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#include "muscle.h"
#include "profile.h"
#include "pwpath.h"
SCORE FastScorePath2(const ProfPos *PA, unsigned uLengthA,
const ProfPos *PB, unsigned uLengthB, const PWPath &Path)
{
const unsigned uEdgeCount = Path.GetEdgeCount();
Log("Edge SS PLA PLB Match Gap Total\n");
Log("---- -- --- --- ----- --- -----\n");
char cType = 'S';
SCORE scoreTotal = 0;
for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
{
const PWEdge &Edge = Path.GetEdge(uEdgeIndex);
const char cPrevType = cType;
cType = Edge.cType;
const unsigned uPrefixLengthA = Edge.uPrefixLengthA;
const unsigned uPrefixLengthB = Edge.uPrefixLengthB;
bool bGap = false;
bool bMatch = false;
SCORE scoreGap = 0;
SCORE scoreMatch = 0;
switch (cType)
{
case 'M':
{
if (0 == uPrefixLengthA || 0 == uPrefixLengthB)
Quit("FastScorePath2, M zero length");
const ProfPos &PPA = PA[uPrefixLengthA - 1];
const ProfPos &PPB = PB[uPrefixLengthB - 1];
bMatch = true;
scoreMatch = ScoreProfPos2(PPA, PPB);
if ('D' == cPrevType)
{
bGap = true;
assert(uPrefixLengthA > 1);
scoreGap = PA[uPrefixLengthA-2].m_scoreGapClose;
}
else if ('I' == cPrevType)
{
bGap = true;
assert(uPrefixLengthB > 1);
scoreGap = PB[uPrefixLengthB-2].m_scoreGapClose;
}
break;
}
case 'D':
{
if (0 == uPrefixLengthA)
Quit("FastScorePath2, D zero length");
const ProfPos &PPA = PA[uPrefixLengthA - 1];
bGap = true;
switch (cPrevType)
{
case 'S':
scoreGap = PPA.m_scoreGapOpen;
break;
case 'M':
scoreGap = PPA.m_scoreGapOpen;
break;
case 'D':
// scoreGap = g_scoreGapExtend;
scoreGap = 0;
break;
case 'I':
Quit("FastScorePath2 DI");
}
break;
}
case 'I':
{
if (0 == uPrefixLengthB)
Quit("FastScorePath2, I zero length");
const ProfPos &PPB = PB[uPrefixLengthB - 1];
bGap = true;
switch (cPrevType)
{
case 'S':
scoreGap = PPB.m_scoreGapOpen;
break;
case 'M':
scoreGap = PPB.m_scoreGapOpen;
break;
case 'I':
scoreGap = 0;
// scoreGap = g_scoreGapExtend;
break;
case 'D':
Quit("FastScorePath2 DI");
}
break;
}
case 'U':
{
Quit("FastScorePath2 U");
}
default:
Quit("FastScorePath2: invalid type %c", cType);
}
Log("%4u %c%c %4u %4u ", uEdgeIndex, cPrevType, cType,
uPrefixLengthA, uPrefixLengthB);
if (bMatch)
Log("%7.1f ", scoreMatch);
else
Log(" ");
if (bGap)
Log("%7.1f ", scoreGap);
else
Log(" ");
SCORE scoreEdge = scoreMatch + scoreGap;
scoreTotal += scoreEdge;
Log("%7.1f %7.1f", scoreEdge, scoreTotal);
Log("\n");
}
SCORE scoreGap = 0;
// if (!g_bTermGapsHalf)
switch (cType)
{
case 'M':
scoreGap = 0;
break;
case 'D':
{
const ProfPos &LastPPA = PA[uLengthA - 1];
scoreGap = LastPPA.m_scoreGapClose;
break;
}
case 'I':
{
const ProfPos &LastPPB = PB[uLengthB - 1];
scoreGap = LastPPB.m_scoreGapClose;
break;
}
case 'U':
Quit("Unaligned regions not supported");
case 'S':
break;
default:
Quit("Invalid type %c", cType);
}
Log(" %cE %4u %4u %7.1f\n", cType, uLengthA, uLengthB, scoreGap);
scoreTotal += scoreGap;
Log("Total = %g\n", scoreTotal);
return scoreTotal;
}
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