Lines Matching refs:m_cd
45 …m_cd(cd), m_clusteringThreshold(identityThreshold), m_replacingThreshold(identityThreshold), m_ac(… in BEGIN_SCOPE()
51 int numNormal = m_cd->GetNumRows(); in swapSequences()
90 m_cd->EraseTheseRows(selectedNormalRows); in swapSequences()
105 ReMasterCdWithoutUnifiedBlocks(m_cd, newMaster, true); in swapSequences()
108 m_cd->EraseTheseRows(rows); in swapSequences()
110 m_cd->ResetPending(); in swapSequences()
111 m_cd->EraseSequences(); in swapSequences()
245 AlignmentCollection ac(m_cd);// default, pending only in findStructuralPendings()
254 AlignmentCollection ac(m_cd);// default, pending only in promotePendingRows()
259 m_cd->AddSeqAlign(ac.getSeqAlign(*newMaster)); in promotePendingRows()
260 *newMaster = m_cd->GetNumRows() - 1; in promotePendingRows()
264 m_cd->AddSeqAlign(ac.getSeqAlign(*sit)); in promotePendingRows()
268 m_cd->ErasePendingRows(rows); in promotePendingRows()