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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/textfile.h"
namespace muscle {
#define TRACE 0
const int MAX_LINE = 4096;
const int MAX_HEADINGS = 32;
static TLS<char[MAX_HEADINGS]> Heading;
static TLS<unsigned> HeadingCount(0);
static TLS<SCOREMATRIX> Mx;
static void LogMx()
{
Log("Matrix\n");
Log(" ");
for (int i = 0; i < 20; ++i)
Log(" %c", LetterToChar(i));
Log("\n");
for (int i = 0; i < 20; ++i)
{
Log("%c ", LetterToChar(i));
for (int j = 0; j < 20; ++j)
Log("%5.1f", Mx.get()[i][j]);
Log("\n");
}
Log("\n");
}
static unsigned MxCharToLetter(char c)
{
for (unsigned Letter = 0; Letter < HeadingCount.get(); ++Letter)
if (Heading.get()[Letter] == c)
return Letter;
Quit("Letter '%c' has no heading", c);
return 0;
}
DYN_PTR_SCOREMATRIX ReadMx(TextFile &File)
{
// Find column headers
char Line[MAX_LINE];
for (;;)
{
bool EndOfFile = File.GetLine(Line, sizeof(Line));
if (EndOfFile)
Quit("Premature EOF in matrix file");
if (Line[0] == '#')
continue;
else if (Line[0] == ' ')
break;
else
Quit("Invalid line in matrix file: '%s'", Line);
}
// Read column headers
HeadingCount.get() = 0;
for (char *p = Line; *p; ++p)
{
char c = *p;
if (!isspace(c))
Heading.get()[HeadingCount.get()++] = c;
}
if (HeadingCount.get() > 0 && Heading.get()[HeadingCount.get()-1] == '*')
--HeadingCount.get();
// AED 22/12/2006: don't force a 20 char matrix since nt matrices will have only 4
// if (HeadingCount.get() < 20)
// Quit("Error in matrix file: < 20 headers, line='%s'", Line);
#if TRACE
{
Log("ReadMx\n");
Log("%d headings: ", HeadingCount.get());
for (unsigned i = 0; i < HeadingCount.get(); ++i)
Log("%c", Heading.get()[i]);
Log("\n");
}
#endif
// Zero out matrix
for (int i = 0; i < MAX_ALPHA; ++i)
for (int j = 0; j < MAX_ALPHA; ++j)
Mx.get()[i][j] = 0.0;
// Read data lines
for (unsigned RowIndex = 0; RowIndex < HeadingCount.get(); ++RowIndex)
{
bool EndOfFile = File.GetTrimLine(Line, sizeof(Line));
if (EndOfFile)
Quit("Premature EOF in matrix file");
#if TRACE
Log("Line=%s\n", Line);
#endif
if (Line[0] == '#')
continue;
char c = Line[0];
#if TRACE
Log("Row char=%c\n", c);
#endif
if (!IsResidueChar(c))
continue;
unsigned RowLetter = CharToLetter(c);
if (RowLetter >= 20)
continue;
#if TRACE
Log("Row letter = %u\n", RowLetter);
#endif
char *p = Line + 1;
char *maxp = p + strlen(Line);
for (unsigned Col = 0; Col < HeadingCount.get() - 1; ++Col)
{
if (p >= maxp)
Quit("Too few fields in line of matrix file: '%s'", Line);
while (isspace(*p))
++p;
char *Value = p;
while (!isspace(*p))
++p;
float v = (float) atof(Value);
char HeaderChar = Heading.get()[Col];
if (IsResidueChar(HeaderChar))
{
unsigned ColLetter = CharToLetter(HeaderChar);
if (ColLetter >= 20)
continue;
Mx.get()[RowLetter][ColLetter] = v;
}
p += 1;
}
}
// Sanity check for symmetry
for (int i = 0; i < 20; ++i)
for (int j = 0; j < i; ++j)
{
if (Mx.get()[i][j] != Mx.get()[j][i])
{
Warning("Matrix is not symmetrical, %c->%c=%g, %c->%c=%g",
CharToLetter(i),
CharToLetter(j),
Mx.get()[i][j],
CharToLetter(j),
CharToLetter(i),
Mx.get()[j][i]);
goto ExitLoop;
}
}
ExitLoop:;
if (g_bVerbose.get())
LogMx();
SCOREMATRIX& sm = Mx.get();
return &sm;
}
}
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