const MultiSequence &MSA1, const MultiSequence &MSA2,

const vector<MySparseMx *> &SparseMxVec,

uint Index1, uint Index2,

uint TargetPairCount, string &Path)

{

const uint SeqCount1 = MSA1.GetNumSequences();

const uint SeqCount2 = MSA2.GetNumSequences();

asserta(SeqCount1 > 0);

asserta(SeqCount2 > 0);

asserta(MSA1.IsAligned());

asserta(MSA2.IsAligned());

const uint ColCount1 = MSA1.GetColCount();

const uint ColCount2 = MSA2.GetColCount();

vector<uint> SeqIndexes1;

vector<uint> SeqIndexes2;

GetPairs(SeqCount1, SeqCount2, TargetPairCount,

SeqIndexes1, SeqIndexes2);

const uint PairCount = SIZE(SeqIndexes1);

asserta(SIZE(SeqIndexes2) == PairCount);

vector<MySparseMx *> SparseMxs;

float AvgEA = GetPostPairsAlignedFlat(ProgressStr, MSA1, MSA2,

SeqIndexes1, SeqIndexes2, SparseMxs);

const uint L1 = ColCount1;

const uint L2 = ColCount2;

float *Post = AllocPost(L1, L2);

CalcPosteriorFlat3(MSA1, MSA2, SeqIndexes1, SeqIndexes2, SparseMxs, Post);

for (uint i = 0; i < PairCount; ++i)

delete SparseMxs[i];

SparseMxs.clear();

float *DPRows = AllocDPRows(L1, L2);

char *TB = AllocTB(L1, L2);

CalcAlnFlat(Post, ColCount1, ColCount2, DPRows, TB, Path);

delete Post;

delete DPRows;

delete TB;

return AvgEA;