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domain_aln.hpp File Reference

Several functions related to domain alignment. More...

#include <algorithm>
#include <map>
#include <stack>
#include <utility>
#include <vector>
#include "Library.hpp"
#include "../Sequence/ProteinSequenceSet.hpp"
#include "../Annotation/DomainArchitecture.hpp"
#include "../utils/MatrixStack.hpp"
#include "../utils/ThreadPool.hpp"
#include "consistency_aln.hpp"

Go to the source code of this file.

Classes

struct  MDAT::Opt_DA
 Structure to contain the MDA options. More...
 

Namespaces

namespace  MDAT
 The general namespace of this project.
 

Functions

void MDAT::rads_align_archi (const Opt_DA &opts, const DomainArchitecture &doms1, const DomainArchitecture &doms2, MatrixStack< 3, std::pair< int, char > > &matrices)
 Aligning two Architectures. More...
 
void MDAT::rads_traceback_archi (Library< DomainArchitectureSet > &lib, const DomainArchitecture &arch1, const DomainArchitecture &arch2, const MatrixStack< 3, std::pair< int, char > > &matrices)
 Traceback for the RADS dynamic programming. More...
 
Matrix< float > * MDAT::all_rads_pair_align_archi (Library< DomainArchitectureSet > &lib, const ProteinSequenceSet< Default > &seqSet, const Opt_DA &opts)
 Produces all pairwise alignments. More...
 
Matrix< float > * MDAT::all_rads_pair_align_archi (Library< DomainArchitectureSet > &lib, const ProteinSequenceSet< Default > &seqSet, const Opt_DA &opts, unsigned int n_threads)
 
void MDAT::refine (DomainArchitectureSet &set)
 Refinement of domain alignment by shifting domains to increase number of identical domains in a column. More...
 

Detailed Description

Several functions related to domain alignment.

Many function in this file are based on RADS. (http://rads.uni-muenster.de/)