ProteoWizard
Functions | Variables
Serializer_mzML_Test.cpp File Reference
#include "Serializer_mzML.hpp"
#include "Diff.hpp"
#include "References.hpp"
#include "examples.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "boost/iostreams/positioning.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <cstring>

Go to the source code of this file.

Functions

void testWriteRead (const MSData &msd, const Serializer_mzML::Config &config, const DiffConfig &diffcfg)
 
void testWriteRead ()
 
int main (int argc, char *argv[])
 

Variables

ostream * os_ = 0
 

Function Documentation

◆ testWriteRead() [1/2]

void testWriteRead ( const MSData msd,
const Serializer_mzML::Config config,
const DiffConfig diffcfg 
)

Definition at line 42 of file Serializer_mzML_Test.cpp.

43{
44 if (os_) *os_ << "testWriteRead() " << config << endl;
45
46 Serializer_mzML mzmlSerializer(config);
47
48 ostringstream oss;
49 mzmlSerializer.write(oss, msd);
50
51 if (os_) *os_ << "oss:\n" << oss.str() << endl;
52
53 shared_ptr<istringstream> iss(new istringstream(oss.str()));
54 MSData msd2;
55 mzmlSerializer.read(iss, msd2);
56
58
59 Diff<MSData, DiffConfig> diff(msd, msd2, diffcfg);
60 if (os_ && diff) *os_ << diff << endl;
62}
void diff(const string &filename1, const string &filename2)
ostream * os_
MSData <-> mzML stream serialization.
PWIZ_API_DECL void resolve(ParamContainer &paramContainer, const MSData &msd)
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Definition diff_std.hpp:143
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition MSData.hpp:850
#define unit_assert(x)
Definition unit.hpp:85

References diff(), os_, pwiz::msdata::Serializer_mzML::read(), pwiz::msdata::References::resolve(), unit_assert, and pwiz::msdata::Serializer_mzML::write().

◆ testWriteRead() [2/2]

void testWriteRead ( )

Definition at line 65 of file Serializer_mzML_Test.cpp.

66{
67 MSData msd;
69 for (int zloop=2;zloop--;) // run through once without zlib, then with
70 {
71 DiffConfig diffcfg;
73
74 if (!zloop) // retest with compression
76
78 testWriteRead(msd, config, diffcfg);
79
81 testWriteRead(msd, config, diffcfg);
82
83 config.indexed = false;
84 testWriteRead(msd, config, diffcfg);
85
86 // lossy compression, increase allowable mismatch
87 diffcfg.precision = 0.01;
89 testWriteRead(msd, config, diffcfg);
90
92 testWriteRead(msd, config, diffcfg);
93
96 testWriteRead(msd, config, diffcfg);
97
98 if (!zloop) // provoke numpress temp. disable
99 {
102 testWriteRead(msd, config, diffcfg);
103 }
104 }
105
106}
void testWriteRead()
MS_intensity_array
intensity array: A data array of intensity values.
Definition cv.hpp:2151
PWIZ_API_DECL void initializeTiny(MSData &msd)
std::map< cv::CVID, Numpress > numpressOverrides
configuration struct for diffing MSData types
Definition Diff.hpp:206
Serializer_mzML configuration.
BinaryDataEncoder::Config binaryDataEncoderConfig
configuration for binary data encoding in write() note: byteOrder is ignored (mzML always little endi...
bool indexed
(indexed==true): read/write with <indexedmzML> wrapper

References pwiz::msdata::Serializer_mzML::Config::binaryDataEncoderConfig, pwiz::msdata::BinaryDataEncoder::Config::compression, pwiz::msdata::BinaryDataEncoder::Compression_Zlib, pwiz::msdata::Serializer_mzML::Config::indexed, pwiz::msdata::examples::initializeTiny(), MS_intensity_array, pwiz::msdata::BinaryDataEncoder::Config::numpress, pwiz::msdata::BinaryDataEncoder::Numpress_Linear, pwiz::msdata::BinaryDataEncoder::Numpress_None, pwiz::msdata::BinaryDataEncoder::Numpress_Pic, pwiz::msdata::BinaryDataEncoder::Numpress_Slof, pwiz::msdata::BinaryDataEncoder::Config::numpressLinearErrorTolerance, pwiz::msdata::BinaryDataEncoder::Config::numpressOverrides, pwiz::msdata::BinaryDataEncoder::Config::numpressSlofErrorTolerance, pwiz::data::BaseDiffConfig::precision, pwiz::msdata::BinaryDataEncoder::Config::precision, pwiz::msdata::BinaryDataEncoder::Precision_32, pwiz::msdata::BinaryDataEncoder::Precision_64, testWriteRead(), and unit_assert.

Referenced by main(), and testWriteRead().

◆ main()

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

Definition at line 109 of file Serializer_mzML_Test.cpp.

110{
111 TEST_PROLOG(argc, argv)
112
113 try
114 {
115 if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
117 }
118 catch (exception& e)
119 {
120 TEST_FAILED(e.what())
121 }
122 catch (...)
123 {
124 TEST_FAILED("Caught unknown exception.")
125 }
126
128}
#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 testWriteRead().

Variable Documentation

◆ os_

ostream* os_ = 0

Definition at line 39 of file Serializer_mzML_Test.cpp.

Referenced by main(), and testWriteRead().