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#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");
}
}
}
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