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cTheoreticalSpectrumList.h
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1
7#ifndef _CTHEORETICALSPECTRUMLIST_H
8#define _CTHEORETICALSPECTRUMLIST_H
9
10#include <algorithm>
11#include <list>
12#include <QMutex>
13
14#include "parallel/cSpectrumAnalyzerThreadMS1.h"
15#include "parallel/cSpectrumComparatorThreadMS1.h"
16#include "parallel/cSpectrumComparatorThreadMS2.h"
17#include "parallel/cSpectrumGeneratorThreadMS1.h"
18
19class cMainThread;
20
21
25class cTheoreticalSpectrumList {
26
27 vector<vector<cTheoreticalSpectrum> > theoreticalspectra;
28 list<cTheoreticalSpectrum> spectrumbuffer;
29 cMainThread* os;
30 cParameters* parameters;
31 cDeNovoGraph* graph;
32
33 double currentworstscore;
34
35 QMutex mutex;
36
37 double getCurrentWorstScore();
38
39 void computeNumbersOfCompletedSeries(int fileid);
40
41 void fixRegularExpression(string& s);
42
43public:
44
45
49 cTheoreticalSpectrumList();
50
51
55 void clear();
56
57
62 void clear(int fileid);
63
64
71 void initialize(cMainThread& os, cParameters& parameters, cDeNovoGraph* graph);
72
73
79 void add(int fileid, cTheoreticalSpectrum& theoreticalspectrum);
80
81
88 cTheoreticalSpectrum& get(int fileid, int order);
89
90
95 int size();
96
97
103 int size(int fileid);
104
105
110 void resize(int size);
111
112
118 void resize(int fileid, int size);
119
120
128 int parallelCompareAndStore(int fileid, cCandidateSet& candidates, bool& terminatecomputation);
129
130
139 double updatekNNList(cTheoreticalSpectrum& theoreticalspectrum, int theoreticalpeaksrealsize, double score, regex* rxsearchedsequence);
140
141
146 void sortAndFitSize(int fileid);
147
148};
149
150
151#endif
152
cSpectrumAnalyzerThreadMS1.h
The thread for an initial check of LC-MS and MSI spectra.
cSpectrumComparatorThreadMS1.h
The thread for comparison of a theoretical spectrum with a peak list (MS1 level).
cSpectrumComparatorThreadMS2.h
The thread for comparison of a theoretical spectrum with a peak list (MS2 level).
cSpectrumGeneratorThreadMS1.h
The thread for generating a theoretical spectrum (MS1 level).
cCandidateSet
The class representing a set of peptide sequence candidates.
Definition: cCandidateSet.h:18
cDeNovoGraph
The class implementing the de novo graph.
Definition: cDeNovoGraph.h:46
cMainThread
The class representing a thread launched by the command 'Search->Run'.
Definition: cMainThread.h:34
cParameters
The class storing parameters of the application.
Definition: cParameters.h:82
cTheoreticalSpectrum
The class representing a theoretical mass spectrum.
Definition: cTheoreticalSpectrum.h:106
cTheoreticalSpectrumList
The class representing lists of theoretical spectra.
Definition: cTheoreticalSpectrumList.h:25
cTheoreticalSpectrumList::initialize
void initialize(cMainThread &os, cParameters &parameters, cDeNovoGraph *graph)
Initialize the list.
Definition: cTheoreticalSpectrumList.cpp:71
cTheoreticalSpectrumList::cTheoreticalSpectrumList
cTheoreticalSpectrumList()
The constructor.
Definition: cTheoreticalSpectrumList.cpp:50
cTheoreticalSpectrumList::parallelCompareAndStore
int parallelCompareAndStore(int fileid, cCandidateSet &candidates, bool &terminatecomputation)
Parallel comparison of theoretical spectra with an experimental spectrum.
Definition: cTheoreticalSpectrumList.cpp:108
cTheoreticalSpectrumList::resize
void resize(int size)
Resize the vector of files.
Definition: cTheoreticalSpectrumList.cpp:98
cTheoreticalSpectrumList::size
int size()
Get the number of files.
Definition: cTheoreticalSpectrumList.cpp:88
cTheoreticalSpectrumList::updatekNNList
double updatekNNList(cTheoreticalSpectrum &theoreticalspectrum, int theoreticalpeaksrealsize, double score, regex *rxsearchedsequence)
Update the kNN list of peptide sequence candidates (thread-safe).
Definition: cTheoreticalSpectrumList.cpp:398
cTheoreticalSpectrumList::add
void add(int fileid, cTheoreticalSpectrum &theoreticalspectrum)
Add a spectrum to the list.
Definition: cTheoreticalSpectrumList.cpp:78
cTheoreticalSpectrumList::get
cTheoreticalSpectrum & get(int fileid, int order)
Get a reference to a spectrum.
Definition: cTheoreticalSpectrumList.cpp:83
cTheoreticalSpectrumList::sortAndFitSize
void sortAndFitSize(int fileid)
Sort the list according to a score defined by cParameters::scoretype and crop the list according cPar...
Definition: cTheoreticalSpectrumList.cpp:512
cTheoreticalSpectrumList::clear
void clear()
Clear the class.
Definition: cTheoreticalSpectrumList.cpp:55