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#include "muscle.h"
#include "msa.h"
#include "profile.h"
#define TRACE 0
static void LogF(FCOUNT f)
{
if (f > -0.00001 && f < 0.00001)
Log(" ");
else
Log(" %5.3f", f);
}
static const char *LocalScoreToStr(SCORE s)
{
static char str[16];
if (s < -1e10 || s > 1e10)
return " *";
sprintf(str, "%5.1f", s);
return str;
}
#if DOUBLE_AFFINE
void ListProfile(const ProfPos *Prof, unsigned uLength, const MSA *ptrMSA)
{
Log(" Pos Occ LL LG GL GG Open Close Open2 Clos2\n");
Log(" --- --- -- -- -- -- ---- ----- ----- -----\n");
for (unsigned n = 0; n < uLength; ++n)
{
const ProfPos &PP = Prof[n];
Log("%5u", n);
LogF(PP.m_fOcc);
LogF(PP.m_LL);
LogF(PP.m_LG);
LogF(PP.m_GL);
LogF(PP.m_GG);
Log(" %s", LocalScoreToStr(-PP.m_scoreGapOpen));
Log(" %s", LocalScoreToStr(-PP.m_scoreGapClose));
Log(" %s", LocalScoreToStr(-PP.m_scoreGapOpen2));
Log(" %s", LocalScoreToStr(-PP.m_scoreGapClose2));
if (0 != ptrMSA)
{
const unsigned uSeqCount = ptrMSA->GetSeqCount();
Log(" ");
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
Log("%c", ptrMSA->GetChar(uSeqIndex, n));
}
Log("\n");
}
Log("\n");
Log(" Pos G");
for (unsigned n = 0; n < g_AlphaSize; ++n)
Log(" %c", LetterExToChar(n));
Log("\n");
Log(" --- -");
for (unsigned n = 0; n < g_AlphaSize; ++n)
Log(" -----");
Log("\n");
for (unsigned n = 0; n < uLength; ++n)
{
const ProfPos &PP = Prof[n];
Log("%5u", n);
if (-1 == PP.m_uResidueGroup)
Log(" -", PP.m_uResidueGroup);
else
Log(" %d", PP.m_uResidueGroup);
for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter)
{
FCOUNT f = PP.m_fcCounts[uLetter];
if (f == 0.0)
Log(" ");
else
Log(" %5.3f", f);
}
if (0 != ptrMSA)
{
const unsigned uSeqCount = ptrMSA->GetSeqCount();
Log(" ");
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
Log("%c", ptrMSA->GetChar(uSeqIndex, n));
}
Log("\n");
}
}
#endif // DOUBLE_AFFINE
#if SINGLE_AFFINE
void ListProfile(const ProfPos *Prof, unsigned uLength, const MSA *ptrMSA)
{
Log(" Pos Occ LL LG GL GG Open Close\n");
Log(" --- --- -- -- -- -- ---- -----\n");
for (unsigned n = 0; n < uLength; ++n)
{
const ProfPos &PP = Prof[n];
Log("%5u", n);
LogF(PP.m_fOcc);
LogF(PP.m_LL);
LogF(PP.m_LG);
LogF(PP.m_GL);
LogF(PP.m_GG);
Log(" %5.1f", -PP.m_scoreGapOpen);
Log(" %5.1f", -PP.m_scoreGapClose);
if (0 != ptrMSA)
{
const unsigned uSeqCount = ptrMSA->GetSeqCount();
Log(" ");
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
Log("%c", ptrMSA->GetChar(uSeqIndex, n));
}
Log("\n");
}
Log("\n");
Log(" Pos G");
for (unsigned n = 0; n < g_AlphaSize; ++n)
Log(" %c", LetterExToChar(n));
Log("\n");
Log(" --- -");
for (unsigned n = 0; n < g_AlphaSize; ++n)
Log(" -----");
Log("\n");
for (unsigned n = 0; n < uLength; ++n)
{
const ProfPos &PP = Prof[n];
Log("%5u", n);
if (-1 == PP.m_uResidueGroup)
Log(" -", PP.m_uResidueGroup);
else
Log(" %d", PP.m_uResidueGroup);
for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter)
{
FCOUNT f = PP.m_fcCounts[uLetter];
if (f == 0.0)
Log(" ");
else
Log(" %5.3f", f);
}
if (0 != ptrMSA)
{
const unsigned uSeqCount = ptrMSA->GetSeqCount();
Log(" ");
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
Log("%c", ptrMSA->GetChar(uSeqIndex, n));
}
Log("\n");
}
}
#endif
void SortCounts(const FCOUNT fcCounts[], unsigned SortOrder[])
{
static unsigned InitialSortOrder[MAX_ALPHA] =
{
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19
};
memcpy(SortOrder, InitialSortOrder, g_AlphaSize*sizeof(unsigned));
bool bAny = true;
while (bAny)
{
bAny = false;
for (unsigned n = 0; n < g_AlphaSize - 1; ++n)
{
unsigned i1 = SortOrder[n];
unsigned i2 = SortOrder[n+1];
if (fcCounts[i1] < fcCounts[i2])
{
SortOrder[n+1] = i1;
SortOrder[n] = i2;
bAny = true;
}
}
}
}
static unsigned AminoGroupFromFCounts(const FCOUNT fcCounts[])
{
bool bAny = false;
unsigned uConsensusResidueGroup = RESIDUE_GROUP_MULTIPLE;
for (unsigned uLetter = 0; uLetter < 20; ++uLetter)
{
if (0 == fcCounts[uLetter])
continue;
const unsigned uResidueGroup = ResidueGroup[uLetter];
if (bAny)
{
if (uResidueGroup != uConsensusResidueGroup)
return RESIDUE_GROUP_MULTIPLE;
}
else
{
bAny = true;
uConsensusResidueGroup = uResidueGroup;
}
}
return uConsensusResidueGroup;
}
static unsigned NucleoGroupFromFCounts(const FCOUNT fcCounts[])
{
bool bAny = false;
unsigned uConsensusResidueGroup = RESIDUE_GROUP_MULTIPLE;
for (unsigned uLetter = 0; uLetter < 4; ++uLetter)
{
if (0 == fcCounts[uLetter])
continue;
const unsigned uResidueGroup = uLetter;
if (bAny)
{
if (uResidueGroup != uConsensusResidueGroup)
return RESIDUE_GROUP_MULTIPLE;
}
else
{
bAny = true;
uConsensusResidueGroup = uResidueGroup;
}
}
return uConsensusResidueGroup;
}
unsigned ResidueGroupFromFCounts(const FCOUNT fcCounts[])
{
switch (g_Alpha)
{
case ALPHA_Amino:
return AminoGroupFromFCounts(fcCounts);
case ALPHA_DNA:
case ALPHA_RNA:
return NucleoGroupFromFCounts(fcCounts);
}
Quit("ResidueGroupFromFCounts: bad alpha");
return 0;
}
ProfPos *ProfileFromMSA(const MSA &a)
{
const unsigned uSeqCount = a.GetSeqCount();
const unsigned uColCount = a.GetColCount();
// Yuck -- cast away const (inconsistent design here).
SetMSAWeightsMuscle((MSA &) a);
ProfPos *Pos = new ProfPos[uColCount];
unsigned uHydrophobicRunLength = 0;
for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
{
ProfPos &PP = Pos[uColIndex];
PP.m_bAllGaps = a.IsGapColumn(uColIndex);
FCOUNT fcGapStart;
FCOUNT fcGapEnd;
FCOUNT fcGapExtend;
FCOUNT fOcc;
a.GetFractionalWeightedCounts(uColIndex, g_bNormalizeCounts, PP.m_fcCounts,
&fcGapStart, &fcGapEnd, &fcGapExtend, &fOcc,
&PP.m_LL, &PP.m_LG, &PP.m_GL, &PP.m_GG);
PP.m_fOcc = fOcc;
SortCounts(PP.m_fcCounts, PP.m_uSortOrder);
PP.m_uResidueGroup = ResidueGroupFromFCounts(PP.m_fcCounts);
for (unsigned i = 0; i < g_AlphaSize; ++i)
{
SCORE scoreSum = 0;
for (unsigned j = 0; j < g_AlphaSize; ++j)
scoreSum += PP.m_fcCounts[j]*(*g_ptrScoreMatrix)[i][j];
PP.m_AAScores[i] = scoreSum;
}
SCORE sStartOcc = (SCORE) (1.0 - fcGapStart);
SCORE sEndOcc = (SCORE) (1.0 - fcGapEnd);
PP.m_fcStartOcc = sStartOcc;
PP.m_fcEndOcc = sEndOcc;
PP.m_scoreGapOpen = sStartOcc*g_scoreGapOpen/2;
PP.m_scoreGapClose = sEndOcc*g_scoreGapOpen/2;
#if DOUBLE_AFFINE
PP.m_scoreGapOpen2 = sStartOcc*g_scoreGapOpen2/2;
PP.m_scoreGapClose2 = sEndOcc*g_scoreGapOpen2/2;
#endif
// PP.m_scoreGapExtend = (SCORE) ((1.0 - fcGapExtend)*scoreGapExtend);
#if PAF
if (ALHPA_Amino == g_Alpha && sStartOcc > 0.5)
{
extern SCORE PAFactor(const FCOUNT fcCounts[]);
SCORE paf = PAFactor(PP.m_fcCounts);
PP.m_scoreGapOpen *= paf;
PP.m_scoreGapClose *= paf;
}
#endif
}
#if HYDRO
if (ALPHA_Amino == g_Alpha)
Hydro(Pos, uColCount);
#endif
#if TRACE
{
Log("ProfileFromMSA\n");
ListProfile(Pos, uColCount, &a);
}
#endif
return Pos;
}
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