SCORE lp2Fast(SCORE x)
{
assert(x >= 0);
const int iTableSize = 1000;
const double dRange = 20.0;
const double dScale = dRange/iTableSize;
static SCORE dValue[iTableSize];
static bool bInit = false;
if (!bInit)
{
for (int i = 0; i < iTableSize; ++i)
dValue[i] = (SCORE) lp2(i*dScale);
bInit = true;
}
if (x >= dRange)
return 0.0;
int i = (int) (x/dScale);
assert(i >= 0 && i < iTableSize);
SCORE dResult = dValue[i];
assert(BTEq(dResult, lp2(x)));
return dResult;
}
bool ScoreEq(SCORE s1, SCORE s2)
{
return BTEq(s1, s2);
}
// The usual sum-of-pairs objective score: sum the score
// of the alignment of each pair of sequences.
SCORE ObjScoreSP(const MSA &msa, SCORE MatchScore[])
{
#if TRACE
Log("==================ObjScoreSP==============\n");
Log("msa=\n");
msa.LogMe();
#endif
g_SPScoreLetters = 0;
g_SPScoreGaps = 0;
if (0 != MatchScore)
{
const unsigned uColCount = msa.GetColCount();
for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
MatchScore[uColIndex] = 0;
}
const unsigned uSeqCount = msa.GetSeqCount();
SCORE scoreTotal = 0;
unsigned uPairCount = 0;
#if TRACE
Log("Seq1 Seq2 wt1 wt2 Letters Gaps Unwt.Score Wt.Score Total\n");
Log("---- ---- ------ ------ ---------- ---------- ---------- ---------- ----------\n");
#endif
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)
{
const WEIGHT w1 = msa.GetSeqWeight(uSeqIndex1);
for (unsigned uSeqIndex2 = uSeqIndex1 + 1; uSeqIndex2 < uSeqCount; ++uSeqIndex2)
{
const WEIGHT w2 = msa.GetSeqWeight(uSeqIndex2);
const WEIGHT w = w1*w2;
SCORE scoreLetters = ScoreSeqPairLetters(msa, uSeqIndex1, msa, uSeqIndex2);
SCORE scoreGaps = ScoreSeqPairGaps(msa, uSeqIndex1, msa, uSeqIndex2);
SCORE scorePair = scoreLetters + scoreGaps;
++uPairCount;
scoreTotal += w*scorePair;
g_SPScoreLetters += w*scoreLetters;
g_SPScoreGaps += w*scoreGaps;
#if TRACE
Log("%4d %4d %6.3f %6.3f %10.2f %10.2f %10.2f %10.2f %10.2f >%s >%s\n",
uSeqIndex1,
uSeqIndex2,
w1,
w2,
scoreLetters,
scoreGaps,
scorePair,
scorePair*w1*w2,
scoreTotal,
msa.GetSeqName(uSeqIndex1),
msa.GetSeqName(uSeqIndex2));
#endif
}
}
#if TEST_SPFAST
{
SCORE f = ObjScoreSPFast(msa);
Log("Fast = %.6g\n", f);
Log("Brute = %.6g\n", scoreTotal);
if (BTEq(f, scoreTotal))
Log("Agree\n");
else
Log("** DISAGREE **\n");
}
#endif
// return scoreTotal / uPairCount;
return scoreTotal;
}
static SCORE ScoreColLetters(const MSA &msa, unsigned uColIndex)
{
MuscleContext *ctx = getMuscleContext();
SCOREMATRIX &Mx = *ctx->params.g_ptrScoreMatrix;
unsigned &g_AlphaSize = ctx->alpha.g_AlphaSize;
const unsigned uSeqCount = msa.GetSeqCount();
#if BRUTE_LETTERS
SCORE BruteScore = 0;
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)
{
unsigned uLetter1 = msa.GetLetterEx(uSeqIndex1, uColIndex);
if (uLetter1 >= g_AlphaSize)
continue;
WEIGHT w1 = msa.GetSeqWeight(uSeqIndex1);
for (unsigned uSeqIndex2 = uSeqIndex1 + 1; uSeqIndex2 < uSeqCount; ++uSeqIndex2)
{
unsigned uLetter2 = msa.GetLetterEx(uSeqIndex2, uColIndex);
if (uLetter2 >= g_AlphaSize)
continue;
WEIGHT w2 = msa.GetSeqWeight(uSeqIndex2);
BruteScore += w1*w2*Mx[uLetter1][uLetter2];
}
}
#endif
double N = 0;
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)
{
WEIGHT w = msa.GetSeqWeight(uSeqIndex1);
N += w;
}
if (N <= 0)
return 0;
FCOUNT Freqs[20];
memset(Freqs, 0, sizeof(Freqs));
SCORE Score = 0;
for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)
{
unsigned uLetter = msa.GetLetterEx(uSeqIndex1, uColIndex);
if (uLetter >= g_AlphaSize)
continue;
WEIGHT w = msa.GetSeqWeight(uSeqIndex1);
Freqs[uLetter] += w;
Score -= w*w*Mx[uLetter][uLetter];
}
for (unsigned uLetter1 = 0; uLetter1 < g_AlphaSize; ++uLetter1)
{
const FCOUNT f1 = Freqs[uLetter1];
Score += f1*f1*Mx[uLetter1][uLetter1];
for (unsigned uLetter2 = uLetter1 + 1; uLetter2 < g_AlphaSize; ++uLetter2)
{
const FCOUNT f2 = Freqs[uLetter2];
Score += 2*f1*f2*Mx[uLetter1][uLetter2];
}
}
Score /= 2;
#if BRUTE_LETTERS
assert(BTEq(BruteScore, Score));
#endif
return Score;
}
