Lines Matching defs:acf
76 AlignedCodonFrame acf = new AlignedCodonFrame(); in testFindAlignedSequence() local
116 AlignedCodonFrame acf = new AlignedCodonFrame(); in testGetMappedRegion() local
177 AlignedCodonFrame acf = new AlignedCodonFrame(); in testGetMappedCodons() local
214 AlignedCodonFrame acf = new AlignedCodonFrame(); in testGetMappedCodons_dnaVariants() local
251 AlignedCodonFrame acf = new AlignedCodonFrame(); in testGetMappedCodons_forSubSequences() local
332 AlignedCodonFrame acf = new AlignedCodonFrame(); in testIsRealisableWith() local
391 AlignedCodonFrame acf = new AlignedCodonFrame(); in testRealiseWith() local
436 AlignedCodonFrame acf = new AlignedCodonFrame(); in testGetMappedRegion_eitherWay() local
492 AlignedCodonFrame acf = new AlignedCodonFrame(); in testAddMap() local
518 AlignedCodonFrame acf = new AlignedCodonFrame(); in testGetCoveringMapping() local
584 AlignedCodonFrame acf = new AlignedCodonFrame(); in testMarkMappedRegion() local
664 AlignedCodonFrame acf = new AlignedCodonFrame(); in testGetCoveringCodonMapping() local