source: branches/lib/GDE/MUSCLE/src/glbalign.cpp

#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