ProteoWizard
ProteinList_DecoyGenerator.hpp
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1//
2// $Id$
3//
4//
5// Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
6//
7// Copyright 2010 Vanderbilt University - Nashville, TN 37232
8//
9// Licensed under the Apache License, Version 2.0 (the "License");
10// you may not use this file except in compliance with the License.
11// You may obtain a copy of the License at
12//
13// http://www.apache.org/licenses/LICENSE-2.0
14//
15// Unless required by applicable law or agreed to in writing, software
16// distributed under the License is distributed on an "AS IS" BASIS,
17// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18// See the License for the specific language governing permissions and
19// limitations under the License.
20//
21
22
23#ifndef _PROTEINLIST_DECOYGENERATOR_HPP_
24#define _PROTEINLIST_DECOYGENERATOR_HPP_
25
26
29#include <boost/cstdint.hpp>
30
31
32namespace pwiz {
33namespace analysis {
34
35
36using namespace pwiz::proteome;
37
38
39/// ProteinList decoy generator for creating decoy proteins on the fly
41{
42 public:
43
44 /// client-implemented generator predicate -- called during construction of
45 /// ProteinList_DecoyGenerator to create a decoy protein from a target protein
47 {
48 /// return a decoy protein based on an input target protein
49 virtual ProteinPtr generate(const Protein& protein) const = 0;
50
51 /// return the string prefixed to a protein id to indicate it is a decoy
52 virtual const std::string& decoyPrefix() const {return decoyPrefix_;}
53
54 virtual ~Predicate() {}
55
56 protected:
57 std::string decoyPrefix_;
58 };
59
60 typedef boost::shared_ptr<Predicate> PredicatePtr;
61
62 ProteinList_DecoyGenerator(const ProteinListPtr& original, const PredicatePtr& predicate);
63
64 /// \name ProteinList interface
65 //@{
66 virtual size_t size() const;
67 virtual size_t find(const std::string& id) const;
68 virtual ProteinPtr protein(size_t index, bool getSequence = true) const;
69 //@}
70
71 private:
72 struct Impl;
73 boost::shared_ptr<Impl> impl_;
76};
77
78
79/// creates a reversed copy of every target protein with the specified decoy string prefixed to the id
87
88
89/// creates a randomly shuffled copy of every target protein with the specified decoy string prefixed to the id
91{
92 public:
93 ProteinList_DecoyGeneratorPredicate_Shuffled(const std::string& decoyPrefix, boost::uint32_t randomSeed = 0u);
94
95 virtual ProteinPtr generate(const Protein& protein) const;
96
97 private:
98 struct Impl;
99 boost::shared_ptr<Impl> impl_;
100};
101
102
103} // namespace analysis
104} // namespace pwiz
105
106
107#endif // _PROTEINLIST_DECOYGENERATOR_HPP_
#define PWIZ_API_DECL
Definition Export.hpp:32
ProteinList decoy generator for creating decoy proteins on the fly.
virtual size_t find(const std::string &id) const
ProteinList_DecoyGenerator & operator=(const ProteinList_DecoyGenerator &)
ProteinList_DecoyGenerator(const ProteinListPtr &original, const PredicatePtr &predicate)
ProteinList_DecoyGenerator(const ProteinList_DecoyGenerator &)
virtual ProteinPtr protein(size_t index, bool getSequence=true) const
creates a reversed copy of every target protein with the specified decoy string prefixed to the id
virtual ProteinPtr generate(const Protein &protein) const
return a decoy protein based on an input target protein
ProteinList_DecoyGeneratorPredicate_Reversed(const std::string &decoyPrefix)
creates a randomly shuffled copy of every target protein with the specified decoy string prefixed to ...
ProteinList_DecoyGeneratorPredicate_Shuffled(const std::string &decoyPrefix, boost::uint32_t randomSeed=0u)
virtual ProteinPtr generate(const Protein &protein) const
return a decoy protein based on an input target protein
Inheritable pass-through implementation for wrapping a ProteinList.
boost::shared_ptr< Protein > ProteinPtr
boost::shared_ptr< ProteinList > ProteinListPtr
client-implemented generator predicate – called during construction of ProteinList_DecoyGenerator to ...
virtual const std::string & decoyPrefix() const
return the string prefixed to a protein id to indicate it is a decoy
virtual ProteinPtr generate(const Protein &protein) const =0
return a decoy protein based on an input target protein