#include "alignment.h"
#include "chromSimMatrix.h"
#include "gapPenalty.h"
#include "affinealignobj.h"
#include "affinealignment.h"
#include "constrainMat.h"

Include dependency graph for CppInterface.hpp:

Go to the source code of this file.

Namespaces
	DIAlign
	Generic namespace for all classes and functions of DIAlign.

Functions
void	DIAlign::alignChromatogramsCpp (AffineAlignObj &obj, const std::vector< std::vector< double > > &r1, const std::vector< std::vector< double > > &r2, std::string alignType, const std::vector< double > &tA, const std::vector< double > &tB, const std::string &normalization, const std::string &simType, double B1p=0.0, double B2p=0.0, int noBeef=0, double goFactor=0.125, double geFactor=40, double cosAngleThresh=0.3, bool OverlapAlignment=true, double dotProdThresh=0.96, double gapQuantile=0.5, bool hardConstrain=false, double samples4gradient=100.0)
	Align two pairs of chromatograms derived from two LC-MS/MS experiments A and B. More...

SimMatrix	DIAlign::getSimilarityMatrix (const std::vector< std::vector< double >> &d1, const std::vector< std::vector< double >> &d2, const std::string &Normalization, const std::string &SimType, double cosAngleThresh, double dotProdThresh)
	Calculates similarity matrix of two fragment-ion chromatogram groups or extracted-ion chromatograms (XICs) derived from two LC-MS/MS experiments A and B. More...

void	DIAlign::doAffineAlignment (AffineAlignObj &obj, const SimMatrix &s, double goPenalty, double gePenalty, bool OverlapAlignment)
	Performs affine alignment on a given alignment object. More...

void	DIAlign::getAffineAlignedIndices (AffineAlignObj &obj, int bandwidth=0)
	Compute path using AffineAlignObj. More...

Namespaces

Functions