X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyNode.java;h=23eeec1731affab68de9132a038c52be8d6cc0b5;hb=c11ce93b4619a0bbfcad671407e4bc98ff6e7a41;hp=01416eb215ccb437f4bd1df9820ab28327ab9965;hpb=397137f4f105810096dc6034ccc1e1013ed11644;p=jalview.git diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java index 01416eb..23eeec1 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java @@ -49,23 +49,20 @@ import org.forester.util.ForesterUtil; */ public final class PhylogenyNode implements Comparable { - public enum NH_CONVERSION_SUPPORT_VALUE_STYLE { - NONE, IN_SQUARE_BRACKETS, AS_INTERNAL_NODE_NAMES; - } private static long NODE_COUNT = 0; - private byte _indicator; - private long _id; - private int _sum_ext_nodes; - private float _x; - private float _y; - private double _distance_parent = PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT; + 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; /** @@ -77,13 +74,22 @@ public final class PhylogenyNode implements Comparable { 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 ); + } } - public boolean isEmpty() { + 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 ); + setId( PhylogenyNode.getNodeCount() ); + PhylogenyNode.increaseNodeCount(); + setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!). } /** @@ -99,16 +105,26 @@ 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 @@ -121,9 +137,6 @@ 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 @@ -219,9 +232,10 @@ public final class PhylogenyNode implements Comparable { } } - // --------------------------------------------------------- - // Obtaining of Nodes - // --------------------------------------------------------- + final public List getAllDescendants() { + return _descendants; + } + /** * Returns a List containing references to all external children of this * PhylogenyNode. @@ -272,10 +286,6 @@ public final class PhylogenyNode implements Comparable { return _branch_data; } - final BranchData getBranchDataDirectly() { - return _branch_data; - } - /** * This return child node n of this node. * @@ -375,6 +385,13 @@ 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() { @@ -401,6 +418,10 @@ 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 @@ -479,28 +500,6 @@ 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 long getId() { - return _id; - } - - final public String getName() { - return getNodeData().getNodeName(); - } - - final public List getAllDescendants() { - return _descendants; - } - final public int getNumberOfDescendants() { if ( _descendants == null ) { return 0; @@ -596,30 +595,6 @@ 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. */ @@ -635,6 +610,10 @@ 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). * @@ -647,11 +626,6 @@ public final class PhylogenyNode implements Comparable { return ( getNumberOfDescendants() < 1 ); } - /** - * 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." ); @@ -659,11 +633,6 @@ public final class PhylogenyNode implements Comparable { return ( getChildNodeIndex() == 0 ); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ final public boolean isFirstExternalNode() { if ( isInternal() ) { return false; @@ -716,11 +685,6 @@ public final class PhylogenyNode implements Comparable { return ( getChildNodeIndex() == ( getParent().getNumberOfDescendants() - 1 ) ); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ final public boolean isLastExternalNode() { if ( isInternal() ) { return false; @@ -735,28 +699,6 @@ 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. * @@ -801,6 +743,12 @@ 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; } @@ -840,15 +788,6 @@ 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. */ @@ -871,19 +810,6 @@ 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 @@ -901,18 +827,6 @@ 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 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; - } - - /** * Sets the _parent PhylogenyNode of this PhylogenyNode to n. */ final public void setParent( final PhylogenyNode n ) { @@ -953,13 +867,28 @@ 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() @@ -982,29 +911,19 @@ 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 ); - } - if ( ForesterUtil.isContainsParanthesesableNhCharacter( data ) ) { - sb.append( '\'' ); - sb.append( data ); - sb.append( '\'' ); + else if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getSymbol() ) ) { + data = getNodeData().getSequence().getSymbol(); } - 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() ); @@ -1022,39 +941,14 @@ public final class PhylogenyNode implements Comparable { } /** - * 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( ":" ); @@ -1122,33 +1016,53 @@ 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() { - --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 (long) - */ - synchronized final public static long getNodeCount() { - return 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() { - ++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. + * 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 long i ) { - PhylogenyNode.NODE_COUNT = i; + final private void addChildNode( final PhylogenyNode child ) { + getDescendants().add( child ); } public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException, @@ -1169,12 +1083,37 @@ public final class PhylogenyNode implements Comparable { return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores ); } - 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 ); - 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; } }