Searched refs:alignmentObj (Results 1 – 2 of 2) sorted by relevance
92 alignmentObj.clearSecStruct1(); in align()93 alignmentObj.clearSecStruct2(); in align()121 alignmentObj.resetAlign(); in align()296 && (alignmentObj.getNumSeqs() - alignmentObj.getProfile1NumSeqs() > 1)) in sequencesAlignToProfile()350 alignmentObj.fixGaps(); in sequencesAlignToProfile()362 _length = alignmentObj.getSeqLength(alignmentObj.getProfile1NumSeqs() + 1); in sequencesAlignToProfile()498 alignmentObj.fixGaps(); in profileAlign()619 alignmentObj.resetProfile1(); in profileAlign()620 alignmentObj.resetProfile2(); in profileAlign()1144 alignmentOutput.createAlignmentOutput(&alignmentObj, 1, alignmentObj.getNumSeqs()); in outputNow()[all …]
48 Alignment* getAlignmentPtr(){return &alignmentObj;} in getAlignmentPtr()70 Alignment alignmentObj; variable