source: branches/stable/GDE/MUSCLE/src/msf.cpp

#include "muscle.h"
#include <stdio.h>
#include <ctype.h>
#include "msa.h"
#include "textfile.h"

const int MAX_NAME = 63;

const unsigned uCharsPerLine = 50;
const unsigned uCharsPerBlock = 10;

// Truncate at first white space or MAX_NAME, whichever comes
// first, then pad with blanks up to PadLength.
static const char *GetPaddedName(const char *Name, int PadLength)
        {
        static char PaddedName[MAX_NAME+1];
        memset(PaddedName, ' ', MAX_NAME);
        size_t n = strcspn(Name, " \t");
        memcpy(PaddedName, Name, n);
        PaddedName[PadLength] = 0;
        return PaddedName;
        }

static const char *strfind(const char *s, const char *t)
        {
        size_t n = strcspn(s, t);
        if (0 == n)
                return 0;
        return s + n;
        }

// GCG checksum code kindly provided by Eric Martel.
unsigned MSA::GetGCGCheckSum(unsigned uSeqIndex) const
        {
        unsigned CheckSum = 0;
        const unsigned uColCount = GetColCount();
        for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
                {
                unsigned c = (unsigned) GetChar(uSeqIndex, uColIndex);
                CheckSum += c*(uColIndex%57 + 1);
                CheckSum %= 10000;              
                }
        return CheckSum;
        }

static void MSFFixGaps(MSA &a)
        {
        const int SeqCount = a.GetSeqCount();
        const int ColCount = a.GetColCount();
        for (int SeqIndex = 0; SeqIndex < SeqCount; ++SeqIndex)
                {
                for (int ColIndex = 0; ColIndex < ColCount; ++ColIndex)
                        if (a.IsGap(SeqIndex, ColIndex))
                                a.SetChar(SeqIndex, ColIndex, '.');
                }
        }

void MSA::ToMSFFile(TextFile &File, const char *ptrComment) const
        {
// Cast away const, yuck
        SetMSAWeightsMuscle((MSA &) *this);
        MSFFixGaps((MSA &) *this);

        File.PutString("PileUp\n");
        
        if (0 != ptrComment)
                File.PutFormat("Comment: %s\n", ptrComment);
        else
                File.PutString("\n");

        char seqtype = (g_Alpha == ALPHA_DNA || g_Alpha == ALPHA_RNA) ? 'N' : 'A';
        File.PutFormat("  MSF: %u  Type: %c  Check: 0000  ..\n\n",
          GetColCount(), seqtype);

        int iLongestNameLength = 0;
        for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)
                {
                const char *Name = GetSeqName(uSeqIndex);
                const char *PaddedName = GetPaddedName(Name, MAX_NAME);
                int iLength = (int) strcspn(PaddedName, " \t");
                if (iLength > iLongestNameLength)
                        iLongestNameLength = iLength;
                }
                
        for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)
                {
                const char *Name = GetSeqName(uSeqIndex);
                const char *PaddedName = GetPaddedName(Name, iLongestNameLength);
                File.PutFormat(" Name: %s", PaddedName);
                File.PutFormat("  Len: %u  Check: %5u  Weight: %g\n",
                  GetColCount(), GetGCGCheckSum(uSeqIndex), GetSeqWeight(uSeqIndex));
                }
        File.PutString("\n//\n");
        if (0 == GetColCount())
                return;

        unsigned uLineCount = (GetColCount() - 1)/uCharsPerLine + 1;
        for (unsigned uLineIndex = 0; uLineIndex < uLineCount; ++uLineIndex)
                {
                File.PutString("\n");
                unsigned uStartColIndex = uLineIndex*uCharsPerLine;
                unsigned uEndColIndex = uStartColIndex + uCharsPerLine - 1;
                if (uEndColIndex >= GetColCount())
                        uEndColIndex = GetColCount() - 1;
                for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)
                        {
                        const char *Name = GetSeqName(uSeqIndex);
                        const char *PaddedName = GetPaddedName(Name, iLongestNameLength);
                        File.PutFormat("%s   ", PaddedName);
                        for (unsigned uColIndex = uStartColIndex; uColIndex <= uEndColIndex;
                          ++uColIndex)
                                {
                                if (0 == uColIndex%uCharsPerBlock)
                                        File.PutString(" ");
                                char c = GetChar(uSeqIndex, uColIndex);
                                File.PutFormat("%c", c);
                                }
                        File.PutString("\n");
                        }
                }
        }