Serializer_protXML_Test.cpp File Reference

#include "pwiz/utility/misc/Std.hpp"
#include "pwiz/data/identdata/DefaultReaderList.hpp"
#include "pwiz/data/identdata/IdentDataFile.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "Serializer_protXML.hpp"
#include "Diff.hpp"
#include "References.hpp"
#include "examples.hpp"
#include "pwiz/utility/misc/Filesystem.hpp"
#include "pwiz/data/proteome/Digestion.hpp"
#include "TextWriter.hpp"
#include "boost/range/adaptor/transformed.hpp"
#include "boost/range/algorithm/max_element.hpp"
#include "boost/range/algorithm/min_element.hpp"
#include <cstring>

Go to the source code of this file.

Functions
void	testSerialize (const string &example_data_dir)
int	main (int argc, char **argv)

Variables
ostream *	os_ = 0

---

Function Documentation

void testSerialize

(

const string &

example_data_dir

)

Definition at line 50 of file Serializer_protXML_Test.cpp.

References pwiz::data::BaseDiffConfig::ignoreVersions, os_, pwiz::identdata::ReaderList::read(), and unit_assert.

{
    DefaultReaderList readers;
    Reader::Config readerConfig;
        DiffConfig diffconfig;
    diffconfig.ignoreVersions = true;

    {
    // verify that loading protXML with reachable pepXML source files gives more 
    // (well, different) data than pepXML alone
    IdentData mzid0,mzid1;
    readers.read(example_data_dir+"/example.pep.xml", mzid0, readerConfig);
    readers.read(example_data_dir+"/example.prot.xml", mzid1, readerConfig);
    Diff<IdentData, DiffConfig> diff0(diffconfig);
    diff0(mzid0, mzid1);
    unit_assert(diff0);
    }

    {
    // verify that adding protxml to pepXML is equivalent to loading protXML with reachable
    // pepXML source files 
    IdentData mzid0,mzid1;
    readers.read(example_data_dir+"/example.pep.xml", mzid0, readerConfig);
    readers.read(example_data_dir+"/example.prot.xml", mzid0, readerConfig);
    readers.read(example_data_dir+"/example.prot.xml", mzid1, readerConfig);
    Diff<IdentData, DiffConfig> diff1(diffconfig);
    diff1(mzid0, mzid1);
    if (os_ && diff1) *os_ << diff1 << endl; 
    unit_assert(!diff1);
    }

    {
    // verify that loading protXML is the same as loading a known-good mzIdentML file
    IdentData mzid0,mzid1;
    readers.read(example_data_dir+"/example.prot.xml", mzid0, readerConfig);
    readers.read(example_data_dir+"/example.prot.mzid", mzid1, readerConfig);
    Diff<IdentData, DiffConfig> diff2(diffconfig);
    diff2(mzid0, mzid1);
    if (os_ && diff2) *os_ << diff2 << endl; 
    else if (diff2) cout << diff2 << endl; 
    unit_assert(!diff2);
    }
}

int main	(	int	argc,
		char **	argv
	)

Definition at line 95 of file Serializer_protXML_Test.cpp.

References e(), os_, TEST_EPILOG, TEST_FAILED, TEST_PROLOG, and testSerialize().

{
    TEST_PROLOG(argc, argv)

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        std::string srcparent(argv[0]);
        size_t pos = srcparent.find("build");

        if (pos == std::string::npos) {
            srcparent = __FILE__; // nonstandard build, maybe?  try using source file name
            // something like \ProteoWizard\pwiz\pwiz\data\identdata\Serializer_ProtXML_Test.cpp
            pos = srcparent.rfind("pwiz");
        }
        srcparent.resize(pos);
        string example_data_dir = srcparent + "example_data";
        testSerialize(example_data_dir);
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

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Variable Documentation

ostream* os_ = 0

Definition at line 48 of file Serializer_protXML_Test.cpp.