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FeatureDetectorSimpleTest.cpp File Reference
#include "FeatureDetectorSimple.hpp"
#include "PeakFamilyDetectorFT.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/data/msdata/MSDataFile.hpp"
#include "pwiz/data/msdata/Serializer_mzML.hpp"
#include "boost/iostreams/positioning.hpp"
#include "boost/filesystem/path.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Classes

struct  mzrtEqual
 

Functions

void testFeatureDetectorSimple (const bfs::path &datadir)
 
int main (int argc, char *argv[])
 

Variables

ostream * os_ = 0
 
double mz_epsilon = .005
 
double rt_epsilon = 10
 

Function Documentation

◆ testFeatureDetectorSimple()

void testFeatureDetectorSimple ( const bfs::path &  datadir)

Definition at line 61 of file FeatureDetectorSimpleTest.cpp.

62{
63
64 if (os_) *os_ << "testFeatureDetectorSimple() ... " << endl;
65
66 // instantiate PeakFamilyDetectorFT
67 // (from PeakFamilyDetectorFTTest.cpp)
68
69 ostream* os_log_ = 0; // don't log peak family detection
70
72 config.log = os_log_;
74 boost::shared_ptr<PeakFamilyDetectorFT> detector(new PeakFamilyDetectorFT(config));
75 FeatureDetectorSimple fds(detector);
76
77 // instantiate MSData from test file
78
79 MSDataFile msd((datadir / "FeatureDetectorTest_Bombesin.mzML").string());
80
81 FeatureField output_features;
82 fds.detect(msd, output_features);
83
84 // instantiate the bombesin +2 feature that we know is correct, with calculated mzMonoisotopic and eyeballed retentionTime
85
86 FeaturePtr bombesin2_truth(new Feature());
87 bombesin2_truth->mz = 810.4148;
88 bombesin2_truth->retentionTime = 1866;
89
90 FeatureField::iterator bombesin2_hopeful = find_if(output_features.begin(), output_features.end(), mzrtEqual(bombesin2_truth));
91
92 // assert that it is found, correctly, in the data
93 unit_assert(bombesin2_hopeful != output_features.end());
94
95
96 if (os_) *os_ << "\n[FeatureDetectorSimple] Bombesin detected at charge state +2 ... " << endl << *bombesin2_hopeful << endl;
97
98
99 // do the same for the +3 feature
100
101 FeaturePtr bombesin3_truth(new Feature());
102 bombesin3_truth->mz = 540.6123;
103 bombesin3_truth->retentionTime = 1866;
104
105 FeatureField::iterator bombesin3_hopeful = find_if(output_features.begin(), output_features.end(), mzrtEqual(bombesin3_truth));
106
107 // assert that it is found, correctly, in the data
108 unit_assert(bombesin3_hopeful != output_features.end());
109
110
111 if (os_) *os_ << "\n[FeatureDetectorSimple] Bombesin detected at charge state +3 ... " << endl << *bombesin3_hopeful << endl;
112
113 return;
114
115}
ostream * os_
FeatureDetectorSimple detects 'rectangular' features, ie number of peaks in isotope envelope is the s...
FT-specific implementation of PeakFamilyDetector.
boost::shared_ptr< Feature > FeaturePtr
Definition PeakData.hpp:292
MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT.
Definition MZRTField.hpp:95
static CalibrationParameters thermo_FT()
MSData object plus file I/O.
#define unit_assert(x)
Definition unit.hpp:85

References pwiz::analysis::PeakFamilyDetectorFT::Config::cp, pwiz::analysis::FeatureDetectorSimple::detect(), pwiz::analysis::PeakFamilyDetectorFT::Config::log, os_, pwiz::data::CalibrationParameters::thermo_FT(), and unit_assert.

Referenced by main().

◆ main()

int main ( int  argc,
char *  argv[] 
)

Definition at line 117 of file FeatureDetectorSimpleTest.cpp.

118{
119 TEST_PROLOG(argc, argv)
120
121 try
122 {
123 bfs::path datadir = ".";
124
125 for (int i=1; i<argc; i++)
126 {
127 if (!strcmp(argv[i],"-v"))
128 os_ = &cout;
129 else
130 // hack to allow running unit test from a different directory:
131 // Jamfile passes full path to specified input file.
132 // we want the path, so we can ignore filename
133 datadir = bfs::path(argv[i]).branch_path();
134 }
135
137 }
138 catch (exception& e)
139 {
140 TEST_FAILED(e.what())
141 }
142 catch (...)
143 {
144 TEST_FAILED("Caught unknown exception.")
145 }
146
148}
void testFeatureDetectorSimple(const bfs::path &datadir)
#define TEST_EPILOG
Definition unit.hpp:183
#define TEST_FAILED(x)
Definition unit.hpp:177
#define TEST_PROLOG(argc, argv)
Definition unit.hpp:175

References os_, TEST_EPILOG, TEST_FAILED, TEST_PROLOG, and testFeatureDetectorSimple().

Variable Documentation

◆ os_

ostream* os_ = 0

Definition at line 40 of file FeatureDetectorSimpleTest.cpp.

Referenced by main(), and testFeatureDetectorSimple().

◆ mz_epsilon

double mz_epsilon = .005

Definition at line 42 of file FeatureDetectorSimpleTest.cpp.

Referenced by mzrtEqual::operator()().

◆ rt_epsilon

double rt_epsilon = 10

Definition at line 43 of file FeatureDetectorSimpleTest.cpp.

Referenced by mzrtEqual::operator()().