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fragment_scoring_utilities.hh
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2 // vi: set ts=2 noet:
3 //
4 // (c) Copyright Rosetta Commons Member Institutions.
5 // (c) This file is part of the Rosetta software suite and is made available under license.
6 // (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
7 // (c) For more information, see http://www.rosettacommons.org. Questions about this can be
8 // (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.
9 
10 /// @file protocols/frag_picker/scores/fragment_scoring_utilities.hh
11 /// @brief functions and data types common for fragment scoring
12 /// @author Dominik Gront
13 
14 #ifndef INCLUDED_protocols_frag_picker_scores_fragment_scoring_utilities_hh
15 #define INCLUDED_protocols_frag_picker_scores_fragment_scoring_utilities_hh
16 
17 // type headers
18 #include <core/types.hh>
19 #include <utility/vector1.hh>
20 
21 #include <algorithm>
22 
23 namespace protocols {
24 namespace frag_picker {
25 namespace scores {
26 
27 using namespace core;
28 
30 
31 
32 void do_one_line(Size start_i,Size start_j,Matrix & small_scores,Size frag_len,Matrix & frag_scores);
33 void rolling_score(Matrix & small_scores,Size frag_len,Matrix & frag_scores);
34 void create_cache(utility::vector1<Size> & frag_sizes,Size query_len,Size longest_vall_chunk,utility::vector1<Matrix> & cache);
35 void allocate_matrix(Size i_size,Size j_size,Matrix & dst);
36 
37 
38 } // scores
39 } // frag_picker
40 } // protocols
41 
42 #endif /* INCLUDED_protocols_frag_picker_scores_fragment_scoring_utilities_HH */