umms.core.alignment.FeatureSequenceAlignment Member List

This is the complete list of members for umms.core.alignment.FeatureSequenceAlignment, including all inherited members.

DEFAULT_GAP_EXTEND_PENALTY	umms.core.alignment.FeatureSequenceAlignment	static
DEFAULT_GAP_OPEN_PENALTY	umms.core.alignment.FeatureSequenceAlignment	static
DEFAULT_MATCH_SCORE	umms.core.alignment.FeatureSequenceAlignment	static
DEFAULT_MISMATCH_SCORE	umms.core.alignment.FeatureSequenceAlignment	static
FeatureSequenceAlignment(String featureBedFile, String genomeFasta)	umms.core.alignment.FeatureSequenceAlignment
FeatureSequenceAlignment(Collection< Gene > genes, String genomeFasta)	umms.core.alignment.FeatureSequenceAlignment
FeatureSequenceAlignment(String featureBedFile, String genomeFasta, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty)	umms.core.alignment.FeatureSequenceAlignment
FeatureSequenceAlignment(Collection< Gene > genes, Map< String, broad.core.sequence.Sequence > chrs, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty)	umms.core.alignment.FeatureSequenceAlignment
FeatureSequenceAlignment(Collection< Gene > genes, String genomeFasta, float matchScore, float mismatchScore, float gapOpenPenalty, float gapExtendPenalty)	umms.core.alignment.FeatureSequenceAlignment
getAllPairwiseAntisenseAlignments(float minAlignLength, float minPctIdentity)	umms.core.alignment.FeatureSequenceAlignment
getAllPairwiseSenseAlignments(float minAlignLength, float minPctIdentity)	umms.core.alignment.FeatureSequenceAlignment
main(String[] args)	umms.core.alignment.FeatureSequenceAlignment	static
writeAllAntisenseAlignmentsToBed(String outBedFile, int minAlignLength, float minPctIdentity)	umms.core.alignment.FeatureSequenceAlignment
writeAllAntisenseAlignmentsToBed(String outBedFile, boolean append, int minAlignLength, float minPctIdentity)	umms.core.alignment.FeatureSequenceAlignment
writeAllSenseAlignmentsToBed(String outBedFile, int minAlignLength, float minPctIdentity)	umms.core.alignment.FeatureSequenceAlignment
writeAllSenseAlignmentsToBed(String outBedFile, boolean append, int minAlignLength, float minPctIdentity)	umms.core.alignment.FeatureSequenceAlignment