void Test()
{
SetListFileName("c:\\tmp\\lobster.log", false);
DistCalcTest DC;
Tree tree;
UPGMA2(DC, tree, LINKAGE_Avg);
}
void TestEstrings()
{
SetListFileName("c:\\tmp\\muscle.log", false);
//{
//short es1[] = { -1, 1, -1, 0 };
//short es2[] = { 1, -1, 2, 0 };
//short esa[] = { -2, 1, -1, 0 };
//test(es1, es2, esa);
//}
//{
//short es1[] = { 2, -1, 2, 0 };
//short es2[] = { 1, -1, 3, -1, 1, 0 };
//short esa[] = { 1, -1, 1, -1, 1, -1, 1, 0 };
//test(es1, es2, esa);
//}
//{
//short es1[] = { -1, 3, 0 };
//short es2[] = { 2, -1, 2, 0 };
//short esa[] = { -1, 1, -1, 2, 0 };
//test(es1, es2, esa);
//}
//{
//short es1[] = { -1, 1, -1, 1, 0};
//short es2[] = { 4, 0 };
//short esa[] = { -1, 1, -1, 1, 0};
//test(es1, es2, esa);
//}
//{
//short es1[] = { 1, -1, 1, -1, 0};
//short es2[] = { 4, 0 };
//short esa[] = { 1, -1, 1, -1, 0};
//test(es1, es2, esa);
//}
//{
//short es1[] = { 1, -1, 1, -1, 0};
//short es2[] = { -1, 4, -1, 0 };
//short esa[] = { -1, 1, -1, 1, -2, 0};
//test(es1, es2, esa);
//}
{
short es1[] = { 106, -77, 56, -2, 155, -3, 123, -2, 0};
short es2[] = { 50, -36, 34, -3, 12, -6, 1, -6, 18, -17, 60, -5, 349, -56, 0 };
short esa[] = { 0 };
test(es1, es2, esa);
}
exit(0);
}
void TestBiPart()
{
SetListFileName("c:\\tmp\\lobster.log", false);
Tree tree;
TextFile fileIn("c:\\tmp\\test.phy");
tree.FromFile(fileIn);
tree.LogMe();
const unsigned uNodeCount = tree.GetNodeCount();
unsigned *Leaves1 = new unsigned[uNodeCount];
unsigned *Leaves2 = new unsigned[uNodeCount];
PhyEnumEdgeState ES;
bool bDone = false;
for (;;)
{
unsigned uCount1 = uInsane;
unsigned uCount2 = uInsane;
bool bOk = PhyEnumBiParts(tree, ES, Leaves1, &uCount1, Leaves2, &uCount2);
Log("PEBP=%d ES.Init=%d ES.ni1=%d ES.ni2=%d\n",
bOk,
ES.m_bInit,
ES.m_uNodeIndex1,
ES.m_uNodeIndex2);
if (!bOk)
break;
Log("\n");
Log("Part1: ");
for (unsigned n = 0; n < uCount1; ++n)
Log(" %d(%s)", Leaves1[n], tree.GetLeafName(Leaves1[n]));
Log("\n");
Log("Part2: ");
for (unsigned n = 0; n < uCount2; ++n)
Log(" %d(%s)", Leaves2[n], tree.GetLeafName(Leaves2[n]));
Log("\n");
}
}
void SPTest()
{
SetPPScore(PPSCORE_SV);
SetListFileName("c:\\tmp\\muscle.log", false);
TextFile file1("c:\\tmp\\msa1.afa");
TextFile file2("c:\\tmp\\msa2.afa");
MSA msa1;
MSA msa2;
msa1.FromFile(file1);
msa2.FromFile(file2);
Log("msa1=\n");
msa1.LogMe();
Log("msa2=\n");
msa2.LogMe();
const unsigned uColCount = msa1.GetColCount();
if (msa2.GetColCount() != uColCount)
Quit("Different lengths");
const unsigned uSeqCount1 = msa1.GetSeqCount();
const unsigned uSeqCount2 = msa2.GetSeqCount();
const unsigned uSeqCount = uSeqCount1 + uSeqCount2;
MSA::SetIdCount(uSeqCount);
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)
{
msa1.SetSeqWeight(uSeqIndex1, 1.0);
msa1.SetSeqId(uSeqIndex1, uSeqIndex1);
}
for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)
{
msa2.SetSeqWeight(uSeqIndex2, 1.0);
msa2.SetSeqId(uSeqIndex2, uSeqCount1 + uSeqIndex2);
}
MSA alnA;
MSA alnB;
char strPathA[1024];
char strPathB[1024];
MakePath(uColCount, INDELS, strPathA);
MakePath(uColCount, INDELS, strPathB);
PWPath PathA;
PWPath PathB;
PathA.FromStr(strPathA);
PathB.FromStr(strPathB);
Log("PathA=\n");
PathA.LogMe();
Log("PathB=\n");
PathB.LogMe();
AlignTwoMSAsGivenPath(PathA, msa1, msa2, alnA);
AlignTwoMSAsGivenPath(PathB, msa1, msa2, alnB);
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
alnA.SetSeqWeight(uSeqIndex, 1.0);
alnB.SetSeqWeight(uSeqIndex, 1.0);
}
unsigned Seqs1[1024];
unsigned Seqs2[1024];
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)
Seqs1[uSeqIndex1] = uSeqIndex1;
for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)
Seqs2[uSeqIndex2] = uSeqCount1 + uSeqIndex2;
MSA msaA1;
MSA msaA2;
MSA msaB1;
MSA msaB2;
MSAFromSeqSubset(alnA, Seqs1, uSeqCount1, msaA1);
MSAFromSeqSubset(alnB, Seqs1, uSeqCount1, msaB1);
MSAFromSeqSubset(alnA, Seqs2, uSeqCount2, msaA2);
MSAFromSeqSubset(alnB, Seqs2, uSeqCount2, msaB2);
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)
{
msaA1.SetSeqWeight(uSeqIndex1, 1.0);
msaB1.SetSeqWeight(uSeqIndex1, 1.0);
}
for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)
{
msaA2.SetSeqWeight(uSeqIndex2, 1.0);
msaB2.SetSeqWeight(uSeqIndex2, 1.0);
}
Log("msaA1=\n");
msaA1.LogMe();
Log("msaB1=\n");
msaB1.LogMe();
Log("msaA2=\n");
msaA2.LogMe();
Log("msaB2=\n");
msaB2.LogMe();
Log("alnA=\n");
alnA.LogMe();
Log("AlnB=\n");
alnB.LogMe();
Log("\nSPA\n---\n");
SCORE SPA = ObjScoreSP(alnA);
Log("\nSPB\n---\n");
SCORE SPB = ObjScoreSP(alnB);
Log("\nXPA\n---\n");
SCORE XPA = ObjScoreXP(msaA1, msaA2);
Log("\nXPB\n---\n");
SCORE XPB = ObjScoreXP(msaB1, msaB2);
Log("SPA=%.4g SPB=%.4g Diff=%.4g\n", SPA, SPB, SPA - SPB);
Log("XPA=%.4g XPB=%.4g Diff=%.4g\n", XPA, XPB, XPA - XPB);
}