PhylogenyNodeIterator it = iteratorPostorder(); it.hasNext(); ) {
320 final PhylogenyNode n = it.next();
321 if ( n.isExternal() ) {
322 _external_nodes_set.add( n );
326 return _external_nodes_set;
330 * Returns the number of duplications of this Phylogeny (int). A return
331 * value of -1 indicates that the number of duplications is unknown.
333 // public int getNumberOfDuplications() {
334 // return _number_of_duplications;
335 // } // getNumberOfDuplications()
337 * Sets the number of duplications of this Phylogeny (int). A value of -1
338 * indicates that the number of duplications is unknown.
341 * set to true for clean NH format
343 // public void setNumberOfDuplications( int i ) {
345 // _number_of_duplications = -1;
348 // _number_of_duplications = i;
350 // } // setNumberOfDuplications( int )
352 * Returns the first external PhylogenyNode.
354 public PhylogenyNode getFirstExternalNode() {
356 throw new FailedConditionCheckException( "attempt to obtain first external node of empty phylogeney" );
358 PhylogenyNode node = getRoot();
359 while ( node.isInternal() ) {
360 node = node.getFirstChildNode();
366 * This calculates the height for rooted, tree-shaped phylogenies. The
367 * height is the longest distance from the root to an external node. Please
368 * note. Child nodes of collapsed nodes are ignored -- which is useful for
369 * display purposes but might be misleading for other applications.
371 * @return the height for rooted, tree-shaped phylogenies
373 public double getHeight() {
377 return calculateSubtreeHeight( getRoot() );
380 public Identifier getIdentifier() {
385 * Returns the name of this Phylogeny.
387 public String getName() {
392 * Finds the PhylogenyNode of this Phylogeny which has a matching ID number.
393 * @return PhylogenyNode with matching ID, null if not found
395 public PhylogenyNode getNode( final int id ) throws NoSuchElementException {
397 throw new NoSuchElementException( "attempt to get node in an empty phylogeny" );
399 if ( ( getIdToNodeMap() == null ) || getIdToNodeMap().isEmpty() ) {
402 return getIdToNodeMap().get( id );
406 * Returns a PhylogenyNode of this Phylogeny which has a matching name.
407 * Throws an Exception if seqname is not present in this or not unique.
410 * name (String) of PhylogenyNode to find
411 * @return PhylogenyNode with matchin name
413 public PhylogenyNode getNode( final String name ) {
417 final List<PhylogenyNode> nodes = getNodes( name );
418 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
419 throw new IllegalArgumentException( "node named \"" + name + "\" not found" );
421 if ( nodes.size() > 1 ) {
422 throw new IllegalArgumentException( "node named \"" + name + "\" not unique" );
424 return nodes.get( 0 );
428 * This is time-inefficient since it runs a iterator each time it is called.
431 public int getNodeCount() {
436 for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); it.next() ) {
443 * Returns a List with references to all Nodes of this Phylogeny which have
447 * name (String) of Nodes to find
448 * @return Vector of references to Nodes of this Phylogeny with matching
450 * @see #getNodesWithMatchingSpecies(String)
452 public List<PhylogenyNode> getNodes( final String name ) {
456 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
457 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
458 final PhylogenyNode n = iter.next();
459 if ( n.getName().equals( name ) ) {
466 public List<PhylogenyNode> getNodesViaSequenceName( final String seq_name ) {
470 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
471 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
472 final PhylogenyNode n = iter.next();
473 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getName().equals( seq_name ) ) {
480 public List<PhylogenyNode> getNodesViaTaxonomyCode( final String taxonomy_code ) {
484 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
485 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
486 final PhylogenyNode n = iter.next();
487 if ( n.getNodeData().isHasTaxonomy()
488 && n.getNodeData().getTaxonomy().getTaxonomyCode().equals( taxonomy_code ) ) {
496 * Returns a Vector with references to all Nodes of this Phylogeny which
497 * have a matching species name.
500 * species name (String) of Nodes to find
501 * @return Vector of references to Nodes of this Phylogeny with matching
503 * @see #getNodes(String)
505 public List<PhylogenyNode> getNodesWithMatchingSpecies( final String specname ) {
509 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
510 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
511 final PhylogenyNode n = iter.next();
512 if ( PhylogenyMethods.getSpecies( n ).equals( specname ) ) {
519 public PhylogenyNode getNodeViaSequenceName( final String seq_name ) {
523 final List<PhylogenyNode> nodes = getNodesViaSequenceName( seq_name );
524 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
525 throw new IllegalArgumentException( "node with sequence named [" + seq_name + "] not found" );
527 if ( nodes.size() > 1 ) {
528 throw new IllegalArgumentException( "node with sequence named [" + seq_name + "] not unique" );
530 return nodes.get( 0 );
533 public PhylogenyNode getNodeViaTaxonomyCode( final String taxonomy_code ) {
537 final List<PhylogenyNode> nodes = getNodesViaTaxonomyCode( taxonomy_code );
538 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
539 throw new IllegalArgumentException( "node with taxonomy code \"" + taxonomy_code + "\" not found" );
541 if ( nodes.size() > 1 ) {
542 throw new IllegalArgumentException( "node with taxonomy code \"" + taxonomy_code + "\" not unique" );
544 return nodes.get( 0 );
547 public int getNumberOfBranches() {
552 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); iter.next() ) {
561 public int getNumberOfInternalNodes() {
566 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
567 if ( iter.next().isInternal() ) {
578 * Returns the sum of external Nodes of this Phylogeny (int).
580 public int getNumberOfExternalNodes() {
584 return getExternalNodes().size();
588 * Returns all paralogs of the external PhylogenyNode n of this Phylogeny.
589 * paralog are returned as List of node references.
591 * PRECONDITION: This tree must be binary and rooted, and speciation -
592 * duplication need to be assigned for each of its internal Nodes.
594 * Returns null if this Phylogeny is empty or if n is internal.
596 * (Last modified: 11/22/00) Olivier CHABROL :
597 * olivier.chabrol@univ-provence.fr
600 * external PhylogenyNode whose orthologs are to be returned
601 * @return Vector of references to all orthologous Nodes of PhylogenyNode n
602 * of this Phylogeny, null if this Phylogeny is empty or if n is
605 public List<PhylogenyNode> getParalogousNodes( final PhylogenyNode n, final String[] taxonomyCodeRange ) {
606 PhylogenyNode node = n;
607 PhylogenyNode prev = null;
608 final List<PhylogenyNode> v = new ArrayList<PhylogenyNode>();
609 final Map<PhylogenyNode, List<String>> map = new HashMap<PhylogenyNode, List<String>>();
610 getTaxonomyMap( getRoot(), map );
611 if ( !node.isExternal() || isEmpty() ) {
614 final String searchNodeSpeciesId = PhylogenyMethods.getTaxonomyIdentifier( n );
615 if ( !node.isExternal() || isEmpty() ) {
618 List<String> taxIdList = null;
619 final List<String> taxonomyCodeRangeList = Arrays.asList( taxonomyCodeRange );
620 while ( !node.isRoot() ) {
622 node = node.getParent();
623 taxIdList = map.get( node );
624 if ( node.isDuplication() && isContains( taxIdList, taxonomyCodeRangeList ) ) {
625 if ( node.getChildNode1() == prev ) {
626 v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode2()
627 .getAllExternalDescendants() ) );
630 v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode1()
631 .getAllExternalDescendants() ) );
638 public Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> getRelevantSequenceRelationTypes() {
639 if ( _relevant_sequence_relation_types == null ) {
640 _relevant_sequence_relation_types = new Vector<SEQUENCE_RELATION_TYPE>();
642 return _relevant_sequence_relation_types;
646 * Returns the root PhylogenyNode of this Phylogeny.
648 public PhylogenyNode getRoot() {
652 public Collection<Sequence> getSequenceRelationQueries() {
653 return _sequenceRelationQueries;
656 public String getType() {
661 * Deletes this Phylogeny.
670 _id_to_node_map = null;
674 setAllowMultipleParents( Phylogeny.ALLOW_MULTIPLE_PARENTS_DEFAULT );
678 * Returns whether this is a completely binary tree (i.e. all internal nodes
682 public boolean isCompletelyBinary() {
686 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
687 final PhylogenyNode node = iter.next();
688 if ( node.isInternal() && ( node.getNumberOfDescendants() != 2 ) ) {
696 * Checks whether a Phylogeny object is deleted (or empty).
698 * @return true if the tree is deleted (or empty), false otherwise
700 public boolean isEmpty() {
701 return ( getRoot() == null );
704 public boolean isRerootable() {
709 * Returns true is this Phylogeny is rooted.
711 public boolean isRooted() {
715 public boolean isTree() {
719 public PhylogenyNodeIterator iteratorExternalForward() {
720 return new ExternalForwardIterator( this );
723 public PhylogenyNodeIterator iteratorLevelOrder() {
724 return new LevelOrderTreeIterator( this );
727 public PhylogenyNodeIterator iteratorPostorder() {
728 return new PostorderTreeIterator( this );
731 public PhylogenyNodeIterator iteratorPreorder() {
732 return new PreorderTreeIterator( this );
736 * Resets the ID numbers of the nodes of this Phylogeny in level order,
737 * starting with start_label (for the root). <br>
738 * WARNING. After this method has been called, node IDs are no longer
741 public void levelOrderReID() {
745 _id_to_node_map = null;
747 for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); ) {
748 final PhylogenyNode node = it.next();
749 if ( node.isRoot() ) {
750 node.setId( PhylogenyNode.getNodeCount() );
753 node.setId( node.getParent().getId() + 1 );
754 if ( node.getId() > max ) {
759 PhylogenyNode.setNodeCount( max + 1 );
763 * Prints descriptions of all external Nodes of this Phylogeny to
766 public void printExtNodes() {
770 for( final PhylogenyNodeIterator iter = iteratorExternalForward(); iter.hasNext(); ) {
771 System.out.println( iter.next() + "\n" );
776 * (Re)counts the number of children for each PhylogenyNode of this
777 * Phylogeny. As an example, this method needs to be called after a
778 * Phylogeny has been reRooted and it is to be displayed.
780 * @param consider_collapsed_nodes
781 * set to true to take into account collapsed nodes (collapsed
782 * nodes have 1 child).
784 public void recalculateNumberOfExternalDescendants( final boolean consider_collapsed_nodes ) {
788 for( final PhylogenyNodeIterator iter = iteratorPostorder(); iter.hasNext(); ) {
789 final PhylogenyNode node = iter.next();
790 if ( node.isExternal() || ( consider_collapsed_nodes && node.isCollapse() ) ) {
791 node.setSumExtNodes( 1 );
795 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
796 sum += node.getChildNode( i ).getNumberOfExternalNodes();
798 node.setSumExtNodes( sum );
804 * Places the root of this Phylogeny on the parent branch of the
805 * PhylogenyNode with a corresponding ID. The new root is always placed on
806 * the middle of the branch. If the resulting reRooted Phylogeny is to be
807 * used any further, in most cases the following methods have to be called
808 * on the resulting Phylogeny:
810 * <li>recalculateNumberOfExternalDescendants(boolean)
811 * <li>recalculateAndReset()
814 * ID (int) of PhylogenyNode of this Phylogeny
816 public void reRoot( final int id ) {
817 reRoot( getNode( id ) );
821 * Places the root of this Phylogeny on Branch b. The new root is always
822 * placed on the middle of the branch b.
825 public void reRoot( final PhylogenyBranch b ) {
826 final PhylogenyNode n1 = b.getFirstNode();
827 final PhylogenyNode n2 = b.getSecondNode();
828 if ( n1.isExternal() ) {
831 else if ( n2.isExternal() ) {
834 else if ( ( n2 == n1.getChildNode1() ) || ( n2 == n1.getChildNode2() ) ) {
837 else if ( ( n1 == n2.getChildNode1() ) || ( n1 == n2.getChildNode2() ) ) {
840 else if ( ( n1.getParent() != null ) && n1.getParent().isRoot()
841 && ( ( n1.getParent().getChildNode1() == n2 ) || ( n1.getParent().getChildNode2() == n2 ) ) ) {
845 throw new IllegalArgumentException( "reRoot( Branch b ): b is not a branch." );
850 * Places the root of this Phylogeny on the parent branch PhylogenyNode n.
851 * The new root is always placed on the middle of the branch.
853 * If the resulting reRooted Phylogeny is to be used any further, in most
854 * cases the following three methods have to be called on the resulting
857 * <li>recalculateNumberOfExternalDescendants(boolean) <li>recalculateAndReset()
860 * (Last modified: 10/01/01)
863 * PhylogenyNode of this Phylogeny\
865 public void reRoot( final PhylogenyNode n ) {
869 public void reRoot( final PhylogenyNode n, final double distance_n_to_parent ) {
870 if ( isEmpty() || ( getNumberOfExternalNodes() < 2 ) ) {
877 else if ( n.getParent().isRoot() ) {
878 if ( ( n.getParent().getNumberOfDescendants() == 2 ) && ( distance_n_to_parent >= 0 ) ) {
879 final double d = n.getParent().getChildNode1().getDistanceToParent()
880 + n.getParent().getChildNode2().getDistanceToParent();
882 if ( n.getChildNodeIndex() == 0 ) {
883 other = n.getParent().getChildNode2();
886 other = n.getParent().getChildNode1();
888 n.setDistanceToParent( distance_n_to_parent );
889 final double dm = d - distance_n_to_parent;
891 other.setDistanceToParent( dm );
894 other.setDistanceToParent( 0 );
897 if ( n.getParent().getNumberOfDescendants() > 2 ) {
898 final int index = n.getChildNodeIndex();
899 final double dn = n.getDistanceToParent();
900 final PhylogenyNode prev_root = getRoot();
901 prev_root.getDescendants().remove( index );
902 final PhylogenyNode new_root = new PhylogenyNode();
903 new_root.setChildNode( 0, n );
904 new_root.setChildNode( 1, prev_root );
905 if ( n.getBranchDataDirectly() != null ) {
906 prev_root.setBranchData( ( BranchData ) n.getBranchDataDirectly().copy() );
909 if ( distance_n_to_parent >= 0 ) {
910 n.setDistanceToParent( distance_n_to_parent );
911 final double d = dn - distance_n_to_parent;
913 prev_root.setDistanceToParent( d );
916 prev_root.setDistanceToParent( 0 );
921 final double d = dn / 2.0;
922 n.setDistanceToParent( d );
923 prev_root.setDistanceToParent( d );
930 PhylogenyNode b = null;
931 PhylogenyNode c = null;
932 final PhylogenyNode new_root = new PhylogenyNode();
933 double distance1 = 0.0;
934 double distance2 = 0.0;
935 BranchData branch_data_1 = null;
936 BranchData branch_data_2 = null;
939 new_root.setChildNode( 0, a );
940 new_root.setChildNode( 1, b );
941 distance1 = c.getDistanceToParent();
942 if ( c.getBranchDataDirectly() != null ) {
943 branch_data_1 = ( BranchData ) c.getBranchDataDirectly().copy();
945 c.setDistanceToParent( b.getDistanceToParent() );
946 if ( b.getBranchDataDirectly() != null ) {
947 c.setBranchData( ( BranchData ) b.getBranchDataDirectly().copy() );
949 if ( a.getBranchDataDirectly() != null ) {
950 b.setBranchData( ( BranchData ) a.getBranchDataDirectly().copy() );
952 // New root is always placed in the middle of the branch:
953 if ( a.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
954 b.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
957 if ( distance_n_to_parent >= 0.0 ) {
958 final double diff = a.getDistanceToParent() - distance_n_to_parent;
959 a.setDistanceToParent( distance_n_to_parent );
960 b.setDistanceToParent( diff >= 0.0 ? diff : 0.0 );
963 final double d = a.getDistanceToParent() / 2.0;
964 a.setDistanceToParent( d );
965 b.setDistanceToParent( d );
968 b.setChildNodeOnly( a.getChildNodeIndex( b ), c );
969 // moving to the old root, swapping references:
970 while ( !c.isRoot() ) {
974 b.setChildNodeOnly( a.getChildNodeIndex( b ), c );
976 distance2 = c.getDistanceToParent();
977 branch_data_2 = c.getBranchDataDirectly();
978 c.setDistanceToParent( distance1 );
979 c.setBranchData( branch_data_1 );
980 distance1 = distance2;
981 branch_data_1 = branch_data_2;
983 // removing the old root:
984 if ( c.getNumberOfDescendants() == 2 ) {
985 final PhylogenyNode node = c.getChildNode( 1 - b.getChildNodeIndex( c ) );
987 if ( ( c.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT )
988 && ( node.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
989 node.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
992 node.setDistanceToParent( ( c.getDistanceToParent() >= 0.0 ? c.getDistanceToParent() : 0.0 )
993 + ( node.getDistanceToParent() >= 0.0 ? node.getDistanceToParent() : 0.0 ) );
995 if ( c.getBranchDataDirectly() != null ) {
996 node.setBranchData( ( BranchData ) c.getBranchDataDirectly().copy() );
998 for( int i = 0; i < b.getNumberOfDescendants(); ++i ) {
999 if ( b.getChildNode( i ) == c ) {
1000 b.setChildNodeOnly( i, node );
1007 c.removeChildNode( b.getChildNodeIndex( c ) );
1009 setRoot( new_root );
1014 * Sets all Nodes of this Phylogeny to not-collapsed.
1016 * In most cases methods adjustNodeCount(false) and recalculateAndReset()
1017 * need to be called after this method has been called.
1019 public void setAllNodesToNotCollapse() {
1023 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1024 final PhylogenyNode node = iter.next();
1025 node.setCollapse( false );
1029 public void setConfidence( final Confidence confidence ) {
1030 _confidence = confidence;
1033 public void setDescription( final String description ) {
1034 _description = description;
1037 public void setDistanceUnit( final String _distance_unit ) {
1038 this._distance_unit = _distance_unit;
1041 public void setIdentifier( final Identifier identifier ) {
1042 _identifier = identifier;
1045 public void setIdToNodeMap( final HashMap<Integer, PhylogenyNode> idhash ) {
1046 _id_to_node_map = idhash;
1050 * Sets the indicators of all Nodes of this Phylogeny to 0.
1052 public void setIndicatorsToZero() {
1056 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1057 iter.next().setIndicator( ( byte ) 0 );
1059 } // setIndicatorsToZero()
1062 * Sets the name of this Phylogeny to s.
1064 public void setName( final String s ) {
1068 public void setRelevantSequenceRelationTypes( final Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> types ) {
1069 _relevant_sequence_relation_types = types;
1072 public void setRerootable( final boolean rerootable ) {
1073 _rerootable = rerootable;
1076 public void setRoot( final PhylogenyNode n ) {
1081 * Sets whether this Phylogeny is rooted or not.
1083 public void setRooted( final boolean b ) {
1085 } // setRooted( boolean )
1087 public void setSequenceRelationQueries( final Collection<Sequence> sequencesByName ) {
1088 _sequenceRelationQueries = sequencesByName;
1091 public void setType( final String type ) {
1095 public String toNewHampshire() {
1096 return toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1099 public String toNewHampshire( final boolean simple_nh,
1100 final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
1102 return new PhylogenyWriter().toNewHampshire( this, simple_nh, true, nh_conversion_support_style )
1105 catch ( final IOException e ) {
1106 throw new Error( "this should not have happend: " + e.getMessage() );
1110 public String toNewHampshireX() {
1112 return new PhylogenyWriter().toNewHampshireX( this ).toString();
1114 catch ( final IOException e ) {
1115 throw new Error( "this should not have happend: " + e.getMessage() );
1119 public String toNexus() {
1120 return toNexus( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1123 public String toNexus( final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) {
1125 return new PhylogenyWriter().toNexus( this, svs ).toString();
1127 catch ( final IOException e ) {
1128 throw new Error( "this should not have happend: " + e.getMessage() );
1132 public String toPhyloXML( final int phyloxml_level ) {
1134 return new PhylogenyWriter().toPhyloXML( this, phyloxml_level ).toString();
1136 catch ( final IOException e ) {
1137 throw new Error( "this should not have happend: " + e.getMessage() );
1141 // ---------------------------------------------------------
1142 // Writing of Phylogeny to Strings
1143 // ---------------------------------------------------------
1145 * Converts this Phylogeny to a New Hampshire X (String) representation.
1147 * @return New Hampshire X (String) representation of this
1148 * @see #toNewHampshireX()
1151 public String toString() {
1152 return toNewHampshireX();
1156 * Removes the root PhylogenyNode this Phylogeny.
1158 public void unRoot() throws RuntimeException {
1160 throw new FailedConditionCheckException( "Attempt to unroot a phylogeny which is not tree-like." );
1165 setIndicatorsToZero();
1166 if ( !isRooted() || ( getNumberOfExternalNodes() <= 1 ) ) {
1173 private HashMap<Integer, PhylogenyNode> getIdToNodeMap() {
1174 return _id_to_node_map;
1178 * Return Node by TaxonomyId Olivier CHABROL :
1179 * olivier.chabrol@univ-provence.fr
1182 * search taxonomy identifier
1184 * sublist node to search
1185 * @return List node with the same taxonomy identifier
1187 private List<PhylogenyNode> getNodeByTaxonomyID( final String taxonomyID, final List<PhylogenyNode> nodes ) {
1188 final List<PhylogenyNode> retour = new ArrayList<PhylogenyNode>();
1189 for( final PhylogenyNode node : nodes ) {
1190 if ( taxonomyID.equals( PhylogenyMethods.getTaxonomyIdentifier( node ) ) ) {
1198 * List all species contains in all leaf under a node Olivier CHABROL :
1199 * olivier.chabrol@univ-provence.fr
1202 * PhylogenyNode whose sub node species are returned
1203 * @return species contains in all leaf under the param node
1205 private List<String> getSubNodeTaxonomy( final PhylogenyNode node ) {
1206 final List<String> taxonomyList = new ArrayList<String>();
1207 final List<PhylogenyNode> childs = node.getAllExternalDescendants();
1208 String speciesId = null;
1209 for( final PhylogenyNode phylogenyNode : childs ) {
1210 // taxId = new Long(phylogenyNode.getTaxonomyID());
1211 speciesId = PhylogenyMethods.getTaxonomyIdentifier( phylogenyNode );
1212 if ( !taxonomyList.contains( speciesId ) ) {
1213 taxonomyList.add( speciesId );
1216 return taxonomyList;
1220 * Create a map [<PhylogenyNode, List<String>], the list contains the
1221 * species contains in all leaf under phylogeny node Olivier CHABROL :
1222 * olivier.chabrol@univ-provence.fr
1225 * the tree root node
1229 private void getTaxonomyMap( final PhylogenyNode node, final Map<PhylogenyNode, List<String>> map ) {
1231 if ( node.isExternal() ) {
1234 map.put( node, getSubNodeTaxonomy( node ) );
1235 getTaxonomyMap( node.getChildNode1(), map );
1236 getTaxonomyMap( node.getChildNode2(), map );
1239 private boolean isAllowMultipleParents() {
1240 return _allow_multiple_parents;
1244 * Util method to check if all element of a list is contains in the
1245 * rangeList. Olivier CHABROL : olivier.chabrol@univ-provence.fr
1250 * the range list to compare
1251 * @return <code>true</code> if all param list element are contains in param
1252 * rangeList, <code>false</code> otherwise.
1254 private boolean isContains( final List<String> list, final List<String> rangeList ) {
1255 if ( list.size() > rangeList.size() ) {
1259 for( final Iterator<String> iterator = list.iterator(); iterator.hasNext(); ) {
1260 l = iterator.next();
1261 if ( !rangeList.contains( l ) ) {
1269 * Hashes the ID number of each PhylogenyNode of this Phylogeny to its
1270 * corresponding PhylogenyNode, in order to make method getNode( id ) run in
1271 * constant time. Important: The user is responsible for calling this method
1272 * (again) after this Phylogeny has been changed/created/renumbered.
1274 private void reHashIdToNodeMap() {
1278 setIdToNodeMap( new HashMap<Integer, PhylogenyNode>() );
1279 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1280 final PhylogenyNode node = iter.next();
1281 getIdToNodeMap().put( node.getId(), node );
1285 private void setAllowMultipleParents( final boolean allow_multiple_parents ) {
1286 _allow_multiple_parents = allow_multiple_parents;