Uses of Class
com.milaboratory.core.alignment.BLASTMatrix

Packages that use BLASTMatrix

Package	Description
com.milaboratory.core.alignment

Uses of BLASTMatrix in com.milaboratory.core.alignment

Methods in com.milaboratory.core.alignment that return BLASTMatrix

Modifier and Type	Method and Description
static BLASTMatrix	BLASTMatrix.valueOf(String name) Returns the enum constant of this type with the specified name.
static BLASTMatrix[]	BLASTMatrix.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in com.milaboratory.core.alignment with parameters of type BLASTMatrix

Modifier and Type	Method and Description
static LinearGapAlignmentScoring<AminoAcidSequence>	LinearGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix) Returns standard amino acid BLAST scoring with #gapPenalty=5
static AffineGapAlignmentScoring<AminoAcidSequence>	AffineGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix) Returns standard AminoAcid BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)
static LinearGapAlignmentScoring<AminoAcidSequence>	LinearGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapPenalty) Returns standard amino acid BLAST scoring
static AffineGapAlignmentScoring<AminoAcidSequence>	AffineGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapOpenPenalty, int gapExtensionPenalty) Returns AminoAcid BLAST scoring