in progress...

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

diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index 3d94dd7..4aefb5c 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -56,7 +56,6 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PostorderTreeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.FailedConditionCheckException;
-import org.forester.util.ForesterUtil;
 
 public class Phylogeny {
 
@@ -131,19 +130,19 @@ public class Phylogeny {
      *            the root-node of a subtree
      * @return the height of the subtree emanating at n
      */
-    public double calculateSubtreeHeight( final PhylogenyNode n ) {
-        if ( n.isExternal() || n.isCollapse() ) {
-            return ForesterUtil.isLargerOrEqualToZero( n.getDistanceToParent() );
+    public double calculateSubtreeHeight( final PhylogenyNode n, final boolean take_collapse_into_account ) {
+        if ( n.isExternal() || ( take_collapse_into_account && n.isCollapse() ) ) {
+            return n.getDistanceToParent() > 0 ? n.getDistanceToParent() : 0;
         }
         else {
             double max = -Double.MAX_VALUE;
             for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
-                final double l = calculateSubtreeHeight( n.getChildNode( i ) );
+                final double l = calculateSubtreeHeight( n.getChildNode( i ),  take_collapse_into_account );
                 if ( l > max ) {
                     max = l;
                 }
             }
-            return max + ForesterUtil.isLargerOrEqualToZero( n.getDistanceToParent() );
+            return max + ( n.getDistanceToParent() > 0 ? n.getDistanceToParent() : 0);
         }
     }
 
@@ -332,28 +331,7 @@ public class Phylogeny {
         return _external_nodes_set;
     }
 
-    /**
-     * Returns the number of duplications of this Phylogeny (int). A return
-     * value of -1 indicates that the number of duplications is unknown.
-     */
-    // public int getNumberOfDuplications() {
-    // return _number_of_duplications;
-    // } // getNumberOfDuplications()
-    /**
-     * Sets the number of duplications of this Phylogeny (int). A value of -1
-     * indicates that the number of duplications is unknown.
-     *
-     * @param clean_nh
-     *            set to true for clean NH format
-     */
-    // public void setNumberOfDuplications( int i ) {
-    // if ( i < 0 ) {
-    // _number_of_duplications = -1;
-    // }
-    // else {
-    // _number_of_duplications = i;
-    // }
-    // } // setNumberOfDuplications( int )
+ 
     /**
      * Returns the first external PhylogenyNode.
      */
@@ -370,17 +348,15 @@ public class Phylogeny {
 
     /**
      * This calculates the height for rooted, tree-shaped phylogenies. The
-     * height is the longest distance from the root to an external node. Please
-     * note. Child nodes of collapsed nodes are ignored -- which is useful for
-     * display purposes but might be misleading for other applications.
+     * height is the longest distance from the root to an external node.
      *
      * @return the height for rooted, tree-shaped phylogenies
      */
-    public double getHeight() {
+    public double calculateHeight(final boolean take_collapse_into_account) {
         if ( isEmpty() ) {
             return 0.0;
         }
-        return calculateSubtreeHeight( getRoot() );
+        return calculateSubtreeHeight( getRoot(), take_collapse_into_account );
     }
 
     public Identifier getIdentifier() {
@@ -1087,7 +1063,7 @@ public class Phylogeny {
      */
     public void setRooted( final boolean b ) {
         _rooted = b;
-    } // setRooted( boolean )
+    }
 
     public void setSequenceRelationQueries( final Collection<Sequence> sequencesByName ) {
         _sequenceRelationQueries = sequencesByName;