void CalvinCHPQuantificationFileUpdaterTest::testQuantification()
{
CreateReferenceFile();
CalvinCHPQuantificationFileUpdater upd;
upd.Initialize(TEST_FILE);
upd.UpdateQuantification(0, 123.0f);
upd.UpdateQuantification(2, 222.0f);
CHPQuantificationData data;
CHPQuantificationFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(TEST_FILE));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data));
CPPUNIT_ASSERT(data.GetEntryCount() == 4);
ProbeSetQuantificationData e;
data.GetQuantificationEntry(0, e);
CPPUNIT_ASSERT(e.name == "1");
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.quantification, 123.0f, 0.000001f);
data.GetQuantificationEntry(1, e);
CPPUNIT_ASSERT(e.name == "2");
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.quantification, 20.0f, 0.000001f);
data.GetQuantificationEntry(2, e);
CPPUNIT_ASSERT(e.name == "3");
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.quantification, 222.0f, 0.000001f);
data.GetQuantificationEntry(3, e);
CPPUNIT_ASSERT(e.name == "4");
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.quantification, 40.0f, 0.000001f);
}
/*
* Read the file.
*/
bool FusionCHPQuantificationData::Read()
{
CHPQuantificationFileReader reader;
reader.SetFilename(filename);
try
{
reader.Read(chpData);
return true;
}
catch(...)
{
return false;
}
}
void CHPQuantificationFileReaderTest::testReadId()
{
CHPQuantificationData data;
CHPQuantificationFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename("../data/CHP_quantification_file_id"));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data));
CPPUNIT_ASSERT(data.GetFilename() == "../data/CHP_quantification_file_id");
CPPUNIT_ASSERT(data.GetAlgName() == L"sig");
CPPUNIT_ASSERT(data.GetAlgVersion() == L"1.0");
CPPUNIT_ASSERT(data.GetArrayType() == L"test3");
CPPUNIT_ASSERT(data.GetEntryCount() == 2);
ParameterNameValueTypeList params = data.GetAlgParams();
CPPUNIT_ASSERT(params.size() == 1);
ParameterNameValueTypeList::iterator it=params.begin();
ParameterNameValueType param = *it;
CPPUNIT_ASSERT(param.GetName() == L"an1");
CPPUNIT_ASSERT(param.GetValueText() == L"av1");
params = data.GetSummaryParams();
CPPUNIT_ASSERT(params.size() == 1);
it=params.begin();
param = *it;
CPPUNIT_ASSERT(param.GetName() == L"sn1");
CPPUNIT_ASSERT(param.GetValueText() == L"sv1");
ProbeSetQuantificationData e;
data.GetQuantificationEntry(0, e);
CPPUNIT_ASSERT(e.id == 10);
CPPUNIT_ASSERT(e.quantification == 10.0f);
CPPUNIT_ASSERT(e.name == "");
data.GetQuantificationEntry(1, e);
CPPUNIT_ASSERT(e.id == 20);
CPPUNIT_ASSERT(e.quantification == 20.0f);
CPPUNIT_ASSERT(e.name == "");
}
void CHPQuantificationFileWriterTest::WriteTest()
{
ParameterNameValueTypeList params;
ParameterNameValueType param;
CHPQuantificationData data("CHP_quantification_file");
data.SetAlgName(L"sig");
data.SetAlgVersion(L"1.0");
data.SetArrayType(L"test3");
data.SetEntryCount(2, 10);
param.SetName(L"an1");
param.SetValueText(L"av1");
params.push_back(param);
data.AddAlgParams(params);
params.clear();
param.SetName(L"sn1");
param.SetValueText(L"sv1");
params.push_back(param);
data.AddSummaryParams(params);
CHPQuantificationFileWriter *writer = new CHPQuantificationFileWriter(data);
affymetrix_calvin_data::ProbeSetQuantificationData e;
writer->SeekToDataSet();
e.name = "abc";
e.quantification = 10.0f;
writer->WriteEntry(e);
e.name = "xyz";
e.quantification = 20.0f;
writer->WriteEntry(e);
delete writer;
CPPUNIT_ASSERT(1);
CHPQuantificationData data2;
CHPQuantificationFileReader reader;
reader.SetFilename("CHP_quantification_file");
reader.Read(data2);
CPPUNIT_ASSERT(data2.GetAlgName() == L"sig");
CPPUNIT_ASSERT(data2.GetAlgVersion() == L"1.0");
CPPUNIT_ASSERT(data2.GetArrayType() == L"test3");
CPPUNIT_ASSERT(data2.GetEntryCount() == 2);
ParameterNameValueTypeList p = data2.GetAlgParams();
ParameterNameValueTypeList::iterator it = p.begin();
param = *it;
CPPUNIT_ASSERT(param.GetName() == L"an1");
CPPUNIT_ASSERT(param.GetValueText() == L"av1");
p = data2.GetSummaryParams();
it = p.begin();
param = *it;
CPPUNIT_ASSERT(param.GetName() == L"sn1");
CPPUNIT_ASSERT(param.GetValueText() == L"sv1");
data2.GetQuantificationEntry(0, e);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.quantification, 10.0f, 0.0001f);
CPPUNIT_ASSERT(e.name == "abc");
data2.GetQuantificationEntry(1, e);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.quantification, 20.0f, 0.0001f);
CPPUNIT_ASSERT(e.name == "xyz");
}
