Merge branch 'master' of https://github.com/cmzmasek/forester.git into JalviewIntegration

[jalview.git] / forester / java / src / org / forester / pccx / BranchCountingBasedScoringMethod.java

diff --git a/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java b/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java
index 815d13d..fdb9b17 100644 (file)
--- a/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java
+++ b/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java
@@ -6,7 +6,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -16,13 +16,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // 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;
 
@@ -33,7 +33,7 @@ import org.forester.phylogeny.PhylogenyNode;
 
 /*
  * Scoring method according to an idea by Adam Godzik, PhD.
- * 
+ *
  * @author Christian M. Zmasek
  */
 public class BranchCountingBasedScoringMethod implements ScoringMethodForExternalNode {
@@ -50,6 +50,7 @@ public class BranchCountingBasedScoringMethod implements ScoringMethodForExterna
         return score_contribution;
     }
 
+    @Override
     public void calculateScoreForExternalNode( final SortedMap<PhylogenyNode, Double> external_node_scores,
                                                final Phylogeny phylogeny,
                                                final PhylogenyNode external_node,
@@ -64,10 +65,12 @@ public class BranchCountingBasedScoringMethod implements ScoringMethodForExterna
         }
     }
 
+    @Override
     public String getDesciption() {
         return "sum of 1/branch-segment-sum";
     }
 
+    @Override
     public double getNormalizationFactor( final Phylogeny phylogeny ) {
         return ( 1.0 / phylogeny.getNumberOfExternalNodes() );
     }