ProteoWizard
Reader_FASTA.hpp
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1 //
2 // $Id: Reader_FASTA.hpp 1623 2009-12-17 20:58:35Z chambm $
3 //
4 //
5 // Original author: Darren Kessner <darren@proteowizard.org>
6 //
7 // Copyright 2007 Spielberg Family Center for Applied Proteomics
8 // Cedars-Sinai Medical Center, Los Angeles, California 90048
9 //
10 // Licensed under the Apache License, Version 2.0 (the "License");
11 // you may not use this file except in compliance with the License.
12 // You may obtain a copy of the License at
13 //
14 // http://www.apache.org/licenses/LICENSE-2.0
15 //
16 // Unless required by applicable law or agreed to in writing, software
17 // distributed under the License is distributed on an "AS IS" BASIS,
18 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19 // See the License for the specific language governing permissions and
20 // limitations under the License.
21 //
22 
23 
24 #ifndef _READER_FASTA_HPP_
25 #define _READER_FASTA_HPP_
26 
27 
29 #include "ProteomeData.hpp"
30 #include "Reader.hpp"
31 
32 
33 namespace pwiz {
34 namespace proteome {
35 
36 
37 /// FASTA -> ProteomeData stream serialization
39 {
40  public:
41 
42  /// Reader_FASTA configuration
44  {
45  /// read with a side-by-side index
46  bool indexed;
47 
48  Config() {}
49  };
50 
51  /// constructor
52  Reader_FASTA(const Config& config = Config());
53 
54  const char* getType() const {return "FASTA";}
55 
56  virtual std::string identify(const std::string& uri,
57  boost::shared_ptr<std::istream> uriStreamPtr) const;
58 
59  /// fill in the ProteomeData structure
60  virtual void read(const std::string& uri,
61  boost::shared_ptr<std::istream> uriStreamPtr,
62  ProteomeData& result) const;
63 
64  private:
67  Reader_FASTA& operator=(Reader_FASTA&);
68 };
69 
70 
71 PWIZ_API_DECL std::ostream& operator<<(std::ostream& os, const Reader_FASTA::Config& config);
72 
73 
74 } // namespace proteome
75 } // namespace pwiz
76 
77 
78 #endif // _READER_FASTA_HPP_