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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/msa.h"
#include "libMUSCLE/textfile.h"
namespace muscle {
const int BLOCKSIZE = 60;
static char FixChar(char c)
{
switch (c)
{
case '(':
case ')':
case '[':
case ']':
case ':':
case ';':
case ',':
return '_';
}
if (!isprint(c))
return '_';
return c;
}
static void FixName(char Name[])
{
while (char c = *Name)
*Name++ = FixChar(c);
}
void MSA::ToPhySequentialFile(TextFile &File) const
{
const unsigned SeqCount = GetSeqCount();
const unsigned ColCount = GetColCount();
File.PutFormat("%d %d\n", SeqCount, ColCount);
if (0 == ColCount)
return;
for (unsigned Seq = 0; Seq < SeqCount; ++Seq)
{
char Name[11];
const char *ptrName = GetSeqName(Seq);
size_t n = strlen(ptrName);
if (n > 10)
n = 10;
memcpy(Name, ptrName, n);
Name[n] = 0;
FixName(Name);
File.PutFormat("%-10.10s", Name);
int BlockIndex = 0;
int Col = 0;
for (;;)
{
const unsigned MaxCols = (BlockIndex == 0) ? (BLOCKSIZE - 10) : BLOCKSIZE;
for (unsigned ColsThisBlock = 0; ColsThisBlock < MaxCols; ++ColsThisBlock)
{
if (Col == ColCount)
break;
if (ColsThisBlock%10 == 0 && (BlockIndex == 0 || ColsThisBlock > 0))
File.PutChar(' ');
char c = GetChar(Seq, Col);
if (isalpha(c))
c = toupper(c);
File.PutChar(c);
++Col;
}
File.PutChar('\n');
if (Col == ColCount)
break;
++BlockIndex;
}
}
}
void MSA::ToPhyInterleavedFile(TextFile &File) const
{
const unsigned SeqCount = GetSeqCount();
const unsigned ColCount = GetColCount();
File.PutFormat("%d %d\n", SeqCount, ColCount);
if (0 == ColCount)
return;
int Col = 0;
for (;;)
{
const unsigned ColBlockStart = Col;
const unsigned MaxCols = (ColBlockStart == 0) ? (BLOCKSIZE - 10) : BLOCKSIZE;
for (unsigned Seq = 0; Seq < SeqCount; ++Seq)
{
if (0 == ColBlockStart)
{
char Name[11];
const char *ptrName = GetSeqName(Seq);
size_t n = strlen(ptrName);
if (n > 10)
n = 10;
memcpy(Name, ptrName, n);
Name[n] = 0;
FixName(Name);
File.PutFormat("%-10.10s", Name);
}
Col = ColBlockStart;
for (unsigned ColsThisBlock = 0; ColsThisBlock < MaxCols; ++ColsThisBlock)
{
if (Col == ColCount)
break;
if (ColsThisBlock%10 == 0 && (0 == ColBlockStart || ColsThisBlock > 0))
File.PutChar(' ');
char c = GetChar(Seq, Col);
if (isalpha(c))
c = toupper(c);
File.PutChar(c);
++Col;
}
File.PutChar('\n');
}
if (Col == ColCount)
break;
File.PutChar('\n');
}
}
}
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