C++ (Cpp) SeqVect::GetSeqCount Examples

Example #1

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

void AlignSubFam(SeqVect &vAll, const Tree &GuideTree, unsigned uNodeIndex,
  MSA &msaOut)
	{
	const unsigned uSeqCount = vAll.GetSeqCount();

	const char *InTmp = "asf_in.tmp";
	const char *OutTmp = "asf_out.tmp";

	unsigned *Leaves = new unsigned[uSeqCount];
	unsigned uLeafCount;
	GetLeaves(GuideTree, uNodeIndex, Leaves, &uLeafCount);

	SeqVect v;
	for (unsigned i = 0; i < uLeafCount; ++i)
		{
		unsigned uLeafNodeIndex = Leaves[i];
		unsigned uId = GuideTree.GetLeafId(uLeafNodeIndex);
		Seq &s = vAll.GetSeqById(uId);
		v.AppendSeq(s);
		}

#if	TRACE
	{
	Log("Align subfam[node=%d, size=%d] ", uNodeIndex, uLeafCount);
	for (unsigned i = 0; i < uLeafCount; ++i)
		Log(" %s", v.GetSeqName(i));
	Log("\n");
	}
#endif

	TextFile fIn(InTmp, true);

	v.ToFASTAFile(fIn);
	fIn.Close();

	char CmdLine[4096];
	sprintf(CmdLine, "probcons %s > %s 2> /dev/null", InTmp, OutTmp);
//	sprintf(CmdLine, "muscle -in %s -out %s -maxiters 1", InTmp, OutTmp);
	system(CmdLine);

	TextFile fOut(OutTmp);
	msaOut.FromFile(fOut);

	for (unsigned uSeqIndex = 0; uSeqIndex < uLeafCount; ++uSeqIndex)
		{
		const char *Name = msaOut.GetSeqName(uSeqIndex);
		unsigned uId = vAll.GetSeqIdFromName(Name);
		msaOut.SetSeqId(uSeqIndex, uId);
		}

	unlink(InTmp);
	unlink(OutTmp);

	delete[] Leaves;
	}

Example #2

File: makerootmsa.cpp Project: Unode/ext_apps

void MakeRootMSA(const SeqVect &v, const Tree &GuideTree, ProgNode Nodes[],
  MSA &a)
	{
#if	TRACE
	Log("MakeRootMSA Tree=");
	GuideTree.LogMe();
#endif
	const unsigned uSeqCount = v.GetSeqCount();
	unsigned uColCount = uInsane;
	unsigned uSeqIndex = 0;
	const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
	const unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();
	const PWPath &RootPath = Nodes[uRootNodeIndex].m_Path;
	const unsigned uRootColCount = RootPath.GetEdgeCount();
	const unsigned uEstringSize = uRootColCount + 1;
	short *Estring1 = new short[uEstringSize];
	short *Estring2 = new short[uEstringSize];
	SetProgressDesc("Root alignment");

	unsigned uTreeNodeIndex = GetFirstNodeIndex(GuideTree);
	do
		{
		Progress(uSeqIndex, uSeqCount);

		unsigned uId = GuideTree.GetLeafId(uTreeNodeIndex);
		const Seq &s = *(v[uId]);

		Seq sRootE;
		short *es = MakeRootSeqE(s, GuideTree, uTreeNodeIndex, Nodes, sRootE,
		  Estring1, Estring2);
		Nodes[uTreeNodeIndex].m_EstringL = EstringNewCopy(es);

#if	VALIDATE
		Seq sRoot;
		MakeRootSeq(s, GuideTree, uTreeNodeIndex, Nodes, sRoot);
		if (!sRoot.Eq(sRootE))
			{
			Log("sRoot=");
			sRoot.LogMe();
			Log("sRootE=");
			sRootE.LogMe();
			Quit("Root seqs differ");
			}
#if	TRACE
		Log("MakeRootSeq=\n");
		sRoot.LogMe();
#endif
#endif

		if (uInsane == uColCount)
			{
			uColCount = sRootE.Length();
			a.SetSize(uSeqCount, uColCount);
			}
		else
			{
			assert(uColCount == sRootE.Length());
			}
		a.SetSeqName(uSeqIndex, s.GetName());
		a.SetSeqId(uSeqIndex, uId);
		for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
			a.SetChar(uSeqIndex, uColIndex, sRootE[uColIndex]);
		++uSeqIndex;

		uTreeNodeIndex = GetNextNodeIndex(GuideTree, uTreeNodeIndex);
		}
	while (NULL_NEIGHBOR != uTreeNodeIndex);

	delete[] Estring1;
	delete[] Estring2;

	ProgressStepsDone();
	assert(uSeqIndex == uSeqCount);
	}