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domain_aln.hpp
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1 /*
2  * domain_aln.hpp
3  *
4  * Created on: Sep 11, 2013
5  * Author: ckeme_01
6  */
7 
8 
17 #ifndef DOMAIN_ALN_HPP_
18 #define DOMAIN_ALN_HPP_
19 
20 //C++ header
21 #include <algorithm>
22 #include <map>
23 #include <stack>
24 #include <utility>
25 #include <vector>
26 
27 
28 //MDAT header
29 #include "Library.hpp"
30 #include "../Sequence/ProteinSequenceSet.hpp"
31 #include "../Annotation/DomainArchitecture.hpp"
32 #include "../utils/MatrixStack.hpp"
33 #include "../utils/ThreadPool.hpp"
34 #include "consistency_aln.hpp"
35 
36 
37 
38 namespace MDAT
39 {
40 
41 
42 
46 struct Opt_DA
47 {
48  Opt_DA() : match(0), mismatch(0), matches(), terminal_gop(0), terminal_gep(0), gop(0), gep(0), l_prop(0), scale(0), dmpm_f("")
49  {}
50  int match;
51  int mismatch;
55  int gop;
56  int gep;
57  int l_prop;
58  int scale;
59  std::string dmpm_f;
60 };
61 
62 
63 
73 void rads_align_archi (const Opt_DA &opts, const DomainArchitecture &doms1, const DomainArchitecture &doms2, MatrixStack<3,std::pair<int, char> > &matrices);
74 
75 
86 void
87 rads_traceback_archi(Library<DomainArchitectureSet > &lib, const DomainArchitecture &arch1, const DomainArchitecture &arch2, const MatrixStack<3,std::pair<int, char> > &matrices);
88 
89 
101 
102 
103 
105 all_rads_pair_align_archi(Library<DomainArchitectureSet > &lib, const ProteinSequenceSet<Default> &seqSet, const Opt_DA &opts, unsigned int n_threads);
106 
107 
112 void
114 
115 
116 }
117 
118 
119 
120 #endif /* DOMAIN_ALN_HPP_ */