3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
27 package org.forester.pccx;
29 import java.util.SortedMap;
31 import org.forester.phylogeny.Phylogeny;
32 import org.forester.phylogeny.PhylogenyNode;
35 * Interface providing implementations of scoring methods used by
36 * ExternalNodeBasedCoverageMethod.
38 * @author Christian M. Zmasek
40 public interface ScoringMethodForExternalNode {
43 * This calculates the coverage score for one external node.
46 * @param external_node_scores
47 * SortedMap<PhylogenyNode, Double> in which the external node
48 * scores are stored (node->score)
50 * Phylogeny containing the external nodes to score
51 * @param external_node
52 * PhylogenyNod for which to calculate the score
54 * CoverageCalculationOptions
55 * @param annotate_phylogeny
58 public void calculateScoreForExternalNode( final SortedMap<PhylogenyNode, Double> external_node_scores,
59 final Phylogeny phylogeny,
60 final PhylogenyNode external_node,
61 final CoverageCalculationOptions options );
64 * This returns a short description of this scoring method
66 * @return short description of this scoring method
68 public String getDesciption();
71 * This calculates a normalization factor, so that a normalized score of 1.0
72 * means complete coverage.
76 * Phylogeny containing the external nodes to score
77 * @return normalization factor
79 public double getNormalizationFactor( final Phylogeny phylogeny );