OpenMS  2.4.0
FTPeakDetectController.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2018.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Lukas Mueller, Markus Mueller $
33 // --------------------------------------------------------------------------
34 //
36 //
37 // written by Lukas N Mueller, 30.3.05
38 // Lukas.Mueller@imsb.biol.ethz.ch
39 // Group of Prof. Ruedi Aebersold, IMSB, ETH Hoenggerberg, Zurich
40 //
41 // Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch
42 // December 2010
43 //
44 
45 #pragma once
46 
47 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
48 
49 #include <boost/shared_ptr.hpp>
50 #include <vector>
56 
57 namespace OpenMS
58 {
59 
60  class SUPERHIRN_DLLAPI FTPeakDetectController
61  {
62 
64  // declaration of the private members:
65 
66 private:
67 
69  // declaration of the public members:
70 
71  // LCMS runs
72  //LCMS* THIS_LCMS;
74 // std::vector<SHFeature> fakeFeatureList_;
75  std::vector<LCMS> lcmsRuns_;
76 
77  // paths:
78  std::string targetMzXML;
79  std::string SOURCE_DIR;
80  std::string OUTPUT_DIR;
81 
82 public:
83 
84  typedef std::pair<double, boost::shared_ptr<RawData> > Map;
85  typedef std::vector<Map> Vec;
86 
87 // static bool CREATE_FEATURE_ELUTION_PROFILES;
88 // static bool LCelutionPeakDebugging;
89 // static double LCelutionPeakMassMin;
90 // static double LCelutionPeakMassMax;
91 
92 // static MS2Feature* SearchedM2Feature;
93 
94 // static bool FEATURE_FAKE_INSERTION_BASED_ON_MS2_FEATURE;
95 
96  // class destructor
98 
99  // class constructor
101  // class copy constructor
103 
105  // function for batch processing of mzXML data
106  // parses LC-MS from runs from a directory or file of raw mzXML data:
107  void parseMzXMLData();
108 
110  // mzXML parsing functions for a single MzXML file:
111  // start the scan parsing of a mzXML file:
112  void startScanParsing(Vec datavec);
113 
114  // **** for the MS1 level post processing:
115  // process MS1 level data
116  void process_MS1_level_data_structure(ProcessData *);
117  // adds an elution peak to the LC/MS run:
118  void add_raw_peak_to_LC_MS_run(LCElutionPeak *);
119  // function to add the elution profile to the feature:
120  void addLCelutionProfile(SHFeature *, LCElutionPeak *);
121 
123  // reads already paths of existing LC-MS runs in xml format into the
124  // memory
125  // for now, open file system for every check, but otherwise could be done
126  // in the constructor
127  bool checkIfFeatureExtractionExists(std::string);
128 
129  // **** for the MS2 level post processing:
130  // process MS2 level data
131  void process_MS2_level_data_structure(ProcessData *);
132  // processes the extracted signals on the MS2 level
133  void extract_MS2_elution_features();
134  // combine the MS2 feature trace data to the MS1 features:
135  void associateMS2FeatureToMS1Feature(MS2Feature *);
136  // add an observed MS2 feature to the MS1 feature
137  // if an observation is already there, then
138  // construct a merged MS2 feature
139  void addMS2FeatureToMS1Feature(MS2Feature *, SHFeature *);
140 
141  // construct here fake ms1 features based on a observed MS2 feature
142  // which however could not be matched to a exiting ms1 feature
143  void constructMS1FeatureFromMS2Feature(MS2Feature *);
144 
146  // write a parsed LC/MS into directory:
147  void write_out_parsed_LC_MS(LCMS *);
148  // add fake MS/MS information for the MS1 feature:
149  void addFakeMSMSToFeature(SHFeature *);
150 
151 
153  // overload operators:
154  FTPeakDetectController & operator=(const FTPeakDetectController &);
155  FTPeakDetectController & operator<=(const FTPeakDetectController &);
156  FTPeakDetectController & operator>=(const FTPeakDetectController &);
158  FTPeakDetectController & operator>(const FTPeakDetectController &);
159 
161  // start here all the get / set
162  // function to access the
163  // variables of the class
164 
165  // target file:
166  void set_target_file(std::string in);
167  std::string get_target_file();
168 
169 // get the vector of LC/MS runs:
170 //std::vector<LCMS> getParsedData();
171 //bool getParsedDataEmpty();
172 //std::vector<LCMS>::iterator get_parsed_DATA_START();
173 //std::vector<LCMS>::iterator get_parsed_DATA_END();
174  LCMS * getLCMS();
175  };
176 
177  inline void FTPeakDetectController::set_target_file(std::string in)
178  {
179  targetMzXML = in;
180  }
181 
183  {
184  return targetMzXML;
185  }
186 
187  /*
188  // get the vector of LC/MS runs:
189  inline std::vector<LCMS> FTPeakDetectController::getParsedData()
190  {
191  return lcmsRuns_;
192  }
193 
194  inline bool FTPeakDetectController::getParsedDataEmpty()
195  {
196  return LC_MS_RUNS.empty();
197  }
198 
199  inline std::vector<LCMS>::iterator FTPeakDetectController::get_parsed_DATA_START()
200  {
201  return LC_MS_RUNS.begin();
202  }
203 
204  inline std::vector<LCMS>::iterator FTPeakDetectController::get_parsed_DATA_END()
205  {
206  return LC_MS_RUNS.end();
207  }
208 */
209 
211  {
212  return lcms_;
213  }
214 
215 } // ns
216 
Definition: ProcessData.h:67
std::vector< LCMS > lcmsRuns_
Definition: FTPeakDetectController.h:75
std::vector< Map > Vec
Definition: FTPeakDetectController.h:85
LCMS * getLCMS()
Definition: FTPeakDetectController.h:210
std::string SOURCE_DIR
Definition: FTPeakDetectController.h:79
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::string OUTPUT_DIR
Definition: FTPeakDetectController.h:80
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
Definition: FTPeakDetectController.h:60
Definition: LCMS.h:57
LCMS * lcms_
Definition: FTPeakDetectController.h:73
Definition: MS2Feature.h:55
void set_target_file(std::string in)
Definition: FTPeakDetectController.h:177
std::pair< double, boost::shared_ptr< RawData > > Map
Definition: FTPeakDetectController.h:84
std::string get_target_file()
Definition: FTPeakDetectController.h:182
Definition: LCElutionPeak.h:67
Definition: SHFeature.h:59
std::string targetMzXML
Definition: FTPeakDetectController.h:78