subtree deletion changed

[jalview.git] / forester / java / src / org / forester / phylogeny / PhylogenyNode.java

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index c7a1caf..8dedcd2 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -42,15 +42,15 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.ForesterUtil;
 
-public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode> {
+public final class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode> {
 
-    private static int               _node_count = 0;
+    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;
+    private double                   _distance_parent = PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
     private boolean                  _collapse;
     private PhylogenyNode            _parent;
     private PhylogenyNode            _link;
@@ -64,12 +64,20 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
      * Default constructor for PhylogenyNode.
      */
     public PhylogenyNode() {
-        init();
+        //  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;
+    }
+
     /**
      * Adds PhylogenyNode n to the list of child nodes and sets the _parent of n
      * to this.
@@ -334,6 +342,9 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     }
 
     final public List<PhylogenyNode> getDescendants() {
+        if ( _descendants == null ) {
+            _descendants = new ArrayList<PhylogenyNode>();
+        }
         return _descendants;
     }
 
@@ -486,6 +497,9 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     }
 
     final public int getNumberOfDescendants() {
+        if ( _descendants == null ) {
+            return 0;
+        }
         return _descendants.size();
     }
 
@@ -577,13 +591,12 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
         return result;
     }
 
-    final private void init() {
-        _descendants = new ArrayList<PhylogenyNode>();
-        _parent = null;
-        _id = 0;
-        initializeData();
-    }
-
+    // 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
@@ -591,18 +604,17 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
      * 
      * @see #getLink() (Last modified: 12/20/03)
      */
-    final public 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;
-    }
-
+    //    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.
      */
@@ -624,6 +636,9 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
      * @return true if this PhylogenyNode is external, false otherwise
      */
     final public boolean isExternal() {
+        if ( _descendants == null ) {
+            return true;
+        }
         return ( getNumberOfDescendants() < 1 );
     }
 
@@ -992,7 +1007,7 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     /**
      * Swaps the the two childern of a PhylogenyNode node of this Phylogeny.
      */
-    public void swapChildren() throws RuntimeException {
+    public final void swapChildren() throws RuntimeException {
         if ( isExternal() ) {
             throw new RuntimeException( "attempt to swap descendants of external node" );
         }
@@ -1044,15 +1059,45 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
 
     @Override
     final public String toString() {
-        final StringBuilder sb = new StringBuilder();
-        if ( !ForesterUtil.isEmpty( getName() ) ) {
+        StringBuilder sb = new StringBuilder();
+        if ( ForesterUtil.isEmpty( getName() ) ) {
             sb.append( getName() );
             sb.append( " " );
         }
-        sb.append( "[" );
-        sb.append( getId() );
-        sb.append( "]" );
-        return sb.toString();
+        if ( getNodeData().isHasTaxonomy() ) {
+            if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getScientificName() ) ) {
+                sb.append( getNodeData().getTaxonomy().getScientificName() );
+                sb.append( " " );
+            }
+            else if ( !ForesterUtil.isEmpty( getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+                sb.append( getNodeData().getTaxonomy().getTaxonomyCode() );
+                sb.append( " " );
+            }
+            else if ( getNodeData().getTaxonomy().getIdentifier() != null ) {
+                sb.append( getNodeData().getTaxonomy().getIdentifier().toString() );
+                sb.append( " " );
+            }
+        }
+        if ( getNodeData().isHasSequence() ) {
+            if ( !ForesterUtil.isEmpty( getNodeData().getSequence().getName() ) ) {
+                sb.append( getNodeData().getSequence().getName() );
+                sb.append( " " );
+            }
+            else 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() );
+                sb.append( " " );
+            }
+        }
+        if ( sb.length() <= 1 ) {
+            sb.append( "[" );
+            sb.append( getId() );
+            sb.append( "]" );
+        }
+        return sb.toString().trim();
     }
 
     /**
@@ -1105,7 +1150,7 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     private PhylogenyNode( final String nhx,
                            final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
                            final boolean replace_underscores ) throws NHXFormatException {
-        init();
+        //  init();
         NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores );
         setId( PhylogenyNode.getNodeCount() );
         PhylogenyNode.increaseNodeCount();