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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
pccx
/
ScoringMethodForExternalNode.java
diff --git
a/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java
b/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java
index
5fab38a
..
78a816e
100644
(file)
--- 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
// 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;
package org.forester.pccx;
@@
-34,15
+34,15
@@
import org.forester.phylogeny.PhylogenyNode;
/*
* Interface providing implementations of scoring methods used by
* ExternalNodeBasedCoverageMethod.
/*
* 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.
* @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)
* @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
* 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,
*/
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
/**
* This returns a short description of this scoring method
- *
+ *
* @return short description of this scoring method
*/
public String getDesciption();
* @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.
/**
* 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
* @param phylogeny
* Phylogeny containing the external nodes to score
* @return normalization factor