// Return true on end-of-file
bool Seq::FromFASTAFile(TextFile &File)
{
Clear();
char szLine[MAX_FASTA_LINE];
bool bEof = File.GetLine(szLine, sizeof(szLine));
if (bEof)
return true;
if ('>' != szLine[0])
Quit_Qscore("Expecting '>' in FASTA file %s line %u",
File.GetFileName(), File.GetLineNr());
// Truncate name at first blank
// TODO: This is a hack because readseq does MSF -> FASTA
// conversion in a very strange way with the annotation.
//char *ptrBlank = strchr(szLine, ' ');
//if (0 != ptrBlank)
// *ptrBlank = 0;
size_t n = strlen(szLine);
if (1 == n)
Quit_Qscore("Missing name following '>' in FASTA file %s line %u",
File.GetFileName(), File.GetLineNr());
m_ptrName = new char[n];
strcpy(m_ptrName, szLine + 1);
TEXTFILEPOS Pos = File.GetPos();
for (;;)
{
bEof = File.GetLine(szLine, sizeof(szLine));
if (bEof)
{
if (0 == size())
{
Quit_Qscore("Empty sequence in FASTA file %s line %u",
File.GetFileName(), File.GetLineNr());
return true;
}
return false;
}
if ('>' == szLine[0])
{
if (0 == size())
Quit_Qscore("Empty sequence in FASTA file %s line %u",
File.GetFileName(), File.GetLineNr());
// Rewind to beginning of this line, it's the start of the
// next sequence.
File.SetPos(Pos);
return false;
}
const char *ptrChar = szLine;
while (char c = *ptrChar++)
push_back(c);
Pos = File.GetPos();
}
}
// Return true on end-of-file
bool Seq::FromFASTAFile(TextFile &File)
{
Clear();
char szLine[MAX_FASTA_LINE];
bool bEof = File.GetLine(szLine, sizeof(szLine));
if (bEof)
return true;
if ('>' != szLine[0])
Quit("Expecting '>' in FASTA file %s line %u",
File.GetFileName(), File.GetLineNr());
size_t n = strlen(szLine);
if (1 == n)
Quit("Missing annotation following '>' in FASTA file %s line %u",
File.GetFileName(), File.GetLineNr());
m_ptrName = new char[n];
strcpy(m_ptrName, szLine + 1);
TEXTFILEPOS Pos = File.GetPos();
for (;;)
{
bEof = File.GetLine(szLine, sizeof(szLine));
if (bEof)
{
if (0 == size())
{
Quit("Empty sequence in FASTA file %s line %u",
File.GetFileName(), File.GetLineNr());
return true;
}
return false;
}
if ('>' == szLine[0])
{
if (0 == size())
Quit("Empty sequence in FASTA file %s line %u",
File.GetFileName(), File.GetLineNr());
// Rewind to beginning of this line, it's the start of the
// next sequence.
File.SetPos(Pos);
return false;
}
const char *ptrChar = szLine;
while (char c = *ptrChar++)
{
if (isspace(c))
continue;
if (IsGapChar(c))
continue;
if (!IsResidueChar(c))
{
if (isprint(c))
{
char w = GetWildcardChar();
Warning("Invalid residue '%c' in FASTA file %s line %d, replaced by '%c'",
c, File.GetFileName(), File.GetLineNr(), w);
c = w;
}
else
Quit("Invalid byte hex %02x in FASTA file %s line %d",
(unsigned char) c, File.GetFileName(), File.GetLineNr());
}
c = toupper(c);
push_back(c);
}
Pos = File.GetPos();
}
}