ProteoWizard
Serializer_MGF_Test.cpp
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1//
2// $Id$
3//
4//
5// Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
6//
7// Copyright 2011 Vanderbilt University - Nashville, TN 37232
8//
9// Licensed under the Apache License, Version 2.0 (the "License");
10// you may not use this file except in compliance with the License.
11// You may obtain a copy of the License at
12//
13// http://www.apache.org/licenses/LICENSE-2.0
14//
15// Unless required by applicable law or agreed to in writing, software
16// distributed under the License is distributed on an "AS IS" BASIS,
17// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18// See the License for the specific language governing permissions and
19// limitations under the License.
20//
21
22
23#include "Serializer_MGF.hpp"
24#include "Serializer_mzML.hpp"
25#include "Diff.hpp"
26#include "TextWriter.hpp"
30
31using namespace pwiz::util;
32using namespace pwiz::cv;
33using namespace pwiz::data;
34using namespace pwiz::msdata;
35
36
37ostream* os_ = 0;
38
39
41{
45
46 //SourceFilePtr sourceFile(new SourceFile);
47 //sourceFile->set(MS_multiple_peak_list_nativeID_format);
48 // TODO: sourceFile->set(MS_Matrix_Science_MGF_format);
49 //msd.fileDescription.sourceFilePtrs.push_back(sourceFile);
50
51 shared_ptr<SpectrumListSimple> spectrumList(new SpectrumListSimple);
52 msd.run.spectrumListPtr = spectrumList;
53 spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));
54 spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));
55
56 Spectrum& s20 = *spectrumList->spectra[0];
57 s20.id = "index=0";
58 s20.index = 0;
59 s20.set(MS_spectrum_title, s20.id);
60
62 s20.set(MS_ms_level, 2);
63
68 s20.set(MS_base_peak_m_z, 0.0);
69 s20.set(MS_base_peak_intensity, 20.0);
70 s20.set(MS_total_ion_current, 110.0);
71
72 s20.precursors.resize(1);
73 Precursor& s20precursor = s20.precursors.front();
74 s20precursor.selectedIons.resize(1);
75 s20precursor.selectedIons[0].set(MS_selected_ion_m_z, 445.34, MS_m_z);
76 s20precursor.selectedIons[0].set(MS_peak_intensity, 120053.0, MS_number_of_detector_counts);
77 s20precursor.selectedIons[0].set(MS_charge_state, 2);
78
80 s20.scanList.scans.push_back(Scan());
81 Scan& s20scan = s20.scanList.scans.back();
82 s20scan.set(MS_scan_start_time, 4.0, UO_second);
83
84 s20.setMZIntensityArrays(vector<double>(), vector<double>(), MS_number_of_detector_counts);
85 BinaryData<double>& s20_mz = s20.getMZArray()->data;
86 BinaryData<double>& s20_intensity = s20.getIntensityArray()->data;
87
88 for (int i=0; i<10; i++)
89 s20_mz.push_back(i*2);
90
91 for (int i=0; i<10; i++)
92 s20_intensity.push_back((10-i)*2);
93
94 s20.defaultArrayLength = s20_mz.size();
95
96
97 Spectrum& s21 = *spectrumList->spectra[1];
98 s21.id = "index=1";
99 s21.index = 1;
100 s21.set(MS_spectrum_title, s21.id);
101
102 s21.set(MS_MSn_spectrum);
103 s21.set(MS_ms_level, 2);
104
107 s21.set(MS_lowest_observed_m_z, 3.0);
108 s21.set(MS_highest_observed_m_z, 30.0);
109 s21.set(MS_base_peak_m_z, 3.0);
110 s21.set(MS_base_peak_intensity, 30.0);
111 s21.set(MS_total_ion_current, 165.0);
112
113 s21.precursors.resize(1);
114 Precursor& s21precursor = s21.precursors.front();
115 s21precursor.selectedIons.resize(1);
116 s21precursor.selectedIons[0].set(MS_selected_ion_m_z, 424.24, MS_m_z);
117 s21precursor.selectedIons[0].set(MS_peak_intensity, 4242.0, MS_number_of_detector_counts);
118 s21precursor.selectedIons[0].cvParams.push_back(CVParam(MS_possible_charge_state, 2));
119 s21precursor.selectedIons[0].cvParams.push_back(CVParam(MS_possible_charge_state, 3));
120
122 s21.scanList.scans.push_back(Scan());
123 Scan& s21scan = s21.scanList.scans.back();
124 s21scan.set(MS_scan_start_time, 42.0, UO_second);
125
126 s21.setMZIntensityArrays(vector<double>(), vector<double>(), MS_number_of_detector_counts);
127 BinaryData<double>& s21_mz = s21.getMZArray()->data;
128 BinaryData<double>& s21_intensity = s21.getIntensityArray()->data;
129
130 for (int i=1; i<=10; i++)
131 s21_mz.push_back(i*3);
132
133 for (int i=0; i<10; i++)
134 s21_intensity.push_back((10-i)*3);
135
136 s21.defaultArrayLength = s21_mz.size();
137
138} // initializeTinyMGF()
139
140
141void testWriteRead(const MSData& msd)
142{
143 Serializer_MGF serializer;
144
145 ostringstream oss;
146 serializer.write(oss, msd);
147
148 if (os_) *os_ << "oss:\n" << oss.str() << endl;
149
150 shared_ptr<istringstream> iss(new istringstream(oss.str()));
151 MSData msd2;
152 serializer.read(iss, msd2);
153
154 DiffConfig diffConfig;
155 diffConfig.ignoreIdentity = true;
156 diffConfig.ignoreChromatograms = true;
157
158 Diff<MSData, DiffConfig> diff(msd, msd2, diffConfig);
159 if (os_ && diff) *os_ << diff << endl;
161
162 if (os_)
163 {
164 *os_ << "msd2:\n";
165 Serializer_mzML mzmlSerializer;
166 mzmlSerializer.write(*os_, msd2);
167 *os_ << endl;
168
169 *os_ << "msd2::";
170 TextWriter write(*os_);
171 write(msd2);
172
173 *os_ << endl;
174 }
175}
176
177
179{
180 MSData msd;
182
183 testWriteRead(msd);
184}
185
186
187int main(int argc, char* argv[])
188{
189 TEST_PROLOG(argc, argv)
190
191 try
192 {
193 if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
195 }
196 catch (exception& e)
197 {
198 TEST_FAILED(e.what())
199 }
200 catch (...)
201 {
202 TEST_FAILED("Caught unknown exception.")
203 }
204
206}
207
void diff(const string &filename1, const string &filename2)
int main(int argc, char *argv[])
void initializeTinyMGF(MSData &msd)
ostream * os_
void testWriteRead()
MSData <-> MGF stream serialization.
void read(boost::shared_ptr< std::istream > is, MSData &msd) const
read in MSData object from an MGF istream note: istream may be managed by MSData's SpectrumList,...
void write(std::ostream &os, const MSData &msd, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry=0) const
write MSData object to ostream as MGF; iterationListenerRegistry may be used to receive progress upda...
MSData <-> mzML stream serialization.
void write(std::ostream &os, const MSData &msd, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry=0) const
write MSData object to ostream as mzML; iterationListenerRegistry may be used to receive progress upd...
A custom vector class that can store its contents in either a std::vector or a cli::array (when compi...
void push_back(const T &value)
MS_no_combination
no combination: Use this term if only one scan was recorded or there is no information about scans av...
Definition cv.hpp:3072
MS_highest_observed_m_z
highest observed m/z: Highest m/z value observed in the m/z array.
Definition cv.hpp:2187
MS_possible_charge_state
possible charge state: A possible charge state of the ion in a situation where the charge of an ion i...
Definition cv.hpp:2571
MS_lowest_observed_m_z
lowest observed m/z: Lowest m/z value observed in the m/z array.
Definition cv.hpp:2190
MS_ms_level
ms level: Stages of ms achieved in a multi stage mass spectrometry experiment.
Definition cv.hpp:2139
MS_centroid_spectrum
centroid spectrum: Processing of profile data to produce spectra that contains discrete peaks of zero...
Definition cv.hpp:720
MS_MSn_spectrum
MSn spectrum: MSn refers to multi-stage MS2 experiments designed to record product ion spectra where ...
Definition cv.hpp:2364
MS_negative_scan
negative scan: Polarity of the scan is negative.
Definition cv.hpp:735
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
Definition cv.hpp:384
MS_charge_state
charge state: The charge state of the ion, single or multiple and positive or negatively charged.
Definition cv.hpp:396
MS_spectrum_title
spectrum title: A free-form text title describing a spectrum.
Definition cv.hpp:3075
MS_total_ion_current
total ion current: The sum of all the separate ion currents carried by the ions of different m/z cont...
Definition cv.hpp:1407
MS_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of an selected ion.
Definition cv.hpp:2901
MS_scan_start_time
scan start time: The time that an analyzer started a scan, relative to the start of the MS run.
Definition cv.hpp:309
MS_number_of_detector_counts
number of detector counts: The number of counted events observed in one or a group of elements of a d...
Definition cv.hpp:741
MS_base_peak_intensity
base peak intensity: The intensity of the greatest peak in the mass spectrum.
Definition cv.hpp:2121
MS_base_peak_m_z
base peak m/z: M/z value of the signal of highest intensity in the mass spectrum.
Definition cv.hpp:2118
MS_positive_scan
positive scan: Polarity of the scan is positive.
Definition cv.hpp:738
UO_second
second: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation correspo...
Definition cv.hpp:13833
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum.
Definition cv.hpp:402
boost::shared_ptr< Spectrum > SpectrumPtr
Definition MSData.hpp:573
represents a tag-value pair, where the tag comes from the controlled vocabulary
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Definition diff_std.hpp:143
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
configuration struct for diffing MSData types
Definition Diff.hpp:206
bool ignoreIdentity
ignore members of SpectrumIdentity and ChromatogramIdentity
Definition Diff.hpp:208
This summarizes the different types of spectra that can be expected in the file. This is expected to ...
Definition MSData.hpp:50
FileContent fileContent
this summarizes the different types of spectra that can be expected in the file. This is expected to ...
Definition MSData.hpp:87
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition MSData.hpp:850
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.
Definition MSData.hpp:886
FileDescription fileDescription
information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
Definition MSData.hpp:862
The method of precursor ion selection and activation.
Definition MSData.hpp:312
std::vector< SelectedIon > selectedIons
this list of precursor ions that were selected.
Definition MSData.hpp:329
SpectrumListPtr spectrumListPtr
all mass spectra and the acquisitions underlying them are described and attached here....
Definition MSData.hpp:827
Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile.
Definition MSData.hpp:370
std::vector< Scan > scans
Definition MSData.hpp:397
The structure that captures the generation of a peak list (including the underlying acquisitions)
Definition MSData.hpp:506
void setMZIntensityArrays(const std::vector< double > &mzArray, const std::vector< double > &intensityArray, CVID intensityUnits)
set m/z and intensity arrays separately (they must be the same size)
BinaryDataArrayPtr getIntensityArray() const
get intensity array (may be null)
size_t defaultArrayLength
default length of binary data arrays contained in this element.
Definition MSData.hpp:508
BinaryDataArrayPtr getMZArray() const
get m/z array (may be null)
ScanList scanList
list of scans
Definition MSData.hpp:517
std::vector< Precursor > precursors
list and descriptions of precursors to the spectrum currently being described.
Definition MSData.hpp:520
std::string id
a unique identifier for this spectrum. It should be expected that external files may use this identif...
Definition MSData.hpp:476
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
Definition MSData.hpp:473
Simple writeable in-memory implementation of SpectrumList.
Definition MSData.hpp:717
#define unit_assert(x)
Definition unit.hpp:85
#define TEST_EPILOG
Definition unit.hpp:183
#define TEST_FAILED(x)
Definition unit.hpp:177
#define TEST_PROLOG(argc, argv)
Definition unit.hpp:175