// 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
// 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;
/*
* 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)
* 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,
/**
* This returns a short description of this scoring method
- *
+ *
* @return short description of this scoring method
*/
public String getDesciption();
/**
* 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