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

#include "muscle.h"
#include "msa.h"
#include "objscore.h"

#define TRACE   0

struct GAPINFO
        {
        GAPINFO *Next;
        unsigned Start;
        unsigned End;
        };

static GAPINFO **g_Gaps;
static GAPINFO *g_FreeList;
static unsigned g_MaxSeqCount;
static unsigned g_MaxColCount;
static unsigned g_ColCount;
static bool *g_ColDiff;

static GAPINFO *NewGapInfo()
        {
        if (0 == g_FreeList)
                {
                const int NEWCOUNT = 256;
                GAPINFO *NewList = new GAPINFO[NEWCOUNT];
                g_FreeList = &NewList[0];
                for (int i = 0; i < NEWCOUNT-1; ++i)
                        NewList[i].Next = &NewList[i+1];
                NewList[NEWCOUNT-1].Next = 0;
                }
        GAPINFO *GI = g_FreeList;
        g_FreeList = g_FreeList->Next;
        return GI;
        }

static void FreeGapInfo(GAPINFO *GI)
        {
        GI->Next = g_FreeList;
        g_FreeList = GI;
        }

// TODO: This could be much faster, no need to look
// at all columns.
static void FindIntersectingGaps(const MSA &msa, unsigned SeqIndex)
        {
        const unsigned ColCount = msa.GetColCount();
        bool InGap = false;
        bool Intersects = false;
        unsigned Start = uInsane;
        for (unsigned Col = 0; Col <= ColCount; ++Col)
                {
                bool Gap = ((Col != ColCount) && msa.IsGap(SeqIndex, Col));
                if (Gap)
                        {
                        if (!InGap)
                                {
                                InGap = true;
                                Start = Col;
                                }
                        if (g_ColDiff[Col])
                                Intersects = true;
                        }
                else if (InGap)
                        {
                        InGap = false;
                        if (Intersects)
                                {
                                GAPINFO *GI = NewGapInfo();
                                GI->Start = Start;
                                GI->End = Col - 1;
                                GI->Next = g_Gaps[SeqIndex];
                                g_Gaps[SeqIndex] = GI;
                                }
                        Intersects = false;
                        }
                }
        }

static SCORE Penalty(unsigned Length, bool Term)
        {
        if (0 == Length)
                return 0;
        SCORE s1 = g_scoreGapOpen + g_scoreGapExtend*(Length - 1);
#if     DOUBLE_AFFINE
        SCORE s2 = g_scoreGapOpen2 + g_scoreGapExtend2*(Length - 1);
        if (s1 > s2)
                return s1;
        return s2;
#else
        return s1;
#endif
        }

//static SCORE ScorePair(unsigned Seq1, unsigned Seq2)
//      {
//#if   TRACE
//      {
//      Log("ScorePair(%d,%d)\n", Seq1, Seq2);
//      Log("Gaps seq 1: ");
//      for (GAPINFO *GI = g_Gaps[Seq1]; GI; GI = GI->Next)
//              Log(" %d-%d", GI->Start, GI->End);
//      Log("\n");
//      Log("Gaps seq 2: ");
//      for (GAPINFO *GI = g_Gaps[Seq2]; GI; GI = GI->Next)
//              Log(" %d-%d", GI->Start, GI->End);
//      Log("\n");
//      }
//#endif
//      return 0;
//      }

SCORE ScoreGaps(const MSA &msa, const unsigned DiffCols[], unsigned DiffColCount)
        {
#if     TRACE
        {
        Log("ScoreGaps\n");
        Log("DiffCols ");
        for (unsigned i = 0; i < DiffColCount; ++i)
                Log(" %u", DiffCols[i]);
        Log("\n");
        Log("msa=\n");
        msa.LogMe();
        Log("\n");
        }
#endif
        const unsigned SeqCount = msa.GetSeqCount();
        const unsigned ColCount = msa.GetColCount();
        g_ColCount = ColCount;

        if (SeqCount > g_MaxSeqCount)
                {
                delete[] g_Gaps;
                g_MaxSeqCount = SeqCount + 256;
                g_Gaps = new GAPINFO *[g_MaxSeqCount];
                }
        memset(g_Gaps, 0, SeqCount*sizeof(GAPINFO *));

        if (ColCount > g_MaxColCount)
                {
                delete[] g_ColDiff;
                g_MaxColCount = ColCount + 256;
                g_ColDiff = new bool[g_MaxColCount];
                }

        memset(g_ColDiff, 0, g_ColCount*sizeof(bool));
        for (unsigned i = 0; i < DiffColCount; ++i)
                {
                unsigned Col = DiffCols[i];
                assert(Col < ColCount);
                g_ColDiff[Col] = true;
                }

        for (unsigned SeqIndex = 0; SeqIndex < SeqCount; ++SeqIndex)
                FindIntersectingGaps(msa, SeqIndex);

#if     TRACE
        {
        Log("\n");
        Log("Intersecting gaps:\n");
        Log("      ");
        for (unsigned Col = 0; Col < ColCount; ++Col)
                Log("%c", g_ColDiff[Col] ? '*' : ' ');
        Log("\n");
        Log("      ");
        for (unsigned Col = 0; Col < ColCount; ++Col)
                Log("%d", Col%10);
        Log("\n");
        for (unsigned Seq = 0; Seq < SeqCount; ++Seq)
                {
                Log("%3d:  ", Seq);
                for (unsigned Col = 0; Col < ColCount; ++Col)
                        Log("%c", msa.GetChar(Seq, Col));
                Log("  :: ");
                for (GAPINFO *GI = g_Gaps[Seq]; GI; GI = GI->Next)
                        Log(" (%d,%d)", GI->Start, GI->End);
                Log("  >%s\n", msa.GetSeqName(Seq));
                }
        Log("\n");
        }
#endif

        SCORE Score = 0;
        for (unsigned Seq1 = 0; Seq1 < SeqCount; ++Seq1)
                {
                const WEIGHT w1 = msa.GetSeqWeight(Seq1);
                for (unsigned Seq2 = Seq1 + 1; Seq2 < SeqCount; ++Seq2)
                        {
                        const WEIGHT w2 = msa.GetSeqWeight(Seq2);
//                      const SCORE Pair = ScorePair(Seq1, Seq2);
                        const SCORE Pair = ScoreSeqPairGaps(msa, Seq1, msa, Seq2);
                        Score += w1*w2*Pair;
#if     TRACE
                        Log("Seq1=%u Seq2=%u ScorePair=%.4g w1=%.4g w2=%.4g Sum=%.4g\n",
                          Seq1, Seq2, Pair, w1, w2, Score);
#endif
                        }
                }

        return Score;
        }