X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fpccx%2FScoringMethodForExternalNode.java;h=78a816e8f71b56eb2e81469328df17b896b118b8;hb=f4f1b0cf648f352e9d3dcaa62aef22355cc801ad;hp=5fab38ad9f2c655d7bd0ebbc04239080aeb68cfd;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java b/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java
index 5fab38a..78a816e 100644
--- a/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java
+++ b/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java
@@ -22,7 +22,7 @@
 // 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.pccx;
 
@@ -34,15 +34,15 @@ import org.forester.phylogeny.PhylogenyNode;
 /*
  * Interface providing implementations of scoring methods used by
  * ExternalNodeBasedCoverageMethod.
- * 
+ *
  * @author Christian M. Zmasek
  */
 public interface ScoringMethodForExternalNode {
 
     /**
      * This calculates the coverage score for one external node.
-     * 
-     * 
+     *
+     *
      * @param external_node_scores
      *            SortedMap<PhylogenyNode, Double> in which the external node
      *            scores are stored (node->score)
@@ -52,8 +52,8 @@ public interface ScoringMethodForExternalNode {
      *            PhylogenyNod for which to calculate the score
      * @param options
      *            CoverageCalculationOptions
-     * @param annotate_phylogeny           
-     *            
+     * @param annotate_phylogeny
+     *
      */
     public void calculateScoreForExternalNode( final SortedMap<PhylogenyNode, Double> external_node_scores,
                                                final Phylogeny phylogeny,
@@ -62,7 +62,7 @@ public interface ScoringMethodForExternalNode {
 
     /**
      * This returns a short description of this scoring method
-     * 
+     *
      * @return short description of this scoring method
      */
     public String getDesciption();
@@ -70,8 +70,8 @@ public interface ScoringMethodForExternalNode {
     /**
      * This calculates a normalization factor, so that a normalized score of 1.0
      * means complete coverage.
-     * 
-     * 
+     *
+     *
      * @param phylogeny
      *            Phylogeny containing the external nodes to score
      * @return normalization factor