source: branches/profile/GDE/MUSCLE/src/mhack.cpp

#include "muscle.h"
#include "seqvect.h"
#include "msa.h"

/***
Methionine hack.
Most proteins start with M.
This results in odd-looking alignments with the terminal Ms aligned followed
immediately by gaps.
Hack this by treating terminal M like X.
***/

static bool *M;

void MHackStart(SeqVect &v)
        {
        if (ALPHA_Amino != g_Alpha)
                return;

        const unsigned uSeqCount = v.Length();
        M = new bool[uSeqCount];
        memset(M, 0, uSeqCount*sizeof(bool));
        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                {
                Seq &s = v.GetSeq(uSeqIndex);
                if (0 == s.Length())
                        continue;
                unsigned uId = s.GetId();
                if (s[0] == 'M' || s[0] == 'm')
                        {
                        M[uId] = true;
                        s[0] = 'X';
                        }
                }
        }

void MHackEnd(MSA &msa)
        {
        if (ALPHA_Amino != g_Alpha)
                return;
        if (0 == M)
                return;

        const unsigned uSeqCount = msa.GetSeqCount();
        const unsigned uColCount = msa.GetColCount();
        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                {
                unsigned uId = msa.GetSeqId(uSeqIndex);
                if (M[uId])
                        {
                        for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
                                {
                                if (!msa.IsGap(uSeqIndex, uColIndex))
                                        {
                                        msa.SetChar(uSeqIndex, uColIndex, 'M');
                                        break;
                                        }
                                }
                        }
                }

        delete[] M;
        M = 0;
        }