X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyNode.java;h=819ba7a6b21a62aa805a22afed295f7b1f7da972;hb=5b11e68cf46c363bd5ae256f794871c194776bd7;hp=404553791082c7e32fbcd3d79bcfee330cc2400a;hpb=9794a064aff842558c2afd65c884127f33b2fd5e;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 4045537..819ba7a 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -32,18 +32,26 @@ 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> {
 
+    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;
@@ -70,6 +78,12 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         setSumExtNodes( 1 ); // For ext node, this number is 1 (not 0!!)
     }
 
+    public void removeConnections() {
+        _parent = null;
+        _link = null;
+        _descendants = null;
+    }
+
     /**
      * Adds PhylogenyNode n to the list of child nodes and sets the _parent of n
      * to this.
@@ -77,9 +91,8 @@ 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 );
     }
@@ -97,6 +110,7 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     @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 ) ) {
@@ -187,12 +201,12 @@ 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;
@@ -269,7 +283,6 @@ 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." );
@@ -344,7 +357,6 @@ 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;
     }
@@ -449,7 +461,7 @@ 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() ) {
@@ -475,19 +487,18 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     /**
      * 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;
@@ -722,6 +733,28 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         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.
      * 
@@ -736,13 +769,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     }
 
     // ---------------------------------------------------------
-    // Iterator
-    // ---------------------------------------------------------
-    final public PhylogenyNodeIterator iterateChildNodesForward() {
-        return new ChildNodeIteratorForward( this );
-    }
-
-    // ---------------------------------------------------------
     // Basic printing
     // ---------------------------------------------------------
     /**
@@ -832,7 +858,6 @@ 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;
     }
@@ -869,7 +894,6 @@ 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 );
     }
@@ -889,7 +913,6 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
     /**
      * Sets the _parent PhylogenyNode of this PhylogenyNode to n.
      */
-    @Override
     final public void setParent( final PhylogenyNode n ) {
         _parent = n;
     }
@@ -1051,17 +1074,13 @@ 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( " " );
             }
@@ -1075,15 +1094,19 @@ 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 ( 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() );
@@ -1122,26 +1145,27 @@ public final class PhylogenyNode implements PhylogenyNodeI, Comparable<Phylogeny
         PhylogenyNode._node_count = i;
     }
 
-    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 {
+                           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() );