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#include "muscle.h"
#include "msa.h"
#include "objscore.h"
#include "profile.h"
SCORE ObjScore(const MSA &msa, const unsigned SeqIndexes1[],
unsigned uSeqCount1, const unsigned SeqIndexes2[], unsigned uSeqCount2)
{
const unsigned uSeqCount = msa.GetSeqCount();
OBJSCORE OS = g_ObjScore;
if (g_ObjScore == OBJSCORE_SPM)
{
if (uSeqCount <= 100)
OS = OBJSCORE_XP;
else
OS = OBJSCORE_SPF;
}
MSA msa1;
MSA msa2;
switch (OS)
{
case OBJSCORE_DP:
case OBJSCORE_XP:
MSAFromSeqSubset(msa, SeqIndexes1, uSeqCount1, msa1);
MSAFromSeqSubset(msa, SeqIndexes2, uSeqCount2, msa2);
SetMSAWeightsMuscle(msa1);
SetMSAWeightsMuscle(msa2);
break;
case OBJSCORE_SP:
case OBJSCORE_SPF:
case OBJSCORE_PS:
// Yuck -- casting away const (design flaw)
SetMSAWeightsMuscle((MSA &) msa);
break;
}
switch (OS)
{
case OBJSCORE_SP:
return ObjScoreSP(msa);
case OBJSCORE_DP:
return ObjScoreDP(msa1, msa2);
case OBJSCORE_XP:
return ObjScoreXP(msa1, msa2);
case OBJSCORE_PS:
return ObjScorePS(msa);
case OBJSCORE_SPF:
return ObjScoreSPDimer(msa);
}
Quit("Invalid g_ObjScore=%d", g_ObjScore);
return 0;
}
SCORE ObjScoreIds(const MSA &msa, const unsigned Ids1[],
unsigned uCount1, const unsigned Ids2[], unsigned uCount2)
{
unsigned *SeqIndexes1 = new unsigned[uCount1];
unsigned *SeqIndexes2 = new unsigned[uCount2];
for (unsigned n = 0; n < uCount1; ++n)
SeqIndexes1[n] = msa.GetSeqIndex(Ids1[n]);
for (unsigned n = 0; n < uCount2; ++n)
SeqIndexes2[n] = msa.GetSeqIndex(Ids2[n]);
SCORE dObjScore = ObjScore(msa, SeqIndexes1, uCount1, SeqIndexes2, uCount2);
delete[] SeqIndexes1;
delete[] SeqIndexes2;
return dObjScore;
}
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