ScoreMatrix
Hamming
, JukesCantor
public class NucleotideScores extends Scores
Modifier and Type | Field | Description |
---|---|---|
static NucleotideScores |
CLUSTALW |
|
static NucleotideScores |
IUB |
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) |
Modifier and Type | Method | Description |
---|---|---|
java.lang.String |
getAlphabet() |
|
java.lang.String |
getName() |
|
java.lang.String |
toString() |
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
duplicate, forMatrix, getMatrixString, getScore, includeAdditionalCharacters, includeGaps
public static final NucleotideScores IUB
public static final NucleotideScores CLUSTALW
public NucleotideScores(NucleotideScores scores)
public NucleotideScores(float match, float misMatch)
match
- match scoremisMatch
- mismatch scorepublic NucleotideScores(float match, float misMatch, float ambiguousMatch)
public NucleotideScores(java.lang.String name, float match, float misMatch)
public NucleotideScores(java.lang.String name, float match, float mismatchTransition, float mismatchTransversion)
public NucleotideScores(java.lang.String name, float match, float mismatchTransition, float mismatchTransversion, float ambiguousMatch, boolean useWeightedAmbigousMatches)
public NucleotideScores(Scores scores, double percentmatches)
http://code.google.com/p/jebl2/