X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyNode.java;h=25b33d79650d9cb4db8d1dae9e5914ebbb53b47d;hb=c0439ed8b088887ffea2faf11bc7897333287cb3;hp=9663845ed75fef427b398ad19fdddc28b640c614;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java index 9663845..25b33d7 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java @@ -42,52 +42,76 @@ import org.forester.phylogeny.iterators.PreorderTreeIterator; import org.forester.util.ForesterUtil; /** - * Warning. Implementation of method 'compareTo' only looks at + * Warning. Implementation of method 'compareTo' only looks at * node name. Thus, use of this class in SortedSets might lead * to unexpected behavior. * */ public final class PhylogenyNode implements Comparable { - public enum NH_CONVERSION_SUPPORT_VALUE_STYLE { - NONE, IN_SQUARE_BRACKETS, AS_INTERNAL_NODE_NAMES; - } - private static int _node_count = 0; - private byte _indicator; - private int _id; - private int _sum_ext_nodes; - private float _x; - private float _y; - private double _distance_parent = PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT; + private static long NODE_COUNT = 0; + private BranchData _branch_data; private boolean _collapse; - private PhylogenyNode _parent; - private PhylogenyNode _link; private ArrayList _descendants; + private double _distance_parent = PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT; + private long _id; + private byte _indicator; + private PhylogenyNode _link; private NodeData _node_data; - private BranchData _branch_data; + private PhylogenyNode _parent; + private int _sum_ext_nodes; + private float _x; private float _x_secondary; + private float _y; private float _y_secondary; /** * Default constructor for PhylogenyNode. */ public PhylogenyNode() { - // init(); setId( PhylogenyNode.getNodeCount() ); PhylogenyNode.increaseNodeCount(); setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!) } - public void removeConnections() { - _parent = null; - _link = null; - _descendants = null; + public PhylogenyNode( final String node_name ) { + setId( PhylogenyNode.getNodeCount() ); + PhylogenyNode.increaseNodeCount(); + setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!) + if ( node_name != null ) { + getNodeData().setNodeName( node_name ); + } + } + + private PhylogenyNode( final String nhx, + final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, + final boolean replace_underscores ) throws NHXFormatException, PhyloXmlDataFormatException { + NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores, false, false, false ); + setId( PhylogenyNode.getNodeCount() ); + PhylogenyNode.increaseNodeCount(); + setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!). + } + + private PhylogenyNode( final String nhx, + final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, + final boolean replace_underscores, + final boolean parse_extended_tags ) throws NHXFormatException, PhyloXmlDataFormatException { + NHXParser.parseNHX( nhx, + this, + taxonomy_extraction, + replace_underscores, + false, + false, + parse_extended_tags ); + setId( PhylogenyNode.getNodeCount() ); + PhylogenyNode.increaseNodeCount(); + setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!). } /** * Adds PhylogenyNode n to the list of child nodes and sets the _parent of n * to this. - * + * * @param n * the PhylogenyNode to add */ @@ -97,16 +121,26 @@ public final class PhylogenyNode implements Comparable { n.setParent( this ); } - /** - * Adds PhylogenyNode n to the list of child nodes. But does NOT set the - * _parent of n to this. - * - * @see addAsChild( PhylogenyNode n ) - * @param n - * the PhylogenyNode to add - */ - final private void addChildNode( final PhylogenyNode child ) { - getDescendants().add( child ); + public final int calculateDepth() { + PhylogenyNode n = this; + int steps = 0; + while ( n._parent != null ) { + steps++; + n = n._parent; + } + return steps; + } + + public final double calculateDistanceToRoot() { + PhylogenyNode n = this; + double d = 0.0; + while ( n._parent != null ) { + if ( n._distance_parent > 0.0 ) { + d += n._distance_parent; + } + n = n._parent; + } + return d; } @Override @@ -119,15 +153,12 @@ public final class PhylogenyNode implements Comparable { return getName().compareTo( n.getName() ); } - // --------------------------------------------------------- - // Copy and delete Nodes, copy subtress - // --------------------------------------------------------- /** * Returns a new PhylogenyNode which has its data copied from this * PhylogenyNode. Links to the other Nodes in the same Phylogeny are NOT * copied (e.g. _link to _parent). Field "_link" IS copied. - * - * @see #getLink() + * + * @see #getLink() */ final public PhylogenyNode copyNodeData() { final PhylogenyNode node = new PhylogenyNode(); @@ -153,8 +184,8 @@ public final class PhylogenyNode implements Comparable { * Returns a new PhylogenyNode which has the same data as this * PhylogenyNode. Links to the other Nodes in the same Phylogeny are NOT * copied (e.g. _link to _parent). Field "_link" IS copied. - * - * @see #getLink() + * + * @see #getLink() */ final public PhylogenyNode copyNodeDataShallow() { final PhylogenyNode node = new PhylogenyNode(); @@ -175,8 +206,8 @@ public final class PhylogenyNode implements Comparable { @Override /** * Based on node name, sequence, and taxonomy. - * - * + * + * */ final public boolean equals( final Object o ) { if ( this == o ) { @@ -217,13 +248,11 @@ public final class PhylogenyNode implements Comparable { } } - // --------------------------------------------------------- - // Obtaining of Nodes - // --------------------------------------------------------- + /** * Returns a List containing references to all external children of this * PhylogenyNode. - * + * * @return List of references to external Nodes */ final public List getAllExternalDescendants() { @@ -251,7 +280,7 @@ public final class PhylogenyNode implements Comparable { /** * Returns a List containing references to all names of the external * children of this PhylogenyNode. - * + * * @return List of references to names of external Nodes */ final public List getAllExternalDescendantsNames() { @@ -270,13 +299,9 @@ public final class PhylogenyNode implements Comparable { return _branch_data; } - final BranchData getBranchDataDirectly() { - return _branch_data; - } - /** * This return child node n of this node. - * + * * @param n * the index of the child to get * @return the child node with index n @@ -315,7 +340,7 @@ public final class PhylogenyNode implements Comparable { /** * This gets the child node index of this node. *

- * + * * @return the child node index of this node * @throws UnsupportedOperationException * if this node is a root node @@ -329,7 +354,7 @@ public final class PhylogenyNode implements Comparable { * parent *

* [last modified Aug 14, 2006 by CMZ] - * + * * @return the child node index of this node * @throws UnsupportedOperationException * if this node is a root node @@ -365,7 +390,7 @@ public final class PhylogenyNode implements Comparable { * Convenience method. Returns the first child node of this node. *

* [last modified May 18, 2005 by CMZ] - * + * * @return the first child node of this node */ public final PhylogenyNode getFirstChildNode() { @@ -373,6 +398,13 @@ public final class PhylogenyNode implements Comparable { } /** + * Returns the ID (int) of this PhylogenyNode. + */ + final public long getId() { + return _id; + } + + /** * Returns the _indicator value of this PhylogenyNode. */ public final byte getIndicator() { @@ -383,7 +415,7 @@ public final class PhylogenyNode implements Comparable { * Convenience method. Returns the last child node of this node. *

* [last modified May 18, 2005 by CMZ] - * + * * @return the last child node of this node */ public final PhylogenyNode getLastChildNode() { @@ -399,6 +431,10 @@ public final class PhylogenyNode implements Comparable { return _link; } + final public String getName() { + return getNodeData().getNodeName(); + } + /** * Returns a refernce to the next external PhylogenyNode of this * PhylogenyNode. TODO should be in Phylogeny. Returns null if no next @@ -429,12 +465,12 @@ public final class PhylogenyNode implements Comparable { public final PhylogenyNode getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() { //TODO work on me ~~ - if ( isInternal() && !isCollapse() ) { - throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" ); - } if ( isRoot() ) { return null; } + if ( isInternal() && !isCollapse() ) { + throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" ); + } if ( getParent().isCollapse() ) { throw new UnsupportedOperationException( "attempt to get next external node of node with a collapsed parent" ); } @@ -476,27 +512,9 @@ public final class PhylogenyNode implements Comparable { } return _node_data; } - - final NodeData getNodeDataDirectly() { - return _node_data; - } - - // --------------------------------------------------------- - // Set and get methods for Nodes - // --------------------------------------------------------- - /** - * Returns the ID (int) of this PhylogenyNode. - */ - final public int getId() { - return _id; - } - - final public String getName() { - return getNodeData().getNodeName(); - } - - final public List getAllDescendants() { - return _descendants; + + public final boolean isHasNodeData() { + return ( !( _node_data == null || _node_data.isEmpty() ) ); } final public int getNumberOfDescendants() { @@ -594,35 +612,12 @@ public final class PhylogenyNode implements Comparable { return result; } - // final private void init() { - //_descendants = new ArrayList(); - // _parent = null; //TODO not needed? - // _id = 0; //TODO not needed? - //initializeData(); //TODO not needed? - //} - /** - * Deletes data of this PhylogenyNode. Links to the other Nodes in the - * Phylogeny, the ID and the sum of external nodes are NOT deleted. Field - * "_link" (_link to Nodes in other Phylogeny) IS deleted. - * - * @see #getLink() (Last modified: 12/20/03) - */ - // final private void initializeData() { - // _indicator = 0; - // _x = 0; - // _y = 0; - // //_node_name = ""; - // _distance_parent = PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT; - // _collapse = false; - // _link = null; - // _branch_data = null; - // _node_data = null; - // } /** * Returns whether this PhylogenyNode should be drawn as collapsed. + * Root can not be collapsed. */ final public boolean isCollapse() { - return _collapse; + return _collapse && _parent != null; } /** @@ -633,23 +628,19 @@ public final class PhylogenyNode implements Comparable { return getNodeData().isHasEvent() && getNodeData().getEvent().isDuplication(); } + public boolean isEmpty() { + return ( ( _node_data == null ) || _node_data.isEmpty() ); + } + /** * Checks whether this PhylogenyNode is external (tip). - * + * * @return true if this PhylogenyNode is external, false otherwise */ final public boolean isExternal() { - if ( _descendants == null ) { - return true; - } - return ( getNumberOfDescendants() < 1 ); + return ( _descendants == null ) || ( _descendants.size() == 0 ); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ final public boolean isFirstChildNode() { if ( isRoot() /* and tree is rooted TODO */) { throw new UnsupportedOperationException( "Cannot determine whether the root is the first child node of its _parent." ); @@ -657,11 +648,6 @@ public final class PhylogenyNode implements Comparable { return ( getChildNodeIndex() == 0 ); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ final public boolean isFirstExternalNode() { if ( isInternal() ) { return false; @@ -692,7 +678,7 @@ public final class PhylogenyNode implements Comparable { /** * Checks whether this PhylogenyNode is internal (tip). - * + * * @return true if this PhylogenyNode is external, false otherwise */ final public boolean isInternal() { @@ -703,7 +689,7 @@ public final class PhylogenyNode implements Comparable { * Returns true if this node is the last child node of its _parent. *

* [last modified June 01, 2005 by CMZ] - * + * * @return true if this node is the last child node of its _parent, false * otherwise */ @@ -714,11 +700,6 @@ public final class PhylogenyNode implements Comparable { return ( getChildNodeIndex() == ( getParent().getNumberOfDescendants() - 1 ) ); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ final public boolean isLastExternalNode() { if ( isInternal() ) { return false; @@ -733,31 +714,9 @@ public final class PhylogenyNode implements Comparable { return true; } - public final int calculateDepth() { - PhylogenyNode n = this; - int steps = 0; - while ( n._parent != null ) { - steps++; - n = n._parent; - } - return steps; - } - - public final double calculateDistanceToRoot() { - PhylogenyNode n = this; - double d = 0.0; - while ( n._parent != null ) { - if ( n._distance_parent > 0.0 ) { - d += n._distance_parent; - } - n = n._parent; - } - return d; - } - /** * Checks whether this PhylogenyNode is a root. - * + * * @return true if this PhylogenyNode is the root, false otherwise */ final public boolean isRoot() { @@ -799,6 +758,12 @@ public final class PhylogenyNode implements Comparable { removeChildNode( remove_me.getChildNodeIndex() ); } + public void removeConnections() { + _parent = null; + _link = null; + _descendants = null; + } + final public void setBranchData( final BranchData branch_data ) { _branch_data = branch_data; } @@ -818,14 +783,14 @@ public final class PhylogenyNode implements Comparable { } /** - * Inserts PhylogenyNode n at the specified position i into the list of + * Inserts PhylogenyNode node at the specified position i into the list of * child nodes. This does not allow null slots in the list of child nodes: - * If i is larger than the number of child nodes, n is just added to the - * list, not place at index i. - * + * If i is larger than the number of child nodes, node is just added to the + * list, not placed at index i. + * * @param i * the index of position where to add the child - * @param n + * @param node * the PhylogenyNode to add */ final public void setChildNode( final int i, final PhylogenyNode node ) { @@ -838,15 +803,6 @@ public final class PhylogenyNode implements Comparable { } } - final void setChildNodeOnly( final int i, final PhylogenyNode node ) { - if ( getNumberOfDescendants() <= i ) { - addChildNode( node ); - } - else { - getDescendants().set( i, node ); - } - } - /** * Sets whether this PhylogenyNode should be drawn as collapsed. */ @@ -869,19 +825,6 @@ public final class PhylogenyNode implements Comparable { _indicator = i; } - // -------------------------------------------------------------------- - // Adjust methods (related to Phylogeny construction and - // Phylogeny modification) - // -------------------------------------------------------------------- - /** - * Sets the indicators of all the children of this PhylogenyNode to zero. - */ - final void setIndicatorsToZero() { - for( final PreorderTreeIterator it = new PreorderTreeIterator( this ); it.hasNext(); ) { - it.next().setIndicator( ( byte ) 0 ); - } - } - /** * Sets the linked PhylogenyNode of this PhylogenyNode to n. Currently, this * method is only used for the speciation-_duplication assignment @@ -899,18 +842,6 @@ public final class PhylogenyNode implements Comparable { } /** - * Sets the Id of this PhylogenyNode to i. In most cases, this number - * should not be set to values lower than getNodeCount() -- which this method - * does not allow. - */ - synchronized final protected void setId( final int i ) { - if ( i < getNodeCount() ) { - throw new IllegalArgumentException( "attempt to set node id to a value less than total node count (thus violating the uniqueness of node ids)" ); - } - _id = i; - } - - /** * Sets the _parent PhylogenyNode of this PhylogenyNode to n. */ final public void setParent( final PhylogenyNode n ) { @@ -951,20 +882,35 @@ public final class PhylogenyNode implements Comparable { _y_secondary = y_secondary; } + /** + * Swaps the the two childern of a PhylogenyNode node of this Phylogeny. + */ + public final void swapChildren() throws RuntimeException { + if ( isExternal() ) { + throw new RuntimeException( "attempt to swap descendants of external node" ); + } + if ( getNumberOfDescendants() != 2 ) { + throw new RuntimeException( "attempt to swap descendants of node with " + getNumberOfDescendants() + + " descendants" ); + } + final PhylogenyNode a = getChildNode( 0 ); + final PhylogenyNode b = getChildNode( 1 ); + setChildNode( 0, b ); + setChildNode( 1, a ); + } + // --------------------------------------------------------- // Writing of Nodes to Strings // --------------------------------------------------------- - final public String toNewHampshire( final boolean simple_nh, - final boolean write_distance_to_parent, + final public String toNewHampshire( final boolean write_distance_to_parent, final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) { - final StringBuilder sb = new StringBuilder(); String data = ""; if ( ( svs == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES ) && !isExternal() ) { if ( getBranchData().isHasConfidences() && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) { data = Confidence.FORMATTER.format( ForesterUtil - .round( getBranchData().getConfidence( 0 ).getValue(), - PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ); + .round( getBranchData().getConfidence( 0 ).getValue(), + PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ); } } else if ( !ForesterUtil.isEmpty( getName() ) ) { @@ -980,29 +926,19 @@ public final class PhylogenyNode implements Comparable { else if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getCommonName() ) ) { data = getNodeData().getTaxonomy().getCommonName(); } - else if ( getNodeData().getTaxonomy().getTaxonomyCode() != null ) { - data = getNodeData().getTaxonomy().getTaxonomyCode(); - } } else if ( getNodeData().isHasSequence() ) { if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getName() ) ) { data = getNodeData().getSequence().getName(); } - } - if ( data.length() > 0 ) { - data = ForesterUtil.replaceIllegalNhCharacters( data ); - if ( simple_nh && ( data.length() > 10 ) ) { - data = data.substring( 0, 11 ); + else if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getSymbol() ) ) { + data = getNodeData().getSequence().getSymbol(); } - if ( ForesterUtil.isContainsParanthesesableNhCharacter( data ) ) { - sb.append( '\'' ); - sb.append( data ); - sb.append( '\'' ); - } - else { - sb.append( data ); + else if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getGeneName() ) ) { + data = getNodeData().getSequence().getGeneName(); } } + final StringBuilder sb = ForesterUtil.santitizeStringForNH( data ); if ( write_distance_to_parent && ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { sb.append( ":" ); sb.append( getDistanceToParent() ); @@ -1012,47 +948,22 @@ public final class PhylogenyNode implements Comparable { && ( getBranchData().getConfidence( 0 ).getValue() != Confidence.CONFIDENCE_DEFAULT_VALUE ) ) { sb.append( "[" ); sb.append( Confidence.FORMATTER.format( ForesterUtil - .round( getBranchData().getConfidence( 0 ).getValue(), - PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ) ); + .round( getBranchData().getConfidence( 0 ).getValue(), + PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ) ); sb.append( "]" ); } return sb.toString(); } /** - * Swaps the the two childern of a PhylogenyNode node of this Phylogeny. - */ - public final void swapChildren() throws RuntimeException { - if ( isExternal() ) { - throw new RuntimeException( "attempt to swap descendants of external node" ); - } - if ( getNumberOfDescendants() != 2 ) { - throw new RuntimeException( "attempt to swap descendants of node with " + getNumberOfDescendants() - + " descendants" ); - } - final PhylogenyNode a = getChildNode( 0 ); - final PhylogenyNode b = getChildNode( 1 ); - setChildNode( 0, b ); - setChildNode( 1, a ); - } - - /** * Converts this PhylogenyNode to a New Hampshire X (NHX) String * representation. */ final public String toNewHampshireX() { - final StringBuffer sb = new StringBuffer(); + final StringBuilder sb = new StringBuilder(); final StringBuffer s_nhx = new StringBuffer(); if ( !ForesterUtil.isEmpty( getName() ) ) { - final String name = ForesterUtil.replaceIllegalNhCharacters( getName() ); - if ( ForesterUtil.isContainsParanthesesableNhCharacter( name ) ) { - sb.append( '\'' ); - sb.append( name ); - sb.append( '\'' ); - } - else { - sb.append( name ); - } + sb.append( ForesterUtil.santitizeStringForNH( getName() ) ); } if ( getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { sb.append( ":" ); @@ -1075,6 +986,10 @@ public final class PhylogenyNode implements Comparable { @Override final public String toString() { final StringBuilder sb = new StringBuilder(); + if ( !ForesterUtil.isEmpty( getName() ) ) { + sb.append( getName() ); + sb.append( " " ); + } if ( getNodeData().isHasTaxonomy() ) { if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getScientificName() ) ) { sb.append( getNodeData().getTaxonomy().getScientificName() ); @@ -1098,15 +1013,15 @@ public final class PhylogenyNode implements Comparable { sb.append( getNodeData().getSequence().getSymbol() ); sb.append( " " ); } + if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getGeneName() ) ) { + sb.append( getNodeData().getSequence().getGeneName() ); + sb.append( " " ); + } if ( getNodeData().getSequence().getAccession() != null ) { sb.append( getNodeData().getSequence().getAccession().toString() ); sb.append( " " ); } } - if ( ( sb.length() <= 1 ) && !ForesterUtil.isEmpty( getName() ) ) { - sb.append( getName() ); - sb.append( " " ); - } if ( sb.length() <= 1 ) { sb.append( "[" ); sb.append( getId() ); @@ -1116,60 +1031,112 @@ public final class PhylogenyNode implements Comparable { } /** - * Decreases the total number of all Nodes created so far by one. + * Sets the Id of this PhylogenyNode to i. In most cases, this number + * should not be set to values lower than getNodeCount() -- which this method + * does not allow. */ - final static synchronized void decreaseNodeCount() { - --PhylogenyNode._node_count; + synchronized final protected void setId( final long i ) { + if ( i < getNodeCount() ) { + throw new IllegalArgumentException( "attempt to set node id to a value less than total node count (thus violating the uniqueness of node ids)" ); + } + _id = i; } - /** - * Returns the total number of all Nodes created so far. - * - * @return total number of Nodes (int) - */ - synchronized final public static int getNodeCount() { - return PhylogenyNode._node_count; + final BranchData getBranchDataDirectly() { + return _branch_data; + } + + final NodeData getNodeDataDirectly() { + return _node_data; + } + + final void setChildNodeOnly( final int i, final PhylogenyNode node ) { + if ( getNumberOfDescendants() <= i ) { + addChildNode( node ); + } + else { + getDescendants().set( i, node ); + } } /** - * Increases the total number of all Nodes created so far by one. + * Sets the indicators of all the children of this PhylogenyNode to zero. */ - synchronized final private static void increaseNodeCount() { - ++PhylogenyNode._node_count; + final void setIndicatorsToZero() { + for( final PreorderTreeIterator it = new PreorderTreeIterator( this ); it.hasNext(); ) { + it.next().setIndicator( ( byte ) 0 ); + } } /** - * Sets the total number of all Nodes created so far to i (int). + * Adds PhylogenyNode n to the list of child nodes. But does NOT set the + * _parent of n to this. + * + * @see addAsChild( PhylogenyNode n ) + * @param n + * the PhylogenyNode to add */ - synchronized final static void setNodeCount( final int i ) { - PhylogenyNode._node_count = i; + final private void addChildNode( final PhylogenyNode child ) { + getDescendants().add( child ); } public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException, - PhyloXmlDataFormatException { + PhyloXmlDataFormatException { return new PhylogenyNode( nhx, NHXParser.TAXONOMY_EXTRACTION.NO, false ); } public static PhylogenyNode createInstanceFromNhxString( final String nhx, final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction ) - throws NHXFormatException, PhyloXmlDataFormatException { + throws NHXFormatException, PhyloXmlDataFormatException { return new PhylogenyNode( nhx, taxonomy_extraction, false ); } public static PhylogenyNode createInstanceFromNhxString( final String nhx, final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, final boolean replace_underscores ) - throws NHXFormatException, PhyloXmlDataFormatException { + throws NHXFormatException, PhyloXmlDataFormatException { return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores ); } + + public static PhylogenyNode createInstanceFromNhxString( final String nhx, + final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, + final boolean replace_underscores, + final boolean parse_extended_tags ) + throws NHXFormatException, PhyloXmlDataFormatException { + return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores, parse_extended_tags ); + } - private PhylogenyNode( final String nhx, - final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, - final boolean replace_underscores ) throws NHXFormatException, PhyloXmlDataFormatException { - // init(); - NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores ); - setId( PhylogenyNode.getNodeCount() ); - PhylogenyNode.increaseNodeCount(); - setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!) + /** + * Returns the total number of all Nodes created so far. + * + * @return total number of Nodes (long) + */ + synchronized final public static long getNodeCount() { + return NODE_COUNT; + } + + /** + * Decreases the total number of all Nodes created so far by one. + */ + final static synchronized void decreaseNodeCount() { + --NODE_COUNT; + } + + /** + * Sets the total number of all Nodes created so far to i. + */ + synchronized final static void setNodeCount( final long i ) { + PhylogenyNode.NODE_COUNT = i; + } + + /** + * Increases the total number of all Nodes created so far by one. + */ + synchronized final private static void increaseNodeCount() { + ++NODE_COUNT; + } + + public enum NH_CONVERSION_SUPPORT_VALUE_STYLE { + AS_INTERNAL_NODE_NAMES, IN_SQUARE_BRACKETS, NONE; } }