MDA
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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... | |
Several functions related to domain alignment.
Many function in this file are based on RADS. (http://rads.uni-muenster.de/)