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.PhylogenyNodeI.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() );
148 * Returns a deep copy of this Phylogeny.
150 * (The resulting Phylogeny has its references in the external nodes
151 * corrected, if they are lacking/obsolete in this.)
153 public Phylogeny copy() {
154 return copy( _root );
158 * Returns a shallow copy of this Phylogeny.
160 * (The resulting Phylogeny has its references in the external nodes
161 * corrected, if they are lacking/obsolete in this.)
163 public Phylogeny copyShallow() {
164 return copyShallow( _root );
167 public Phylogeny copyShallow( final PhylogenyNode source ) {
168 final Phylogeny tree = new Phylogeny();
173 tree._rooted = _rooted;
175 tree._description = _description;
177 tree._rerootable = _rerootable;
178 tree._distance_unit = _distance_unit;
179 tree._confidence = _confidence;
180 tree._identifier = _identifier;
181 tree.setAllowMultipleParents( isAllowMultipleParents() );
182 tree._root = PhylogenyMethods.copySubTreeShallow( source );
187 * Returns a deep copy of this Phylogeny.
189 * (The resulting Phylogeny has its references in the external nodes
190 * corrected, if they are lacking/obsolete in this.)
192 public Phylogeny copy( final PhylogenyNode source ) {
193 final Phylogeny tree = new Phylogeny();
198 tree._rooted = _rooted;
199 tree._name = new String( _name );
200 tree._description = new String( _description );
201 tree._type = new String( _type );
202 tree._rerootable = _rerootable;
203 tree._distance_unit = new String( _distance_unit );
204 if ( _confidence != null ) {
205 tree._confidence = ( Confidence ) _confidence.copy();
207 if ( _identifier != null ) {
208 tree._identifier = ( Identifier ) _identifier.copy();
210 tree.setAllowMultipleParents( isAllowMultipleParents() );
211 tree._root = PhylogenyMethods.copySubTree( source );
216 * Need to call clearHashIdToNodeMap() afterwards (not done automatically
217 * to allow client multiple deletions in linear time).
218 * Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this
219 * if tree is to be displayed.
221 * @param remove_us the parent node of the subtree to be deleted
223 public void deleteSubtree( final PhylogenyNode remove_us, final boolean collapse_resulting_node_with_one_desc ) {
224 if ( isEmpty() || ( remove_us.isRoot() && ( getNumberOfExternalNodes() != 1 ) ) ) {
227 if ( remove_us.isRoot() && ( getNumberOfExternalNodes() == 1 ) ) {
230 else if ( !collapse_resulting_node_with_one_desc ) {
231 remove_us.getParent().removeChildNode( remove_us );
234 final PhylogenyNode removed_node = remove_us;
235 final PhylogenyNode p = remove_us.getParent();
237 if ( p.getNumberOfDescendants() == 2 ) {
238 if ( removed_node.isFirstChildNode() ) {
239 setRoot( getRoot().getChildNode( 1 ) );
240 getRoot().setParent( null );
243 setRoot( getRoot().getChildNode( 0 ) );
244 getRoot().setParent( null );
248 p.removeChildNode( removed_node.getChildNodeIndex() );
252 final PhylogenyNode pp = removed_node.getParent().getParent();
253 if ( p.getNumberOfDescendants() == 2 ) {
254 final int pi = p.getChildNodeIndex();
255 if ( removed_node.isFirstChildNode() ) {
256 p.getChildNode( 1 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
257 .getDistanceToParent(), p.getChildNode( 1 ).getDistanceToParent() ) );
258 pp.setChildNode( pi, p.getChildNode( 1 ) );
261 p.getChildNode( 0 ).setDistanceToParent( PhylogenyMethods.addPhylogenyDistances( p
262 .getDistanceToParent(), p.getChildNode( 0 ).getDistanceToParent() ) );
263 pp.setChildNode( pi, p.getChildNode( 0 ) );
267 p.removeChildNode( removed_node.getChildNodeIndex() );
271 remove_us.removeConnections();
272 externalNodesHaveChanged();
275 public void externalNodesHaveChanged() {
276 _external_nodes_set = null;
279 public String[] getAllExternalNodeNames() {
284 final String[] names = new String[ getNumberOfExternalNodes() ];
285 for( final PhylogenyNodeIterator iter = iteratorExternalForward(); iter.hasNext(); ) {
286 names[ i++ ] = new String( iter.next().getName() );
291 public Confidence getConfidence() {
295 public String getDescription() {
299 public String getDistanceUnit() {
300 return _distance_unit;
305 * Warning. The order of the returned nodes is random
306 * -- and hence cannot be relied on.
308 * @return Unordered set of PhylogenyNode
310 public List<PhylogenyNode> getExternalNodes() {
311 if ( _external_nodes_set == null ) {
312 _external_nodes_set = new ArrayList<PhylogenyNode>();
313 for( final PhylogenyNodeIterator it = iteratorPostorder(); it.hasNext(); ) {
314 final PhylogenyNode n = it.next();
315 if ( n.isExternal() ) {
316 _external_nodes_set.add( n );
320 return _external_nodes_set;
324 * Returns the number of duplications of this Phylogeny (int). A return
325 * value of -1 indicates that the number of duplications is unknown.
327 // public int getNumberOfDuplications() {
328 // return _number_of_duplications;
329 // } // getNumberOfDuplications()
331 * Sets the number of duplications of this Phylogeny (int). A value of -1
332 * indicates that the number of duplications is unknown.
335 * set to true for clean NH format
337 // public void setNumberOfDuplications( int i ) {
339 // _number_of_duplications = -1;
342 // _number_of_duplications = i;
344 // } // setNumberOfDuplications( int )
346 * Returns the first external PhylogenyNode.
348 public PhylogenyNode getFirstExternalNode() {
350 throw new FailedConditionCheckException( "attempt to obtain first external node of empty phylogeney" );
352 PhylogenyNode node = getRoot();
353 while ( node.isInternal() ) {
354 node = node.getFirstChildNode();
360 * This calculates the height for rooted, tree-shaped phylogenies. The
361 * height is the longest distance from the root to an external node. Please
362 * note. Child nodes of collapsed nodes are ignored -- which is useful for
363 * display purposes but might be misleading for other applications.
365 * @return the height for rooted, tree-shaped phylogenies
367 public double getHeight() {
371 return calculateSubtreeHeight( getRoot() );
374 public Identifier getIdentifier() {
378 private HashMap<Integer, PhylogenyNode> getIdToNodeMap() {
379 return _id_to_node_map;
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 int 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 * Return Node by TaxonomyId Olivier CHABROL :
427 * olivier.chabrol@univ-provence.fr
430 * search taxonomy identifier
432 * sublist node to search
433 * @return List node with the same taxonomy identifier
435 private List<PhylogenyNode> getNodeByTaxonomyID( final String taxonomyID, final List<PhylogenyNode> nodes ) {
436 final List<PhylogenyNode> retour = new ArrayList<PhylogenyNode>();
437 for( final PhylogenyNode node : nodes ) {
438 if ( taxonomyID.equals( PhylogenyMethods.getTaxonomyIdentifier( node ) ) ) {
446 * Returns a List with references to all Nodes of this Phylogeny which have
450 * name (String) of Nodes to find
451 * @return Vector of references to Nodes of this Phylogeny with matching
453 * @see #getNodesWithMatchingSpecies(String)
455 public List<PhylogenyNode> getNodes( final String name ) {
459 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
460 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
461 final PhylogenyNode n = iter.next();
462 if ( n.getName().equals( name ) ) {
469 public List<PhylogenyNode> getNodesViaSequenceName( final String seq_name ) {
473 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
474 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
475 final PhylogenyNode n = iter.next();
476 if ( n.getNodeData().isHasSequence() && n.getNodeData().getSequence().getName().equals( seq_name ) ) {
483 public List<PhylogenyNode> getNodesViaTaxonomyCode( final String taxonomy_code ) {
487 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
488 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
489 final PhylogenyNode n = iter.next();
490 if ( n.getNodeData().isHasTaxonomy()
491 && n.getNodeData().getTaxonomy().getTaxonomyCode().equals( taxonomy_code ) ) {
499 * Returns a Vector with references to all Nodes of this Phylogeny which
500 * have a matching species name.
503 * species name (String) of Nodes to find
504 * @return Vector of references to Nodes of this Phylogeny with matching
506 * @see #getNodes(String)
508 public List<PhylogenyNode> getNodesWithMatchingSpecies( final String specname ) {
512 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
513 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
514 final PhylogenyNode n = iter.next();
515 if ( PhylogenyMethods.getSpecies( n ).equals( specname ) ) {
522 public PhylogenyNode getNodeViaSequenceName( final String seq_name ) {
526 final List<PhylogenyNode> nodes = getNodesViaSequenceName( seq_name );
527 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
528 throw new IllegalArgumentException( "node with sequence named [" + seq_name + "] not found" );
530 if ( nodes.size() > 1 ) {
531 throw new IllegalArgumentException( "node with sequence named [" + seq_name + "] not unique" );
533 return nodes.get( 0 );
536 public PhylogenyNode getNodeViaTaxonomyCode( final String taxonomy_code ) {
540 final List<PhylogenyNode> nodes = getNodesViaTaxonomyCode( taxonomy_code );
541 if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
542 throw new IllegalArgumentException( "node with taxonomy code \"" + taxonomy_code + "\" not found" );
544 if ( nodes.size() > 1 ) {
545 throw new IllegalArgumentException( "node with taxonomy code \"" + taxonomy_code + "\" not unique" );
547 return nodes.get( 0 );
551 * This is time-inefficient since it runs a iterator each time it is called.
554 public int getNodeCount() {
559 for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); it.next() ) {
565 public int getNumberOfBranches() {
570 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); iter.next() ) {
580 * Returns the sum of external Nodes of this Phylogeny (int).
582 public int getNumberOfExternalNodes() {
586 return getExternalNodes().size();
590 * Returns all paralogs of the external PhylogenyNode n of this Phylogeny.
591 * paralog are returned as List of node references.
593 * PRECONDITION: This tree must be binary and rooted, and speciation -
594 * duplication need to be assigned for each of its internal Nodes.
596 * Returns null if this Phylogeny is empty or if n is internal.
598 * (Last modified: 11/22/00) Olivier CHABROL :
599 * olivier.chabrol@univ-provence.fr
602 * external PhylogenyNode whose orthologs are to be returned
603 * @return Vector of references to all orthologous Nodes of PhylogenyNode n
604 * of this Phylogeny, null if this Phylogeny is empty or if n is
607 public List<PhylogenyNode> getParalogousNodes( final PhylogenyNode n, final String[] taxonomyCodeRange ) {
608 PhylogenyNode node = n;
609 PhylogenyNode prev = null;
610 final List<PhylogenyNode> v = new ArrayList<PhylogenyNode>();
611 final Map<PhylogenyNode, List<String>> map = new HashMap<PhylogenyNode, List<String>>();
612 getTaxonomyMap( getRoot(), map );
613 if ( !node.isExternal() || isEmpty() ) {
616 final String searchNodeSpeciesId = PhylogenyMethods.getTaxonomyIdentifier( n );
617 if ( !node.isExternal() || isEmpty() ) {
620 List<String> taxIdList = null;
621 final List<String> taxonomyCodeRangeList = Arrays.asList( taxonomyCodeRange );
622 while ( !node.isRoot() ) {
624 node = node.getParent();
625 taxIdList = map.get( node );
626 if ( node.isDuplication() && isContains( taxIdList, taxonomyCodeRangeList ) ) {
627 if ( node.getChildNode1() == prev ) {
628 v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode2()
629 .getAllExternalDescendants() ) );
632 v.addAll( getNodeByTaxonomyID( searchNodeSpeciesId, node.getChildNode1()
633 .getAllExternalDescendants() ) );
640 public Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> getRelevantSequenceRelationTypes() {
641 if ( _relevant_sequence_relation_types == null ) {
642 _relevant_sequence_relation_types = new Vector<SEQUENCE_RELATION_TYPE>();
644 return _relevant_sequence_relation_types;
648 * Returns the root PhylogenyNode of this Phylogeny.
650 public PhylogenyNode getRoot() {
654 public Collection<Sequence> getSequenceRelationQueries() {
655 return _sequenceRelationQueries;
659 * List all species contains in all leaf under a node Olivier CHABROL :
660 * olivier.chabrol@univ-provence.fr
663 * PhylogenyNode whose sub node species are returned
664 * @return species contains in all leaf under the param node
666 private List<String> getSubNodeTaxonomy( final PhylogenyNode node ) {
667 final List<String> taxonomyList = new ArrayList<String>();
668 final List<PhylogenyNode> childs = node.getAllExternalDescendants();
669 String speciesId = null;
670 for( final PhylogenyNode phylogenyNode : childs ) {
671 // taxId = new Long(phylogenyNode.getTaxonomyID());
672 speciesId = PhylogenyMethods.getTaxonomyIdentifier( phylogenyNode );
673 if ( !taxonomyList.contains( speciesId ) ) {
674 taxonomyList.add( speciesId );
681 * Create a map [<PhylogenyNode, List<String>], the list contains the
682 * species contains in all leaf under phylogeny node Olivier CHABROL :
683 * olivier.chabrol@univ-provence.fr
690 private void getTaxonomyMap( final PhylogenyNode node, final Map<PhylogenyNode, List<String>> map ) {
692 if ( node.isExternal() ) {
695 map.put( node, getSubNodeTaxonomy( node ) );
696 getTaxonomyMap( node.getChildNode1(), map );
697 getTaxonomyMap( node.getChildNode2(), map );
700 public String getType() {
705 * Hashes the ID number of each PhylogenyNode of this Phylogeny to its
706 * corresponding PhylogenyNode, in order to make method getNode( id ) run in
707 * constant time. Important: The user is responsible for calling this method
708 * (again) after this Phylogeny has been changed/created/renumbered.
710 private void reHashIdToNodeMap() {
714 setIdToNodeMap( new HashMap<Integer, PhylogenyNode>() );
715 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
716 final PhylogenyNode node = iter.next();
717 getIdToNodeMap().put( node.getId(), node );
721 public void clearHashIdToNodeMap() {
722 setIdToNodeMap( null );
726 * Deletes this Phylogeny.
735 _id_to_node_map = null;
739 setAllowMultipleParents( Phylogeny.ALLOW_MULTIPLE_PARENTS_DEFAULT );
742 private boolean isAllowMultipleParents() {
743 return _allow_multiple_parents;
747 * Returns whether this is a completely binary tree (i.e. all internal nodes
751 public boolean isCompletelyBinary() {
755 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
756 final PhylogenyNode node = iter.next();
757 if ( node.isInternal() && ( node.getNumberOfDescendants() != 2 ) ) {
765 * Util method to check if all element of a list is contains in the
766 * rangeList. Olivier CHABROL : olivier.chabrol@univ-provence.fr
771 * the range list to compare
772 * @return <code>true</code> if all param list element are contains in param
773 * rangeList, <code>false</code> otherwise.
775 private boolean isContains( final List<String> list, final List<String> rangeList ) {
776 if ( list.size() > rangeList.size() ) {
780 for( final Iterator<String> iterator = list.iterator(); iterator.hasNext(); ) {
782 if ( !rangeList.contains( l ) ) {
790 * Checks whether a Phylogeny object is deleted (or empty).
792 * @return true if the tree is deleted (or empty), false otherwise
794 public boolean isEmpty() {
795 return ( getRoot() == null );
798 public boolean isRerootable() {
803 * Returns true is this Phylogeny is rooted.
805 public boolean isRooted() {
809 public boolean isTree() {
813 public PhylogenyNodeIterator iteratorExternalForward() {
814 return new ExternalForwardIterator( this );
817 public PhylogenyNodeIterator iteratorLevelOrder() {
818 return new LevelOrderTreeIterator( this );
821 public PhylogenyNodeIterator iteratorPostorder() {
822 return new PostorderTreeIterator( this );
825 public PhylogenyNodeIterator iteratorPreorder() {
826 return new PreorderTreeIterator( this );
830 * Resets the ID numbers of the nodes of this Phylogeny in level order,
831 * starting with start_label (for the root). <br>
832 * WARNING. After this method has been called, node IDs are no longer
835 public void levelOrderReID() {
839 _id_to_node_map = null;
841 for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); ) {
842 final PhylogenyNode node = it.next();
843 if ( node.isRoot() ) {
844 node.setId( PhylogenyNode.getNodeCount() );
847 node.setId( node.getParent().getId() + 1 );
848 if ( node.getId() > max ) {
853 PhylogenyNode.setNodeCount( max + 1 );
856 public void preOrderReId() {
860 setIdToNodeMap( null );
861 int i = PhylogenyNode.getNodeCount();
862 for( final PhylogenyNodeIterator it = iteratorPreorder(); it.hasNext(); ) {
863 it.next().setId( i++ );
865 PhylogenyNode.setNodeCount( i );
869 * Prints descriptions of all external Nodes of this Phylogeny to
872 public void printExtNodes() {
876 for( final PhylogenyNodeIterator iter = iteratorExternalForward(); iter.hasNext(); ) {
877 System.out.println( iter.next() + "\n" );
882 * (Re)counts the number of children for each PhylogenyNode of this
883 * Phylogeny. As an example, this method needs to be called after a
884 * Phylogeny has been reRooted and it is to be displayed.
886 * @param consider_collapsed_nodes
887 * set to true to take into account collapsed nodes (collapsed
888 * nodes have 1 child).
890 public void recalculateNumberOfExternalDescendants( final boolean consider_collapsed_nodes ) {
894 for( final PhylogenyNodeIterator iter = iteratorPostorder(); iter.hasNext(); ) {
895 final PhylogenyNode node = iter.next();
896 if ( node.isExternal() || ( consider_collapsed_nodes && node.isCollapse() ) ) {
897 node.setSumExtNodes( 1 );
901 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
902 sum += node.getChildNode( i ).getNumberOfExternalNodes();
904 node.setSumExtNodes( sum );
910 * Places the root of this Phylogeny on the parent branch of the
911 * PhylogenyNode with a corresponding ID. The new root is always placed on
912 * the middle of the branch. If the resulting reRooted Phylogeny is to be
913 * used any further, in most cases the following methods have to be called
914 * on the resulting Phylogeny:
916 * <li>recalculateNumberOfExternalDescendants(boolean)
917 * <li>recalculateAndReset()
920 * ID (int) of PhylogenyNode of this Phylogeny
922 public void reRoot( final int id ) {
923 reRoot( getNode( id ) );
927 * Places the root of this Phylogeny on Branch b. The new root is always
928 * placed on the middle of the branch b.
931 public void reRoot( final PhylogenyBranch b ) {
932 final PhylogenyNode n1 = b.getFirstNode();
933 final PhylogenyNode n2 = b.getSecondNode();
934 if ( n1.isExternal() ) {
937 else if ( n2.isExternal() ) {
940 else if ( ( n2 == n1.getChildNode1() ) || ( n2 == n1.getChildNode2() ) ) {
943 else if ( ( n1 == n2.getChildNode1() ) || ( n1 == n2.getChildNode2() ) ) {
946 else if ( ( n1.getParent() != null ) && n1.getParent().isRoot()
947 && ( ( n1.getParent().getChildNode1() == n2 ) || ( n1.getParent().getChildNode2() == n2 ) ) ) {
951 throw new IllegalArgumentException( "reRoot( Branch b ): b is not a branch." );
956 * Places the root of this Phylogeny on the parent branch PhylogenyNode n.
957 * The new root is always placed on the middle of the branch.
959 * If the resulting reRooted Phylogeny is to be used any further, in most
960 * cases the following three methods have to be called on the resulting
963 * <li>recalculateNumberOfExternalDescendants(boolean) <li>recalculateAndReset()
966 * (Last modified: 10/01/01)
969 * PhylogenyNode of this Phylogeny\
971 public void reRoot( final PhylogenyNode n ) {
975 public void reRoot( final PhylogenyNode n, final double distance_n_to_parent ) {
976 if ( isEmpty() || ( getNumberOfExternalNodes() < 2 ) ) {
983 else if ( n.getParent().isRoot() ) {
984 if ( ( n.getParent().getNumberOfDescendants() == 2 ) && ( distance_n_to_parent >= 0 ) ) {
985 final double d = n.getParent().getChildNode1().getDistanceToParent()
986 + n.getParent().getChildNode2().getDistanceToParent();
988 if ( n.getChildNodeIndex() == 0 ) {
989 other = n.getParent().getChildNode2();
992 other = n.getParent().getChildNode1();
994 n.setDistanceToParent( distance_n_to_parent );
995 final double dm = d - distance_n_to_parent;
997 other.setDistanceToParent( dm );
1000 other.setDistanceToParent( 0 );
1003 if ( n.getParent().getNumberOfDescendants() > 2 ) {
1004 final int index = n.getChildNodeIndex();
1005 final double dn = n.getDistanceToParent();
1006 final PhylogenyNode prev_root = getRoot();
1007 prev_root.getDescendants().remove( index );
1008 final PhylogenyNode new_root = new PhylogenyNode();
1009 new_root.setChildNode( 0, n );
1010 new_root.setChildNode( 1, prev_root );
1011 if ( n.getBranchDataDirectly() != null ) {
1012 prev_root.setBranchData( ( BranchData ) n.getBranchDataDirectly().copy() );
1014 setRoot( new_root );
1015 if ( distance_n_to_parent >= 0 ) {
1016 n.setDistanceToParent( distance_n_to_parent );
1017 final double d = dn - distance_n_to_parent;
1019 prev_root.setDistanceToParent( d );
1022 prev_root.setDistanceToParent( 0 );
1027 final double d = dn / 2.0;
1028 n.setDistanceToParent( d );
1029 prev_root.setDistanceToParent( d );
1035 PhylogenyNode a = n;
1036 PhylogenyNode b = null;
1037 PhylogenyNode c = null;
1038 final PhylogenyNode new_root = new PhylogenyNode();
1039 double distance1 = 0.0;
1040 double distance2 = 0.0;
1041 BranchData branch_data_1 = null;
1042 BranchData branch_data_2 = null;
1045 new_root.setChildNode( 0, a );
1046 new_root.setChildNode( 1, b );
1047 distance1 = c.getDistanceToParent();
1048 if ( c.getBranchDataDirectly() != null ) {
1049 branch_data_1 = ( BranchData ) c.getBranchDataDirectly().copy();
1051 c.setDistanceToParent( b.getDistanceToParent() );
1052 if ( b.getBranchDataDirectly() != null ) {
1053 c.setBranchData( ( BranchData ) b.getBranchDataDirectly().copy() );
1055 if ( a.getBranchDataDirectly() != null ) {
1056 b.setBranchData( ( BranchData ) a.getBranchDataDirectly().copy() );
1058 // New root is always placed in the middle of the branch:
1059 if ( a.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
1060 b.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
1063 if ( distance_n_to_parent >= 0.0 ) {
1064 final double diff = a.getDistanceToParent() - distance_n_to_parent;
1065 a.setDistanceToParent( distance_n_to_parent );
1066 b.setDistanceToParent( diff >= 0.0 ? diff : 0.0 );
1069 final double d = a.getDistanceToParent() / 2.0;
1070 a.setDistanceToParent( d );
1071 b.setDistanceToParent( d );
1074 b.setChildNodeOnly( a.getChildNodeIndex( b ), c );
1075 // moving to the old root, swapping references:
1076 while ( !c.isRoot() ) {
1080 b.setChildNodeOnly( a.getChildNodeIndex( b ), c );
1082 distance2 = c.getDistanceToParent();
1083 branch_data_2 = c.getBranchDataDirectly();
1084 c.setDistanceToParent( distance1 );
1085 c.setBranchData( branch_data_1 );
1086 distance1 = distance2;
1087 branch_data_1 = branch_data_2;
1089 // removing the old root:
1090 if ( c.getNumberOfDescendants() == 2 ) {
1091 final PhylogenyNode node = c.getChildNode( 1 - b.getChildNodeIndex( c ) );
1092 node.setParent( b );
1093 if ( ( c.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT )
1094 && ( node.getDistanceToParent() == PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
1095 node.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
1098 node.setDistanceToParent( ( c.getDistanceToParent() >= 0.0 ? c.getDistanceToParent() : 0.0 )
1099 + ( node.getDistanceToParent() >= 0.0 ? node.getDistanceToParent() : 0.0 ) );
1101 if ( c.getBranchDataDirectly() != null ) {
1102 node.setBranchData( ( BranchData ) c.getBranchDataDirectly().copy() );
1104 for( int i = 0; i < b.getNumberOfDescendants(); ++i ) {
1105 if ( b.getChildNode( i ) == c ) {
1106 b.setChildNodeOnly( i, node );
1113 c.removeChildNode( b.getChildNodeIndex( c ) );
1115 setRoot( new_root );
1120 * Sets all Nodes of this Phylogeny to not-collapsed.
1122 * In most cases methods adjustNodeCount(false) and recalculateAndReset()
1123 * need to be called after this method has been called.
1125 public void setAllNodesToNotCollapse() {
1129 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1130 final PhylogenyNode node = iter.next();
1131 node.setCollapse( false );
1135 private void setAllowMultipleParents( final boolean allow_multiple_parents ) {
1136 _allow_multiple_parents = allow_multiple_parents;
1139 public void setConfidence( final Confidence confidence ) {
1140 _confidence = confidence;
1143 public void setDescription( final String description ) {
1144 _description = description;
1147 public void setDistanceUnit( final String _distance_unit ) {
1148 this._distance_unit = _distance_unit;
1151 public void setIdentifier( final Identifier identifier ) {
1152 _identifier = identifier;
1155 private void setIdToNodeMap( final HashMap<Integer, PhylogenyNode> idhash ) {
1156 _id_to_node_map = idhash;
1160 * Sets the indicators of all Nodes of this Phylogeny to 0.
1162 public void setIndicatorsToZero() {
1166 for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
1167 iter.next().setIndicator( ( byte ) 0 );
1169 } // setIndicatorsToZero()
1172 * Sets the name of this Phylogeny to s.
1174 public void setName( final String s ) {
1178 public void setRelevantSequenceRelationTypes( final Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> types ) {
1179 _relevant_sequence_relation_types = types;
1182 public void setRerootable( final boolean rerootable ) {
1183 _rerootable = rerootable;
1186 public void setRoot( final PhylogenyNode n ) {
1188 } // setRoot( PhylogenyNode )
1191 * Sets whether this Phylogeny is rooted or not.
1193 public void setRooted( final boolean b ) {
1195 } // setRooted( boolean )
1197 public void setSequenceRelationQueries( final Collection<Sequence> sequencesByName ) {
1198 _sequenceRelationQueries = sequencesByName;
1201 public void setType( final String type ) {
1205 public String toNewHampshire() {
1206 return toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1209 public String toNewHampshire( final boolean simple_nh,
1210 final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
1212 return new PhylogenyWriter().toNewHampshire( this, simple_nh, true, nh_conversion_support_style )
1215 catch ( final IOException e ) {
1216 throw new Error( "this should not have happend: " + e.getMessage() );
1220 public String toNewHampshireX() {
1222 return new PhylogenyWriter().toNewHampshireX( this ).toString();
1224 catch ( final IOException e ) {
1225 throw new Error( "this should not have happend: " + e.getMessage() );
1229 public String toNexus( final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) {
1231 return new PhylogenyWriter().toNexus( this, svs ).toString();
1233 catch ( final IOException e ) {
1234 throw new Error( "this should not have happend: " + e.getMessage() );
1238 public String toNexus() {
1239 return toNexus( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
1242 public String toPhyloXML( final int phyloxml_level ) {
1244 return new PhylogenyWriter().toPhyloXML( this, phyloxml_level ).toString();
1246 catch ( final IOException e ) {
1247 throw new Error( "this should not have happend: " + e.getMessage() );
1251 // ---------------------------------------------------------
1252 // Writing of Phylogeny to Strings
1253 // ---------------------------------------------------------
1255 * Converts this Phylogeny to a New Hampshire X (String) representation.
1257 * @return New Hampshire X (String) representation of this
1258 * @see #toNewHampshireX()
1261 public String toString() {
1262 return toNewHampshireX();
1266 * Removes the root PhylogenyNode this Phylogeny.
1268 public void unRoot() throws RuntimeException {
1270 throw new FailedConditionCheckException( "Attempt to unroot a phylogeny which is not tree-like." );
1275 setIndicatorsToZero();
1276 if ( !isRooted() || ( getNumberOfExternalNodes() <= 1 ) ) {