ScoringMethodForExternalNode

All Known Implementing Classes:

BranchCountingBasedScoringMethod, BranchLengthBasedScoringMethod, LogBranchLengthBasedScoringMethod
```
public interface ScoringMethodForExternalNode
```

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`void`	`calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)`	This calculates the coverage score for one external node.
`java.lang.String`	`getDesciption()`	This returns a short description of this scoring method
`double`	`getNormalizationFactor(Phylogeny phylogeny)`	This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.

- Method Detail
  - calculateScoreForExternalNode
```
void calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.Double> external_node_scores,
                                   Phylogeny phylogeny,
                                   PhylogenyNode external_node,
                                   CoverageCalculationOptions options)
```
    This calculates the coverage score for one external node.
    
    Parameters:
    
    external_node_scores - SortedMap in which the external node scores are stored (node->score)
    
    phylogeny - Phylogeny containing the external nodes to score
    
    external_node - PhylogenyNod for which to calculate the score
    
    options - CoverageCalculationOptions
    
    annotate_phylogeny -
  - getDesciption
```
java.lang.String getDesciption()
```
    This returns a short description of this scoring method
    
    Returns:
    
    short description of this scoring method
  - getNormalizationFactor
```
double getNormalizationFactor(Phylogeny phylogeny)
```
    This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.
    
    Parameters:
    
    phylogeny - Phylogeny containing the external nodes to score
    
    Returns:
    
    normalization factor