コード例 #1
0
    virtual void read(const string& filename, const string& head, MSData& result, int runIndex = 0) const
    {
        if (runIndex != 0)
            throw ReaderFail("[Reader_MGF::read] multiple runs not supported");

        shared_ptr<istream> is(new pwiz::util::random_access_compressed_ifstream(filename.c_str()));
        if (!is.get() || !*is)
            throw runtime_error(("[Reader_MGF::read] Unable to open file " + filename));

        Serializer_MGF serializer;
        serializer.read(is, result);
        fillInCommonMetadata(filename, result);
        result.fileDescription.sourceFilePtrs.back()->set(MS_multiple_peak_list_nativeID_format);
        result.fileDescription.sourceFilePtrs.back()->set(MS_Mascot_MGF_file);
        return;
    }
コード例 #2
0
void testModeMetaDataAndBinaryData()
{
    // initialize list
    MSData msd;
    shared_ptr<SpectrumListSimple> sl(new SpectrumListSimple);
    sl->spectra.push_back(makeSpectrumPtr(0, "S1"));
    sl->spectra.push_back(makeSpectrumPtr(1, "S2"));
    sl->spectra.push_back(makeSpectrumPtr(2, "S3"));
    sl->spectra.push_back(makeSpectrumPtr(3, "S4"));
    msd.run.spectrumListPtr = sl;

    // SpectrumListSimple returns the same shared_ptrs regardless of caching;
    // serializing to MGF and back will produce different shared_ptrs
    boost::shared_ptr<stringstream> ss(new stringstream);
    Serializer_MGF serializer;
    serializer.write(*ss, msd, 0);
    serializer.read(ss, msd);

    // access a series of spectra and make sure the cache behaves appropriately:
    // in metadata-and-binary-data mode, entries in the cache should:
    // - always have metadata
    // - always have binary data

    SpectrumPtr s;

    SpectrumListCache slc(msd.run.spectrumListPtr, MemoryMRUCacheMode_MetaDataAndBinaryData, 2);
    SpectrumListCache::CacheType& cache = slc.spectrumCache();

    unit_assert(cache.empty());
    unit_assert_operator_equal(2, cache.max_size());

    // metadata-only access should not affect the cache
    s = slc.spectrum(0, false);

    if (os_) *os_ << cache << endl;
    unit_assert(cache.empty());
    unit_assert_operator_equal(0, cache.size());

    s = slc.spectrum(1, true);

    // pointers should be equal
    unit_assert_operator_equal(slc.spectrum(1, true), s);

    if (os_) *os_ << cache << endl;
    unit_assert_operator_equal(1, cache.size());
    unit_assert_operator_equal(1, cache.mru().spectrum->index);
    unit_assert(spectrumHasMetadata(*cache.mru().spectrum));
    unit_assert(spectrumHasBinaryData(*cache.mru().spectrum));

    s = slc.spectrum(2, false);

    if (os_) *os_ << cache << endl;
    unit_assert_operator_equal(1, cache.size());
    unit_assert_operator_equal(1, cache.mru().spectrum->index);
    unit_assert(spectrumHasMetadata(*cache.mru().spectrum));
    unit_assert(spectrumHasBinaryData(*cache.mru().spectrum));

    s = slc.spectrum(3, true);

    // pointers should be equal
    unit_assert_operator_equal(slc.spectrum(3, true), s);

    if (os_) *os_ << cache << endl;
    unit_assert_operator_equal(2, cache.size());
    unit_assert_operator_equal(3, cache.mru().spectrum->index);
    unit_assert(spectrumHasMetadata(*cache.mru().spectrum));
    unit_assert(spectrumHasBinaryData(*cache.mru().spectrum));
    unit_assert_operator_equal(1, cache.lru().spectrum->index);
    unit_assert(spectrumHasMetadata(*cache.lru().spectrum));
    unit_assert(spectrumHasBinaryData(*cache.lru().spectrum));

    s = slc.spectrum(2, true);

    if (os_) *os_ << cache << endl;
    unit_assert_operator_equal(2, cache.size());
    unit_assert_operator_equal(2, cache.mru().spectrum->index);
    unit_assert(spectrumHasMetadata(*cache.mru().spectrum));
    unit_assert(spectrumHasBinaryData(*cache.mru().spectrum));
    unit_assert_operator_equal(3, cache.lru().spectrum->index);
    unit_assert(spectrumHasMetadata(*cache.lru().spectrum));
    unit_assert(spectrumHasBinaryData(*cache.lru().spectrum));
}