public class MSA
extends java.lang.Object
Constructor and Description |
---|
MSA(int encodingLength,
java.util.List<java.lang.String> charStreamList,
int[][] itemsJoined,
java.util.Map<java.lang.String,java.lang.Integer> substitutionScoreMap,
java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap,
int incrementLikeSubstitutionScore,
float scaleFactor,
int gapPenalty,
float lengthRatioThreshold) |
Modifier and Type | Method and Description |
---|---|
java.util.List<java.lang.String[]> |
getAlignments(int noClusters) |
java.util.Set<java.lang.Integer> |
getClusterItems(int noClusters) |
java.util.Set<java.lang.Integer> |
getItemElements(int index,
int noClusters) |
public MSA(int encodingLength, java.util.List<java.lang.String> charStreamList, int[][] itemsJoined, java.util.Map<java.lang.String,java.lang.Integer> substitutionScoreMap, java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap, int incrementLikeSubstitutionScore, float scaleFactor, int gapPenalty, float lengthRatioThreshold)