X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyNode.java;h=d37cc3b849b584335b7770a04239f05906d3c92f;hb=803a2b32992b5944b73c6dfcb80ceb58c09b81c1;hp=32fec23463c35d7cb6a66c0dcc4a961881e6720b;hpb=39ad4632ee57d8ab720a7ad08c2ba4cccffa05bb;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 32fec23..d37cc3b 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -23,7 +23,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.phylogeny;
 
@@ -42,69 +42,105 @@ 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 PhylogenyNodeI, Comparable<PhylogenyNode> {
+public final class PhylogenyNode implements Comparable<PhylogenyNode> {
 
-    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<PhylogenyNode> _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
      */
-    @Override
-    final public void addAsChild( final PhylogenyNodeI node ) {
-        final PhylogenyNode n = ( PhylogenyNode ) node;
+    final public void addAsChild( final PhylogenyNode node ) {
+        final PhylogenyNode n = node;
         addChildNode( n );
         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
@@ -117,15 +153,12 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         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();
@@ -151,8 +184,8 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * 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();
@@ -173,8 +206,8 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     @Override
     /**
      * Based on node name, sequence, and taxonomy.
-     * 
-     * 
+     *
+     *
      */
     final public boolean equals( final Object o ) {
         if ( this == o ) {
@@ -215,13 +248,14 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         }
     }
 
-    // ---------------------------------------------------------
-    // Obtaining of Nodes
-    // ---------------------------------------------------------
+    final public List<PhylogenyNode> getAllDescendants() {
+        return _descendants;
+    }
+
     /**
      * Returns a List containing references to all external children of this
      * PhylogenyNode.
-     * 
+     *
      * @return List of references to external Nodes
      */
     final public List<PhylogenyNode> getAllExternalDescendants() {
@@ -249,7 +283,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     /**
      * 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<String> getAllExternalDescendantsNames() {
@@ -268,20 +302,15 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         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
      * @throws IllegalArgumentException
      *             if n is out of bounds
      */
-    @Override
     final public PhylogenyNode getChildNode( final int i ) {
         if ( isExternal() ) {
             throw new UnsupportedOperationException( "attempt to get the child node of an external node." );
@@ -314,7 +343,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     /**
      * This gets the child node index of this node.
      * <p>
-     * 
+     *
      * @return the child node index of this node
      * @throws UnsupportedOperationException
      *             if this node is a root node
@@ -328,7 +357,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * parent
      * <p>
      * [last modified Aug 14, 2006 by CMZ]
-     * 
+     *
      * @return the child node index of this node
      * @throws UnsupportedOperationException
      *             if this node is a root node
@@ -356,7 +385,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * Returns the length of the branch leading to the _parent of this
      * PhylogenyNode (double).
      */
-    @Override
     final public double getDistanceToParent() {
         return _distance_parent;
     }
@@ -365,7 +393,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * Convenience method. Returns the first child node of this node.
      * <p>
      * [last modified May 18, 2005 by CMZ]
-     * 
+     *
      * @return the first child node of this node
      */
     public final PhylogenyNode getFirstChildNode() {
@@ -373,6 +401,13 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     /**
+     * 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 +418,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * Convenience method. Returns the last child node of this node.
      * <p>
      * [last modified May 18, 2005 by CMZ]
-     * 
+     *
      * @return the last child node of this node
      */
     public final PhylogenyNode getLastChildNode() {
@@ -399,6 +434,10 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         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
@@ -461,7 +500,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
             previous_node = current_node;
             current_node = current_node.getParent();
         }
-        if ( index < current_node.getNumberOfDescendants() - 1 ) {
+        if ( index < ( current_node.getNumberOfDescendants() - 1 ) ) {
             current_node = current_node.getChildNode( index + 1 );
         }
         while ( current_node.isInternal() && !current_node.isCollapse() ) {
@@ -477,33 +516,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         return _node_data;
     }
 
-    final NodeData getNodeDataDirectly() {
-        return _node_data;
-    }
-
-    // ---------------------------------------------------------
-    // Set and get methods for Nodes
-    // ---------------------------------------------------------
-    /**
-     * Returns the ID (int) of this PhylogenyNode.
-     */
-    @Override
-    final public int getId() {
-        return _id;
-    }
-
-    /**
-     * Returns the name of this node.
-     */
-    @Override
-    final public String getName() {
-        return getNodeData().getNodeName();
-    }
-
-    final public List<PhylogenyNode> getAllDescendants() {
-        return _descendants;
-    }
-
     final public int getNumberOfDescendants() {
         if ( _descendants == null ) {
             return 0;
@@ -599,30 +611,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         return result;
     }
 
-    // final private void init() {
-    //_descendants = new ArrayList<PhylogenyNode>();
-    //  _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.
      */
@@ -638,9 +626,13 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         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() {
@@ -650,11 +642,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         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." );
@@ -662,11 +649,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         return ( getChildNodeIndex() == 0 );
     }
 
-    /**
-     * DOCUMENT ME!
-     * 
-     * @return DOCUMENT ME!
-     */
     final public boolean isFirstExternalNode() {
         if ( isInternal() ) {
             return false;
@@ -697,7 +679,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
 
     /**
      * Checks whether this PhylogenyNode is internal (tip).
-     * 
+     *
      * @return true if this PhylogenyNode is external, false otherwise
      */
     final public boolean isInternal() {
@@ -708,7 +690,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * Returns true if this node is the last child node of its _parent.
      * <p>
      * [last modified June 01, 2005 by CMZ]
-     * 
+     *
      * @return true if this node is the last child node of its _parent, false
      *         otherwise
      */
@@ -719,11 +701,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         return ( getChildNodeIndex() == ( getParent().getNumberOfDescendants() - 1 ) );
     }
 
-    /**
-     * DOCUMENT ME!
-     * 
-     * @return DOCUMENT ME!
-     */
     final public boolean isLastExternalNode() {
         if ( isInternal() ) {
             return false;
@@ -740,7 +717,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
 
     /**
      * Checks whether this PhylogenyNode is a root.
-     * 
+     *
      * @return true if this PhylogenyNode is the root, false otherwise
      */
     final public boolean isRoot() {
@@ -782,6 +759,12 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         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;
     }
@@ -805,7 +788,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * 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.
-     * 
+     *
      * @param i
      *            the index of position where to add the child
      * @param n
@@ -821,15 +804,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         }
     }
 
-    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.
      */
@@ -841,7 +815,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * Sets the length of the branch leading to the _parent of this
      * PhylogenyNode to double d.
      */
-    @Override
     final public void setDistanceToParent( final double d ) {
         _distance_parent = d;
     }
@@ -853,19 +826,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         _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
@@ -878,27 +838,13 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     /**
      * Sets the name of this node.
      */
-    @Override
     final public void setName( final String node_name ) {
         getNodeData().setNodeName( node_name );
     }
 
     /**
-     * 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.
      */
-    @Override
     final public void setParent( final PhylogenyNode n ) {
         _parent = n;
     }
@@ -937,20 +883,35 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         _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() ) ) {
@@ -966,29 +927,19 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
             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() );
@@ -998,47 +949,22 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
                 && ( 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( ":" );
@@ -1061,6 +987,10 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     @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() );
@@ -1080,18 +1010,22 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
                 sb.append( getNodeData().getSequence().getName() );
                 sb.append( " " );
             }
-            else if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getSymbol() ) ) {
+            if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getSymbol() ) ) {
                 sb.append( getNodeData().getSequence().getSymbol() );
                 sb.append( " " );
             }
-            else if ( getNodeData().getSequence().getAccession() != null ) {
-                sb.append( getNodeData().getTaxonomy().getIdentifier().toString() );
+            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 ( !ForesterUtil.isEmpty( getNodeData().getSequence().getMolecularSequence() ) ) {
+                sb.append( getNodeData().getSequence().getMolecularSequence() );
                 sb.append( " " );
             }
-        }
-        if ( ( sb.length() <= 1 ) && !ForesterUtil.isEmpty( getName() ) ) {
-            sb.append( getName() );
-            sb.append( " " );
         }
         if ( sb.length() <= 1 ) {
             sb.append( "[" );
@@ -1102,60 +1036,112 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     /**
-     * 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 {
-        return new PhylogenyNode( nhx, PhylogenyMethods.TAXONOMY_EXTRACTION.NO, false );
+    PhyloXmlDataFormatException {
+        return new PhylogenyNode( nhx, NHXParser.TAXONOMY_EXTRACTION.NO, false );
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx,
-                                                             final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction )
-            throws NHXFormatException, PhyloXmlDataFormatException {
+                                                             final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction )
+                                                                     throws NHXFormatException, PhyloXmlDataFormatException {
         return new PhylogenyNode( nhx, taxonomy_extraction, false );
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx,
-                                                             final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
+                                                             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 PhylogenyMethods.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;
     }
 }