Lines Matching defs:acf
294 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0)) in testMapProteinAlignmentToCdna_noXrefs() local
460 AlignedCodonFrame acf = new AlignedCodonFrame(); in checkAlignSequenceAs() local
510 AlignedCodonFrame acf = new AlignedCodonFrame(); in testAlignProteinAsDna() local
639 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0)) in testMapProteinAlignmentToCdna_withStartAndStopCodons() local
746 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0)) in testMapProteinAlignmentToCdna_withXrefs() local
811 AlignedCodonFrame acf = protein.getCodonFrame(protein.getSequenceAt(0)) in testMapProteinAlignmentToCdna_prioritiseXrefs() local
1039 AlignedCodonFrame acf = new AlignedCodonFrame(); in testMakeCdsAlignment() local
1266 AlignedCodonFrame acf = new AlignedCodonFrame(); in testMakeCdsAlignment_multipleProteins() local
1463 AlignedCodonFrame acf = new AlignedCodonFrame(); in testAlignSequenceAs_mappedProteinProtein() local
1662 AlignedCodonFrame acf = new AlignedCodonFrame(); in testMakeCdsAlignment_alternativeTranscripts() local
1779 AlignedCodonFrame acf = new AlignedCodonFrame(); in testAlignProteinAsDna_incompleteStartCodon() local
2002 AlignedCodonFrame acf = new AlignedCodonFrame(); in testAlignAs_alternateTranscriptsUngapped() local
2104 AlignedCodonFrame acf = new AlignedCodonFrame(); in testMakeCdsAlignment_filterProducts() local