Package | Description |
---|---|
jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
jebl.evolution.align.scores |
Modifier and Type | Method | Description |
---|---|---|
Scores |
BartonSternberg.getEstimatedScores() |
Modifier and Type | Method | Description |
---|---|---|
static float |
ProfileCharacter.score(ProfileCharacter character1,
ProfileCharacter character2,
Scores scores) |
|
static float |
ProfileCharacter.scoreSelf(ProfileCharacter character,
Scores scores) |
|
void |
Align.setScores(Scores sub) |
Constructor | Description |
---|---|
Align(Scores sub,
float d) |
|
BartonSternberg(Scores scores,
float gapOpen,
float gapExtend,
int refinementIterations,
boolean freeGapsAtEnds,
boolean fastGuide) |
|
MaximalSegmentPair(Scores sub) |
|
NeedlemanWunsch(Scores sub,
float d) |
|
NeedlemanWunschAffine(Scores sub,
float d,
float e) |
|
NeedlemanWunschLinearSpace(Scores sub,
float d) |
|
NeedlemanWunschLinearSpaceAffine(Scores sub,
float openGapPenalty,
float extendGapPenalty) |
|
NeedlemanWunschLinearSpaceAffine(Scores sub,
float d,
float e,
boolean freeGapsAtEnds) |
|
NeedlemanWunschLinearSpaceAffine(Scores sub,
float d,
float e,
boolean freeGapsAtEnds,
boolean applyGapExtendCostToFirstGapResidue) |
|
NonOverlapMultipleLocalAffine(Scores sub,
float d,
float e,
int T) |
|
OldNeedlemanWunschAffine(Scores sub,
float d,
float e) |
|
OverlapAlign(Scores sub,
float d) |
|
SmithWaterman(Scores sub,
float d) |
|
SmithWatermanLinearSpace(Scores sub,
float d) |
|
SmithWatermanLinearSpaceAffine(Scores sub,
float d,
float e) |
Modifier and Type | Class | Description |
---|---|---|
class |
AminoAcidScores |
|
class |
Blosum45 |
|
class |
Blosum50 |
|
class |
Blosum55 |
|
class |
Blosum60 |
|
class |
Blosum62 |
|
class |
Blosum65 |
|
class |
Blosum70 |
|
class |
Blosum75 |
|
class |
Blosum80 |
|
class |
Blosum85 |
|
class |
Blosum90 |
|
class |
Hamming |
|
class |
JukesCantor |
Jukes Cantor assumes equal substitution frequencies and equal nucleotide
equilibrium frequencies.
|
class |
NucleotideScores |
|
class |
Pam100 |
|
class |
Pam110 |
|
class |
Pam120 |
|
class |
Pam130 |
|
class |
Pam140 |
|
class |
Pam150 |
|
class |
Pam160 |
|
class |
Pam170 |
|
class |
Pam180 |
|
class |
Pam190 |
|
class |
Pam200 |
|
class |
Pam210 |
|
class |
Pam220 |
|
class |
Pam230 |
|
class |
Pam240 |
|
class |
Pam250 |
|
class |
SubstScoreMatrix |
Modifier and Type | Method | Description |
---|---|---|
static Scores |
Scores.duplicate(Scores scores) |
|
static Scores |
Scores.forMatrix(ScoreMatrix scoreMatrix) |
|
static Scores |
ScoresFactory.generateScores(java.lang.String nameVal) |
For any matrix.
|
static Scores |
ScoresFactory.generateScores(java.lang.String name,
float val) |
For calculated nucleotide matrices.
|
static Scores |
ScoresFactory.generateScores(java.lang.String name,
int val) |
For Blosum and Pam matrices
|
static Scores |
Scores.includeAdditionalCharacters(Scores scores,
java.lang.String characters) |
includes additional characters in the score matrix which will all have scored zero when compared to other
characters.
|
static Scores |
Scores.includeGaps(Scores scores,
float gapVersusResidueCost,
float gapVersusGapCost) |
Modifier and Type | Method | Description |
---|---|---|
static Scores |
Scores.duplicate(Scores scores) |
|
static Scores |
Scores.includeAdditionalCharacters(Scores scores,
java.lang.String characters) |
includes additional characters in the score matrix which will all have scored zero when compared to other
characters.
|
static Scores |
Scores.includeGaps(Scores scores,
float gapVersusResidueCost,
float gapVersusGapCost) |
Constructor | Description |
---|---|
NucleotideScores(Scores scores,
double percentmatches) |
http://code.google.com/p/jebl2/