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

Packages that use PairwiseSettings

Package	Description
com.hfg.bio.seq.alignment

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

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

Modifier and Type	Method and Description
PairwiseSettings	PairwiseSettings.clone()
PairwiseSettings	PairwiseSeqAligner.getSettings()
PairwiseSettings	PairwiseSeqAlignment.getSettings()
PairwiseSettings	PairwiseSettings.setAlignmentType(PairwiseAlignmentType inValue)
PairwiseSettings	PairwiseSettings.setCalculateStatisticalScores(boolean inValue) Specifies whether or not to calculate an E-value, P-value, and Z score by generating background alignments.
PairwiseSettings	PairwiseSettings.setDumpMatrices(boolean inValue)
PairwiseSettings	PairwiseSettings.setGapPenalties(GapPenalties inValue) Sets the specified gap penalties for both the query and subject.
PairwiseSettings	PairwiseSettings.setGapPenalties(PairwiseSeqType inPairwiseSeqType, GapPenalties inValue)
PairwiseSettings	PairwiseSettings.setMaxLocalAlignmentResults(Integer inValue)
PairwiseSettings	PairwiseSettings.setMinLocalAlignmentLength(Integer inValue)
PairwiseSettings	PairwiseSettings.setMinNumOfBackgroundCycles(int inValue)
PairwiseSettings	PairwiseSettings.setMinQueryMatchLength(Integer inValue) Specifies the minimum number of non-gap characters for the query in the alignment.
PairwiseSettings	PairwiseSettings.setMinRawScore(Integer inValue)
PairwiseSettings	PairwiseSettings.setPenalizeTerminalGaps(boolean inValue)
PairwiseSettings	PairwiseSettings.setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, boolean inValue)
PairwiseSettings	PairwiseSettings.setPenalizeTerminalGaps(PairwiseSeqType inPairwiseSeqType, PairwiseSeqTerminus inPairwiseSeqTerminus, boolean inValue)
PairwiseSettings	PairwiseSettings.setQueryAlignmentType(PairwiseAlignmentType inValue)
PairwiseSettings	PairwiseSettings.setScoreCaseInsensitive(boolean inValue) If specified as true, the scoring matrix's scoreCaseInsensitive() method is used.
PairwiseSettings	PairwiseSettings.setSubjectAlignmentType(PairwiseAlignmentType inValue)
PairwiseSettings	PairwiseSettings.setSubjectTemplateMode(boolean inValue) If specified as true, query gaps are not penalized if they exist in the subject.
PairwiseSettings	PairwiseSettings.setSubstitutionMatrix(SubstitutionMatrix inValue)

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

Modifier and Type	Method and Description
PairwiseSeqAligner	PairwiseSeqAligner.setSettings(PairwiseSettings inValue)
PairwiseSeqAlignment	PairwiseSeqAlignment.setSettings(PairwiseSettings inValue)

Constructors in com.hfg.bio.seq.alignment with parameters of type PairwiseSettings

Constructor and Description
PairwiseSeqAligner(PairwiseSettings inSettings)