Uses of Class
com.hfg.bio.seq.alignment.AlignmentScoring

Packages that use AlignmentScoring

Package	Description
com.hfg.bio.seq.alignment

Uses of AlignmentScoring in com.hfg.bio.seq.alignment

Methods in com.hfg.bio.seq.alignment that return AlignmentScoring

Modifier and Type	Method and Description
AlignmentScoring	AlignmentScoring.clone()
AlignmentScoring	AlignmentScoring.combine(AlignmentScoring inValue)
AlignmentScoring	PairwiseSeqAlignment.getScoring() Returns the alignment scoring object.
AlignmentScoring	AlignmentScoring.incrementComparisonLength()
AlignmentScoring	AlignmentScoring.incrementComparisonLength(int inValue)
AlignmentScoring	AlignmentScoring.incrementNumIdentities()
AlignmentScoring	AlignmentScoring.incrementNumIdentities(int inValue)
AlignmentScoring	AlignmentScoring.setAdjustedPctIdentity(Float inValue) Sets the percent identity that doesn't penalize sequence's terminal gaps.
AlignmentScoring	AlignmentScoring.setComparisonLength(Integer inValue)
AlignmentScoring	AlignmentScoring.setEValue(Float inValue)
AlignmentScoring	AlignmentScoring.setNumIdentities(Integer inValue)
AlignmentScoring	AlignmentScoring.setPValue(Float inValue)
AlignmentScoring	AlignmentScoring.setScore(Float inValue)
AlignmentScoring	AlignmentScoring.setScoringBoundaries(List<Range<Integer>> inValue) Specifies an optional 1-based list of alignment position ranges which should be considered for scoring.
AlignmentScoring	AlignmentScoring.setZScore(Float inValue)

Methods in com.hfg.bio.seq.alignment with parameters of type AlignmentScoring

Modifier and Type	Method and Description
AlignmentScoring	AlignmentScoring.combine(AlignmentScoring inValue)
int	AlignmentScoring.compareTo(AlignmentScoring inObj2)