ProteoWizard
MSDataCache.hpp
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1 //
2 // $Id: MSDataCache.hpp 2241 2010-09-10 23:47:06Z cpaulse $
3 //
4 //
5 // Original author: Darren Kessner <darren@proteowizard.org>
6 //
7 // Copyright 2008 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 _MSDATACACHE_HPP_
25 #define _MSDATACACHE_HPP_
26 
27 
30 #include "MSDataAnalyzer.hpp"
31 
32 
33 namespace pwiz {
34 namespace analysis {
35 
36 
37 using namespace msdata;
38 
39 
40 ///
41 /// simple memory cache for common MSData info
42 ///
43 /// Memory caching is useful to minimize data retrieval expenses:
44 /// - disk I/O and decoding of binary data
45 /// - indirection and pointer validation
46 /// - parameter list searching
47 /// - lexical casting
48 ///
49 /// MSDataCache is a vector of SpectrumInfo objects, but also implements the
50 /// MSDataAnalyzer interface. It can be used in two ways:
51 /// 1) Updated from the outside via MSDataAnalyzer interface
52 /// 2) Automatic updating via spectrumInfo() access method
53 ///
54 /// Spectrum binary data (SpectrumInfo::data) is
55 /// freed from the cache using a LRU (least recently used) algorithm.
56 /// Binary data will be freed only to make room for a new update. The
57 /// default cache size is 1, i.e. only the most recently updated binary
58 /// data array is stored. Note that modifying the SpectrumInfo objects
59 /// directly through the vector interface circumvents the LRU mechanism.
60 ///
61 /// Usage #1: MSDataCache should be placed first in an
62 /// MSDataAnalyzerContainer, so that it receives update() first. Other
63 /// analyzers may then use it (preferably as const MSDataCache&) to access
64 /// spectrum data when they receive update(). On updateRequested(),
65 /// MSDataCache returns UpdateRequest_Ok to indicate that it should
66 /// receive any updates that are requested by other analyzers. If no
67 /// other analyzer requests an update, the cache will not be updated.
68 ///
69 /// Usage #2: Instantiate independently and call open() to set reference to an
70 /// MSData object. Calls to spectrumInfo() will return the requested SpectrumInfo,
71 /// automatically updating the cache via call to SpectrumList::spectrum() if
72 /// necessary.
73 ///
74 class PWIZ_API_DECL MSDataCache : public std::vector<SpectrumInfo>,
75  public MSDataAnalyzer
76 
77 {
78  public:
79 
80  /// MSDataCache configuration
82  {
84  Config(size_t cacheSize = 1) : binaryDataCacheSize(cacheSize) {}
85  };
86 
87  MSDataCache(const Config& config = Config());
88 
89  /// \name MSDataAnalyzer interface
90  //@{
91  virtual void open(const DataInfo& dataInfo);
92 
93  virtual UpdateRequest updateRequested(const DataInfo& dataInfo,
94  const SpectrumIdentity& spectrumIdentity) const
95  {
96  // receive update() only if requested by another analyzer
98  }
99 
100  virtual void update(const DataInfo& dataInfo,
101  const Spectrum& spectrum);
102  //@}
103 
104  /// access to SpectrumInfo with automatic update (open() must be called first)
105  const SpectrumInfo& spectrumInfo(size_t index, bool getBinaryData = false);
106 
107  private:
108  struct Impl;
109  boost::shared_ptr<Impl> impl_;
111  MSDataCache& operator=(MSDataCache&);
112 };
113 
114 
115 } // namespace analysis
116 } // namespace pwiz
117 
118 
119 #endif // _MSDATACACHE_HPP_
120