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

Packages that use GapPenalties

Package	Description
com.hfg.bio.seq.alignment

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

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

Modifier and Type	Method and Description
GapPenalties	GapPenalties.clone()
GapPenalties	MSA_Settings.getGapPenalties(PairwiseSeqType inPairwiseSeqType)
GapPenalties	PairwiseSettings.getGapPenalties(PairwiseSeqType inPairwiseSeqType)
GapPenalties	GapPenalties.setExtensionPenalty(Float inValue)
GapPenalties	GapPenalties.setOpenPenalty(Float inValue)

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

Modifier and Type	Method and Description
MSA_Settings	MSA_Settings.setGapPenalties(GapPenalties inValue) Sets the specified gap penalties for both the query and subject.
PairwiseSettings	PairwiseSettings.setGapPenalties(GapPenalties inValue) Sets the specified gap penalties for both the query and subject.
MSA_Settings	MSA_Settings.setGapPenalties(PairwiseSeqType inPairwiseSeqType, GapPenalties inValue)
PairwiseSettings	PairwiseSettings.setGapPenalties(PairwiseSeqType inPairwiseSeqType, GapPenalties inValue)