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#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;
}
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