Esempi in C++ (Cpp) per TextFile::SetPos

Esempio n. 1

File: qscore_seq.cpp Progetto: ggrekhov/ugene

// 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();
		}
	}

Esempio n. 2

File: seq.cpp Progetto: bigmuscle/bigmuscle

// 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();
		}
	}