C++ TextFile::PutString方法代码示例

void MSA::ToFASTAFile(TextFile &File) const
	{
	const unsigned uColCount = GetColCount();
	assert(uColCount > 0);
	const unsigned uLinesPerSeq = (GetColCount() - 1)/FASTA_BLOCK + 1;
	const unsigned uSeqCount = GetSeqCount();

	for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
		{
		File.PutString(">");
		File.PutString(GetSeqName(uSeqIndex));
		File.PutString("\n");

		unsigned n = 0;
		for (unsigned uLine = 0; uLine < uLinesPerSeq; ++uLine)
			{
			unsigned uLetters = uColCount - uLine*FASTA_BLOCK;
			if (uLetters > FASTA_BLOCK)
				uLetters = FASTA_BLOCK;
			for (unsigned i = 0; i < uLetters; ++i)
				{
				char c = GetChar(uSeqIndex, n);
				File.PutChar(c);
				++n;
				}
			File.PutChar('\n');
			}
		}
	}

void Tree::ToFileNodeRooted(TextFile &File, unsigned uNodeIndex) const
	{
	assert(IsRooted());

	bool bGroup = !IsLeaf(uNodeIndex) || IsRoot(uNodeIndex);
	if (bGroup)
		File.PutString("(\n");

	if (IsLeaf(uNodeIndex))
		File.PutString(GetName(uNodeIndex));
	else
		{
		ToFileNodeRooted(File, GetLeft(uNodeIndex));
		File.PutString(",\n");
		ToFileNodeRooted(File, GetRight(uNodeIndex));
		}

	if (bGroup)
		File.PutString(")");

	if (!IsRoot(uNodeIndex))
		{
		unsigned uParent = GetParent(uNodeIndex);
		if (HasEdgeLength(uNodeIndex, uParent))
			File.PutFormat(":%g", GetEdgeLength(uNodeIndex, uParent));
		}
	File.PutString("\n");
	}

void Seq::ToFASTAFile(TextFile &File) const
	{
	File.PutFormat(">%s\n", m_ptrName);
	unsigned uColCount = Length();
	for (unsigned n = 0; n < uColCount; ++n)
		{
		if (n > 0 && n%60 == 0)
			File.PutString("\n");
		File.PutChar(at(n));
		}
	File.PutString("\n");
	}

void Tree::ToFile(TextFile &File) const
	{
	if (IsRooted())
		{
		ToFileNodeRooted(File, m_uRootNodeIndex);
		File.PutString(";\n");
		return;
		}

// Unrooted.
	unsigned uNodeIndex = GetAnyNonLeafNode();

	File.PutString("(\n");
	ToFileNodeUnrooted(File, m_uNeighbor1[uNodeIndex], uNodeIndex);
	File.PutString(",\n");
	ToFileNodeUnrooted(File, m_uNeighbor2[uNodeIndex], uNodeIndex);
	File.PutString(",\n");
	ToFileNodeUnrooted(File, m_uNeighbor3[uNodeIndex], uNodeIndex);
	File.PutString(");\n");
	}

void Tree::ToFileNodeUnrooted(TextFile &File, unsigned uNodeIndex, unsigned uParent) const
	{
	assert(!IsRooted());

	bool bGroup = !IsLeaf(uNodeIndex);
	if (bGroup)
		File.PutString("(\n");

	if (IsLeaf(uNodeIndex))
		File.PutString(GetName(uNodeIndex));
	else
		{
		ToFileNodeUnrooted(File, GetFirstNeighbor(uNodeIndex, uParent), uNodeIndex);
		File.PutString(",\n");
		ToFileNodeUnrooted(File, GetSecondNeighbor(uNodeIndex, uParent), uNodeIndex);
		}

	if (bGroup)
		File.PutString(")");

	if (HasEdgeLength(uNodeIndex, uParent))
		File.PutFormat(":%g", GetEdgeLength(uNodeIndex, uParent));
	File.PutString("\n");
	}

void MSA::ToAlnFile(TextFile &File) const
	{
	if (getMuscleContext()->params.g_bClwStrict)
		File.PutString("CLUSTAL W (1.81) multiple sequence alignment\n");
	else
		{
		File.PutString("MUSCLE ("
		  MUSCLE_MAJOR_VERSION "." MUSCLE_MINOR_VERSION ")"
		  " multiple sequence alignment\n");
		File.PutString("\n");
		}

	int iLongestNameLength = 0;
	for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)
		{
		const char *ptrName = GetSeqName(uSeqIndex);
		const char *ptrBlank = strchr(ptrName, ' ');
		int iLength;
		if (0 != ptrBlank)
			iLength = (int) (ptrBlank - ptrName);
		else
			iLength = (int) strlen(ptrName);
		if (iLength > iLongestNameLength)
			iLongestNameLength = iLength;
		}
	if (iLongestNameLength > MAX_NAME)
		iLongestNameLength = MAX_NAME;
	if (iLongestNameLength < MIN_NAME)
		iLongestNameLength = MIN_NAME;

	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;
		char Name[MAX_NAME+1];
		for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)
			{
			const char *ptrName = GetSeqName(uSeqIndex);
			const char *ptrBlank = strchr(ptrName, ' ');
			int iLength;
			if (0 != ptrBlank)
				iLength = (int) (ptrBlank - ptrName);
			else
				iLength = (int) strlen(ptrName);
			if (iLength > MAX_NAME)
				iLength = MAX_NAME;
			memset(Name, ' ', MAX_NAME);
			memcpy(Name, ptrName, iLength);
			Name[iLongestNameLength] = 0;

			File.PutFormat("%s      ", Name);
			for (unsigned uColIndex = uStartColIndex; uColIndex <= uEndColIndex;
			  ++uColIndex)
				{
				const char c = GetChar(uSeqIndex, uColIndex);
				File.PutFormat("%c", toupper(c));
				}
			File.PutString("\n");
			}

		memset(Name, ' ', MAX_NAME);
		Name[iLongestNameLength] = 0;
		File.PutFormat("%s      ", Name);
		for (unsigned uColIndex = uStartColIndex; uColIndex <= uEndColIndex;
		  ++uColIndex)
			{
			const char c = GetAlnConsensusChar(*this, uColIndex);
			File.PutChar(c);
			}
		File.PutString("\n");
		}
	}