NucleotideScores (JEBL2 lib API)

java.lang.Object
- jebl.evolution.align.scores.Scores
- - jebl.evolution.align.scores.NucleotideScores

All Implemented Interfaces:

ScoreMatrix

Direct Known Subclasses:

Hamming, JukesCantor
```
public class NucleotideScores
extends Scores
```
Version:

$Id: NucleotideScores.java 916 2008-05-26 03:33:27Z matt_kearse $

Author:

Richard Moir, Alexei Drummond

Field Summary

Fields
Modifier and Type Field Description

static NucleotideScores CLUSTALW

static NucleotideScores IUB
- Fields inherited from class jebl.evolution.align.scores.Scores
  score

Fields
Modifier and Type	Field	Description
`static NucleotideScores`	`CLUSTALW`
`static NucleotideScores`	`IUB`

Constructor Summary

Constructors
Constructor	Description
`NucleotideScores(float match, float misMatch)`
`NucleotideScores(float match, float misMatch, float ambiguousMatch)`
`NucleotideScores(java.lang.String name, float match, float misMatch)`
`NucleotideScores(java.lang.String name, float match, float mismatchTransition, float mismatchTransversion)`
`NucleotideScores(java.lang.String name, float match, float mismatchTransition, float mismatchTransversion, float ambiguousMatch, boolean useWeightedAmbigousMatches)`
`NucleotideScores(NucleotideScores scores)`
`NucleotideScores(Scores scores, double percentmatches)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type Method Description

java.lang.String getAlphabet()

java.lang.String getName()

java.lang.String toString()
- Methods inherited from class java.lang.Object
  equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
- Methods inherited from class jebl.evolution.align.scores.Scores
  duplicate, forMatrix, getMatrixString, getScore, includeAdditionalCharacters, includeGaps

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.String`	`getAlphabet()`
`java.lang.String`	`getName()`
`java.lang.String`	`toString()`

Field Detail

IUB

public static final NucleotideScores IUB

CLUSTALW

public static final NucleotideScores CLUSTALW

Constructor Detail

NucleotideScores

public NucleotideScores(NucleotideScores scores)

NucleotideScores

public NucleotideScores(float match,
                        float misMatch)

Parameters:: match - match score; misMatch - mismatch score

NucleotideScores

public NucleotideScores(float match,
                        float misMatch,
                        float ambiguousMatch)

NucleotideScores

public NucleotideScores(java.lang.String name,
                        float match,
                        float misMatch)

NucleotideScores

public NucleotideScores(java.lang.String name,
                        float match,
                        float mismatchTransition,
                        float mismatchTransversion)

NucleotideScores

public NucleotideScores(java.lang.String name,
                        float match,
                        float mismatchTransition,
                        float mismatchTransversion,
                        float ambiguousMatch,
                        boolean useWeightedAmbigousMatches)

NucleotideScores

public NucleotideScores(Scores scores,
                        double percentmatches)

Method Detail
- getName
```
public java.lang.String getName()
```
  Returns:
  
  human readable name
- getAlphabet
```
public final java.lang.String getAlphabet()
```
  Returns:
  
  a string containing the valid characters for this score matrix.
- toString
```
public java.lang.String toString()
```
  Overrides:
  
  toString in class Scores

Class NucleotideScores

Field Summary

Fields inherited from class jebl.evolution.align.scores.Scores

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from class jebl.evolution.align.scores.Scores

Field Detail

IUB

CLUSTALW

Constructor Detail

NucleotideScores

NucleotideScores

NucleotideScores

NucleotideScores

NucleotideScores

NucleotideScores

NucleotideScores

Method Detail

getName

getAlphabet

toString