C++ (Cpp) Seq::Clear Examples

Example #1

File: estring.cpp Project: Unode/ext_apps

void EstringOp(const short es[], const Seq &sIn, Seq &sOut)
	{
#if	DEBUG
	unsigned uSymbols;
	unsigned uIndels;
	EstringCounts(es, &uSymbols, &uIndels);
	assert(sIn.Length() == uSymbols);
#endif
	sOut.Clear();
	sOut.SetName(sIn.GetName());
	int p = 0;
	for (;;)
		{
		int n = *es++;
		if (0 == n)
			break;
		if (n > 0)
			for (int i = 0; i < n; ++i)
				{
				char c = sIn[p++];
				sOut.push_back(c);
				}
		else
			for (int i = 0; i < -n; ++i)
				sOut.push_back('-');
		}
	}

Example #2

File: refinew.cpp Project: Wyss/mauve-py

static void SeqFromMSACols(const MSA &msa, unsigned uSeqIndex, unsigned uColFrom,
  unsigned uColTo, Seq &s)
	{
	s.Clear();
	s.SetName(msa.GetSeqName(uSeqIndex));
	s.SetId(msa.GetSeqId(uSeqIndex));
	for (unsigned uColIndex = uColFrom; uColIndex <= uColTo; ++uColIndex)
		{
		char c = msa.GetChar(uSeqIndex, uColIndex);
		if (!IsGapChar(c))
			s.AppendChar(c);
		}
	}

Example #3

File: makerootmsa.cpp Project: Unode/ext_apps

static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
	{
	short *esA;
	short *esB;
	PathToEstrings(Path, &esA, &esB);

	const unsigned uSeqLength = s.Length();
	const unsigned uEdgeCount = Path.GetEdgeCount();

	sOut.Clear();
	sOut.SetName(s.GetName());
	unsigned uPos = 0;
	for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)
		{
		const PWEdge &Edge = Path.GetEdge(uEdgeIndex);
		char cType = Edge.cType;
		if (bRight)
			{
			if (cType == 'I')
				cType = 'D';
			else if (cType == 'D')
				cType = 'I';
			}
		switch (cType)
			{
		case 'M':
			sOut.AppendChar(s[uPos++]);
			break;
		case 'D':
			sOut.AppendChar('-');
			break;
		case 'I':
			sOut.AppendChar(s[uPos++]);
			break;
		default:
			Quit("PathSeq, invalid edge type %c", cType);
			}
		}
	}