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=8dedcd20a9989d54049799d8a266d78fa12a6725;hpb=e37b8c622b4d0a46d3dd170e3cd130bca39ee468;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 8dedcd2..23eeec1 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;
 
@@ -32,50 +32,64 @@ import java.util.List;
 
 import org.forester.io.parsers.nhx.NHXFormatException;
 import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.phylogeny.data.BranchData;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.NodeData;
 import org.forester.phylogeny.data.PhylogenyDataUtil;
-import org.forester.phylogeny.iterators.ChildNodeIteratorForward;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.ForesterUtil;
 
-public final class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode> {
+/**
+ * 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<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 reset() {
-        _parent = null;
-        _link = null;
-        _descendants = null;
-        _node_data = null;
-        _branch_data = 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 );
+        setId( PhylogenyNode.getNodeCount() );
+        PhylogenyNode.increaseNodeCount();
+        setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!).
     }
 
     /**
@@ -85,26 +99,36 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * @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
+    // this is poor, as it only compares on names!
     final public int compareTo( final PhylogenyNode o ) {
         final PhylogenyNode n = o;
         if ( ( getName() == null ) || ( n.getName() == null ) ) {
@@ -113,9 +137,6 @@ 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
@@ -195,12 +216,12 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
                 return ( this_data.getTaxonomy().isEqual( other_data.getTaxonomy() ) && this_data.getSequence()
                         .isEqual( other_data.getSequence() ) );
             }
-            else if ( this_data.isHasSequence() && other_data.isHasSequence() ) {
-                return ( this_data.getSequence().isEqual( other_data.getSequence() ) );
-            }
             else if ( this_data.isHasTaxonomy() && other_data.isHasTaxonomy() ) {
                 return ( this_data.getTaxonomy().isEqual( other_data.getTaxonomy() ) );
             }
+            else if ( this_data.isHasSequence() && other_data.isHasSequence() ) {
+                return ( this_data.getSequence().isEqual( other_data.getSequence() ) );
+            }
             else if ( getName().length() > 0 ) {
                 // Node name is not empty, and equal.
                 return true;
@@ -211,9 +232,10 @@ 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.
@@ -264,10 +286,6 @@ 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.
      * 
@@ -277,7 +295,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
      * @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." );
@@ -352,7 +369,6 @@ 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;
     }
@@ -369,6 +385,13 @@ 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() {
@@ -395,6 +418,10 @@ 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
@@ -457,7 +484,7 @@ 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() ) {
@@ -473,29 +500,6 @@ 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 int getNumberOfDescendants() {
         if ( _descendants == null ) {
             return 0;
@@ -591,30 +595,6 @@ 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.
      */
@@ -630,6 +610,10 @@ 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).
      * 
@@ -642,11 +626,6 @@ 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." );
@@ -654,11 +633,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         return ( getChildNodeIndex() == 0 );
     }
 
-    /**
-     * DOCUMENT ME!
-     * 
-     * @return DOCUMENT ME!
-     */
     final public boolean isFirstExternalNode() {
         if ( isInternal() ) {
             return false;
@@ -711,11 +685,6 @@ 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;
@@ -744,13 +713,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     // ---------------------------------------------------------
-    // Iterator
-    // ---------------------------------------------------------
-    final public PhylogenyNodeIterator iterateChildNodesForward() {
-        return new ChildNodeIteratorForward( this );
-    }
-
-    // ---------------------------------------------------------
     // Basic printing
     // ---------------------------------------------------------
     /**
@@ -781,6 +743,12 @@ 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;
     }
@@ -820,15 +788,6 @@ 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.
      */
@@ -840,7 +799,6 @@ 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;
     }
@@ -852,19 +810,6 @@ 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
@@ -877,27 +822,13 @@ 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;
     }
@@ -936,13 +867,28 @@ 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()
@@ -965,29 +911,19 @@ 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 );
+            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() );
@@ -1005,39 +941,14 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     /**
-     * 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( ":" );
@@ -1059,17 +970,13 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
 
     @Override
     final public String toString() {
-        StringBuilder sb = new StringBuilder();
-        if ( ForesterUtil.isEmpty( getName() ) ) {
-            sb.append( getName() );
-            sb.append( " " );
-        }
+        final StringBuilder sb = new StringBuilder();
         if ( getNodeData().isHasTaxonomy() ) {
             if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getScientificName() ) ) {
                 sb.append( getNodeData().getTaxonomy().getScientificName() );
                 sb.append( " " );
             }
-            else if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+            else if ( ( sb.length() <= 1 ) && !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
                 sb.append( getNodeData().getTaxonomy().getTaxonomyCode() );
                 sb.append( " " );
             }
@@ -1083,15 +990,23 @@ 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 ( ( sb.length() <= 1 ) && !ForesterUtil.isEmpty( getName() ) ) {
+            sb.append( getName() );
+            sb.append( " " );
+        }
         if ( sb.length() <= 1 ) {
             sb.append( "[" );
             sb.append( getId() );
@@ -1101,59 +1016,104 @@ 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 {
-        return new PhylogenyNode( nhx, PhylogenyMethods.TAXONOMY_EXTRACTION.NO, false );
+    public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException,
+            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 {
+                                                             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 {
+            throws NHXFormatException, PhyloXmlDataFormatException {
         return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores );
     }
 
-    private PhylogenyNode( final String nhx,
-                           final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
-                           final boolean replace_underscores ) throws NHXFormatException {
-        //  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;
     }
 }