OpenMS  2.5.0
LCMS.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Lukas Mueller, Markus Mueller $
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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>
49 
50 #include <string>
51 #include <vector>
52 #include <map>
53 
54 namespace OpenMS
55 {
56 
57  class SUPERHIRN_DLLAPI LCMS
58  {
59 
61  // declaration of the private members:
62 
63 private:
64 
65  // name of the spectra:
66  std::string spec_name;
67 
68  // vector of object feature:
69  std::vector<SHFeature> feature_list;
70 
71  // a unique spectrum id to identify a spectrum:
73 
74  // MASTER RUN ID:
75  int MASTER_ID;
76 
77  // the LC-MS raw data names and their IDs
78  std::map<int, std::string> raw_spec_names;
79 
80  // alignment error:
81  std::map<double, std::pair<double, double> > ALIGNMENT_ERROR;
82 
84  // declaration of the public members:
85 
86 public:
87 
89 // static double PEP_PROPHET_THERSHOLD;
90 
91  // class destructor
92  ~LCMS();
93 
94  // class constructor
95  LCMS(std::string);
96  LCMS();
97  // copy constructor
98  LCMS(const LCMS *);
99 
100  // copy constructor
101  LCMS(const LCMS &);
102 
103  // show the content of the spectra
104  void show_info();
105 
106  // copy constructor:
107  LCMS & operator=(const LCMS &);
108 
109  // sort the features according their parent mass:
110  void order_by_mass();
111 
112  // function to compare the feature mass:
113  float compare_feature_mass(const void *, const void *);
114 
115  // this structure provides the function to compare
116  // in the sorting algorithm:
117  struct OPERATOR_MZ
118  {
119  // provide the compare function for sort:
120  bool operator()(const SHFeature A, const SHFeature B) const
121  {
122  // check if they have same mass
123  if (A.MONO_MZ == B.MONO_MZ)
124  {
125  return A.TR < B.TR;
126  }
127  else
128  {
129  return A.MONO_MZ < B.MONO_MZ;
130  }
131  }
132 
133  };
134 
135  // this structure provides the function to compare
136  // in the sorting algorithm:
138  {
139  // provide the compare function for sort:
140  bool operator()(const SHFeature A, const SHFeature B) const
141  {
142  // check if they have same mass
143  if (A.feature_ID == B.feature_ID)
144  {
145  return true;
146  }
147  else
148  {
149  return false;
150  }
151  }
152 
153  };
154 
155  // tag the feature with the spectrum id:
156  void tag_peaks_with_spectrum_ID();
157 
158  // count the number of common peaks of a given number of LC-MS:
159  int get_nb_common_peaks(int);
160 
162  // start here all the get / set
163  // function to access the
164  // variables of the class
165 
166  // get the whole feature list:
167  void clear_feature_list();
168  std::vector<SHFeature> get_feature_list();
169  std::vector<SHFeature> * get_feature_list_reference();
170  bool check_feature_list_empty();
171 
172  // access end /start of list:
173  std::vector<SHFeature>::iterator get_feature_list_begin();
174  std::vector<SHFeature>::iterator get_feature_list_end();
175 
176  // add a new feature to the list:
177  void add_feature(SHFeature * in);
178 
179  // remove a feature from the LC/MS run by ID:
180  void remove_feature_by_ID(SHFeature *);
181  void remove_feature_by_ID(int);
182  // remove a feature from the LC/MS run:
183  void remove_feature(SHFeature *);
184  void remove_feature(int i);
185 
186  // remove a feature by iterator and return the iterator to the next element
187  std::vector<SHFeature>::iterator remove_feature_from_list(std::vector<SHFeature>::iterator in);
188 
189  // get number of feature added:
190  unsigned int get_nb_features();
191 
192  std::string get_spec_name();
193  void set_spec_name(std::string in);
194 
195  // set / get spectrum id:
196  int get_spectrum_ID();
197  void set_spectrum_ID(int in);
198 
199  // set the id of all features
200  void setFeatureLCMSID();
201 
202  // search the list of feature for the one with input ID:
203  SHFeature * find_feature_by_ID(int);
204 
205  // access the raw data names:
206  void remove_raw_spec_name(int ID);
207  void add_raw_spec_name(int ID, std::string name);
208  bool check_raw_spec_name_empty();
209  std::map<int, std::string>::iterator get_raw_spec_name_start();
210  std::map<int, std::string>::iterator get_raw_spec_name_end();
211  std::map<int, std::string> get_raw_spec_name_map();
212  int get_nb_raw_specs();
213 
214  std::string get_raw_spec_name(int ID);
215 
216  // compare the LC/MS runs names
217  bool check_LCMS_name(std::string);
218 
219  // check if this LC/MS ID is present in the raw LC/MS runs
220  bool find_LC_MS_by_ID(int);
221 
222  // add the raw spectrum map:
223  void add_raw_spec_name_map(std::map<int, std::string> in);
224 
225  // counts the number of ms features, which contain MS2 info:
226  int get_nb_identified_features();
227 
228  // counts the number of ms features, which contain MS2 info (no thresholding)
229  int get_nb_identified_features(double PepProb_T);
230 
232  // access the alignment error:
233  // save an error:
234  void add_alignment_error(double TR, double ERROR_UP, double ERROR_DOWN);
235 
236  // get alignment error at specific TR:
237  void get_alignment_error(double, double *, double *);
238 
239  // access MASTER run ID:
240  void set_MASTER_ID(int in);
241  int get_MASTER_ID();
242  };
243 
244 }
245 
OpenMS::LCMS::spectrum_id
int spectrum_id
Definition: LCMS.h:72
OpenMS::SHFeature
Definition: SHFeature.h:59
OpenMS::LCMS::spec_name
std::string spec_name
Definition: LCMS.h:66
OpenMS::LCMS::ALIGNMENT_ERROR
std::map< double, std::pair< double, double > > ALIGNMENT_ERROR
Definition: LCMS.h:81
OpenMS::LCMS::OPERATOR_MZ::operator()
bool operator()(const SHFeature A, const SHFeature B) const
Definition: LCMS.h:120
OpenMS::LCMS::MINIMAL_PEP_PROPHET_THERSHOLD
static double MINIMAL_PEP_PROPHET_THERSHOLD
Definition: LCMS.h:88
OpenMS::SHFeature::feature_ID
int feature_ID
Definition: SHFeature.h:133
OpenMS::LCMS::OPERATOR_FeatureCompare
Definition: LCMS.h:137
SHFeature.h
OpenMS::LCMS::OPERATOR_MZ
Definition: LCMS.h:117
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SHFeature::MONO_MZ
double MONO_MZ
Definition: SHFeature.h:129
OpenMS::SHFeature::TR
double TR
Definition: SHFeature.h:128
OpenMS::LCMS::MASTER_ID
int MASTER_ID
Definition: LCMS.h:75
OpenMS::LCMS::feature_list
std::vector< SHFeature > feature_list
Definition: LCMS.h:69
OpenMS::LCMS::OPERATOR_FeatureCompare::operator()
bool operator()(const SHFeature A, const SHFeature B) const
Definition: LCMS.h:140
OpenMS::LCMS
Definition: LCMS.h:57
OpenMS::LCMS::raw_spec_names
std::map< int, std::string > raw_spec_names
Definition: LCMS.h:78