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#include "muscle.h"
#include "pwpath.h"
#include "timing.h"
#include "textfile.h"
#include "msa.h"
#include "profile.h"
#if !VER_3_52
#define COMPARE_SIMPLE 0
#if TIMING
TICKS g_ticksDP = 0;
#endif
#if 1
extern bool g_bKeepSimpleDP;
SCORE NWSmall(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path);
SCORE NWDASmall(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path);
SCORE NWDASimple(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path);
SCORE NWDASimple2(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path);
SCORE GlobalAlignSimple(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path);
SCORE GlobalAlignNoDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path)
{
return GlobalAlign(PA, uLengthA, PB, uLengthB, Path);
}
#if COMPARE_SIMPLE
SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path)
{
#if TIMING
TICKS t1 = GetClockTicks();
#endif
g_bKeepSimpleDP = true;
PWPath SimplePath;
GlobalAlignSimple(PA, uLengthA, PB, uLengthB, SimplePath);
SCORE Score = NWSmall(PA, uLengthA, PB, uLengthB, Path);
if (!Path.Equal(SimplePath))
{
Log("Simple:\n");
SimplePath.LogMe();
Log("Small:\n");
Path.LogMe();
Quit("Paths differ");
}
#if TIMING
TICKS t2 = GetClockTicks();
g_ticksDP += (t2 - t1);
#endif
return Score;
}
#else // COMPARE_SIMPLE
SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path)
{
#if TIMING
TICKS t1 = GetClockTicks();
#endif
SCORE Score = NWSmall(PA, uLengthA, PB, uLengthB, Path);
#if TIMING
TICKS t2 = GetClockTicks();
g_ticksDP += (t2 - t1);
#endif
return Score;
}
#endif
#else // 1
static void AllInserts(PWPath &Path, unsigned uLengthB)
{
Path.Clear();
PWEdge Edge;
Edge.cType = 'I';
Edge.uPrefixLengthA = 0;
for (unsigned uPrefixLengthB = 1; uPrefixLengthB <= uLengthB; ++uPrefixLengthB)
{
Edge.uPrefixLengthB = uPrefixLengthB;
Path.AppendEdge(Edge);
}
}
static void AllDeletes(PWPath &Path, unsigned uLengthA)
{
Path.Clear();
PWEdge Edge;
Edge.cType = 'D';
Edge.uPrefixLengthB = 0;
for (unsigned uPrefixLengthA = 1; uPrefixLengthA <= uLengthA; ++uPrefixLengthA)
{
Edge.uPrefixLengthA = uPrefixLengthA;
Path.AppendEdge(Edge);
}
}
SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path)
{
#if TIMING
TICKS t1 = GetClockTicks();
#endif
if (0 == uLengthA)
{
AllInserts(Path, uLengthB);
return 0;
}
else if (0 == uLengthB)
{
AllDeletes(Path, uLengthA);
return 0;
}
SCORE Score = 0;
if (g_bDiags)
Score = GlobalAlignDiags(PA, uLengthA, PB, uLengthB, Path);
else
Score = GlobalAlignNoDiags(PA, uLengthA, PB, uLengthB, Path);
#if TIMING
TICKS t2 = GetClockTicks();
g_ticksDP += (t2 - t1);
#endif
return Score;
}
SCORE GlobalAlignNoDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path)
{
if (g_bDimer)
return GlobalAlignDimer(PA, uLengthA, PB, uLengthB, Path);
switch (g_PPScore)
{
case PPSCORE_LE:
return GlobalAlignLE(PA, uLengthA, PB, uLengthB, Path);
case PPSCORE_SP:
case PPSCORE_SV:
return GlobalAlignSP(PA, uLengthA, PB, uLengthB, Path);
case PPSCORE_SPN:
return GlobalAlignSPN(PA, uLengthA, PB, uLengthB, Path);
}
Quit("Invalid PP score (GlobalAlignNoDiags)");
return 0;
}
#endif
#endif // !VER_3_52
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