void CHPMultiDataFileReaderTest::testRead()
{
affymetrix_calvin_data::ProbeSetMultiDataExpressionData ex;
affymetrix_calvin_data::ProbeSetMultiDataGenotypeData gn;
ParameterNameValueType param;
CHPMultiDataData data2;
CHPMultiDataFileReader reader;
reader.SetFilename("../data/CHP_MultiData_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(ExpressionMultiDataType) == 1);
CPPUNIT_ASSERT(data2.GetEntryCount(GenotypeMultiDataType) == 2);
// expression
CPPUNIT_ASSERT(data2.GetNumMetricColumns(ExpressionMultiDataType) == 0);
data2.GetExpressionEntry(ExpressionMultiDataType, 0, ex);
CPPUNIT_ASSERT_DOUBLES_EQUAL(ex.quantification, 10.0f, 0.0001f);
CPPUNIT_ASSERT(ex.name == "ex1");
// genotype
CPPUNIT_ASSERT(data2.GetNumMetricColumns(GenotypeMultiDataType) == 2);
CPPUNIT_ASSERT(data2.GetMetricColumnName(GenotypeMultiDataType, 0) == L"int");
CPPUNIT_ASSERT(data2.GetMetricColumnName(GenotypeMultiDataType, 1) == L"float");
data2.GetGenotypeEntry(GenotypeMultiDataType, 0, gn);
CPPUNIT_ASSERT(gn.call == 1);
CPPUNIT_ASSERT_DOUBLES_EQUAL(gn.confidence, 11.0f, 0.0001f);
CPPUNIT_ASSERT(gn.name == "gn1");
CPPUNIT_ASSERT(gn.metrics.size() == 2);
param = gn.metrics[0];
CPPUNIT_ASSERT(param.GetParameterType() == ParameterNameValueType::Int32Type);
CPPUNIT_ASSERT(param.GetValueInt32() == 1);
param = gn.metrics[1];
CPPUNIT_ASSERT(param.GetParameterType() == ParameterNameValueType::FloatType);
CPPUNIT_ASSERT_DOUBLES_EQUAL(param.GetValueFloat(), 2.0f, 0.00001f);
data2.GetGenotypeEntry(GenotypeMultiDataType, 1, gn);
CPPUNIT_ASSERT(gn.call == 2);
CPPUNIT_ASSERT_DOUBLES_EQUAL(gn.confidence, 22.0f, 0.0001f);
CPPUNIT_ASSERT(gn.name == "gn2");
CPPUNIT_ASSERT(gn.metrics.size() == 2);
param = gn.metrics[0];
CPPUNIT_ASSERT(param.GetParameterType() == ParameterNameValueType::Int32Type);
CPPUNIT_ASSERT(param.GetValueInt32() == 2);
param = gn.metrics[1];
CPPUNIT_ASSERT(param.GetParameterType() == ParameterNameValueType::FloatType);
CPPUNIT_ASSERT_DOUBLES_EQUAL(param.GetValueFloat(), 3.0f, 0.00001f);
}
/*
* Read the file.
*/
bool FusionCHPMultiDataData::Read()
{
CHPMultiDataFileReader reader;
reader.SetFilename(filename);
try
{
reader.Read(chpData);
return true;
}
catch(...)
{
return false;
}
}
void CHPMultiDataFileReaderTest::testReadCNV()
{
affymetrix_calvin_data::ProbeSetMultiDataCopyNumberVariationRegionData e;
ParameterNameValueType param;
CHPMultiDataData data2;
CHPMultiDataFileReader reader;
reader.SetFilename("../data/CHP_MultiData_file_cnv");
reader.Read(data2);
CPPUNIT_ASSERT(data2.GetAlgName() == L"canary");
CPPUNIT_ASSERT(data2.GetAlgVersion() == L"1.0");
CPPUNIT_ASSERT(data2.GetArrayType() == L"test3");
CPPUNIT_ASSERT(data2.GetEntryCount(CopyNumberVariationMultiDataType) == 2);
CPPUNIT_ASSERT(data2.GetEntryCount(CopyNumberMultiDataType) == 0);
CPPUNIT_ASSERT(data2.GetEntryCount(GenotypeMultiDataType) == 0);
CPPUNIT_ASSERT(data2.GetEntryCount(ExpressionMultiDataType) == 0);
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.GetCopyNumberVariationEntry(CopyNumberVariationMultiDataType, 0, e);
CPPUNIT_ASSERT(e.call == 1);
CPPUNIT_ASSERT(e.name == "abc");
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.confidenceScore, 1.1f, 0.0001f);
CPPUNIT_ASSERT(e.signal == 100);
data2.GetCopyNumberVariationEntry(CopyNumberVariationMultiDataType, 1, e);
CPPUNIT_ASSERT(e.call == 2);
CPPUNIT_ASSERT(e.name == "xyz");
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.confidenceScore, 2.2, 0.0001f);
CPPUNIT_ASSERT(e.signal == 200);
}
void CalvinCHPMultiDataFileUpdaterTest::testMultiData1()
{
CreateReferenceFile1();
vector<ColumnInfo> cols;
CalvinCHPMultiDataFileUpdater upd;
ProbeSetMultiDataGenotypeData e;
upd.Initialize(TEST1_FILE);
e.call = 11;
e.confidence = 111.0f;
upd.UpdateMultiData(GenotypeMultiDataType, 0, e);
e.call = 22;
e.confidence = 222.0f;
upd.UpdateMultiData(GenotypeMultiDataType, 2, e);
CHPMultiDataData data;
CHPMultiDataFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(TEST1_FILE));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data));
CPPUNIT_ASSERT(data.GetEntryCount(GenotypeMultiDataType) == 4);
data.GetGenotypeEntry(GenotypeMultiDataType, 0, e);
CPPUNIT_ASSERT(e.name == "1");
CPPUNIT_ASSERT(e.call == 11);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.confidence, 111.0f, 0.000001f);
data.GetGenotypeEntry(GenotypeMultiDataType, 1, e);
CPPUNIT_ASSERT(e.name == "2");
CPPUNIT_ASSERT(e.call == 2);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.confidence, 20.0f, 0.000001f);
data.GetGenotypeEntry(GenotypeMultiDataType, 2, e);
CPPUNIT_ASSERT(e.name == "3");
CPPUNIT_ASSERT(e.call == 22);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.confidence, 222.0f, 0.000001f);
data.GetGenotypeEntry(GenotypeMultiDataType, 3, e);
CPPUNIT_ASSERT(e.name == "4");
CPPUNIT_ASSERT(e.call == 4);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.confidence, 40.0f, 0.000001f);
}
void CHPMultiDataFileReaderTest::testReadCN()
{
affymetrix_calvin_data::ProbeSetMultiDataCopyNumberData e;
ParameterNameValueType param;
CHPMultiDataData data2;
CHPMultiDataFileReader reader;
reader.SetFilename("../data/CHP_MultiData_file_cn");
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(CopyNumberMultiDataType) == 2);
CPPUNIT_ASSERT(data2.GetEntryCount(GenotypeMultiDataType) == 0);
CPPUNIT_ASSERT(data2.GetEntryCount(ExpressionMultiDataType) == 0);
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.GetCopyNumberEntry(CopyNumberMultiDataType, 0, e);
CPPUNIT_ASSERT(e.chr == 10);
CPPUNIT_ASSERT(e.position == 11);
CPPUNIT_ASSERT(e.name == "abc");
data2.GetCopyNumberEntry(CopyNumberMultiDataType, 1, e);
CPPUNIT_ASSERT(e.chr == 20);
CPPUNIT_ASSERT(e.position == 21);
CPPUNIT_ASSERT(e.name == "xyz");
}
void CalvinCHPMultiDataFileUpdaterTest::testMultiData3()
{
CreateReferenceFile3();
vector<ColumnInfo> cols;
ByteColumn bcol(L"byte");
cols.push_back(bcol);
UByteColumn ubcol(L"ubyte");
cols.push_back(ubcol);
ShortColumn scol(L"short");
cols.push_back(scol);
UShortColumn uscol(L"ushort");
cols.push_back(uscol);
IntColumn icol(L"int");
cols.push_back(icol);
UIntColumn uicol(L"uint");
cols.push_back(uicol);
FloatColumn fcol(L"float");
cols.push_back(fcol);
ASCIIColumn acol(L"ascii", 7);
cols.push_back(acol);
UnicodeColumn tcol(L"text", 10);
cols.push_back(tcol);
CalvinCHPMultiDataFileUpdater upd;
ProbeSetMultiDataCopyNumberData e;
ProbeSetMultiDataCytoRegionData c;
upd.Initialize(TEST3_FILE);
e.metrics.resize(9);
e.chr = 11;
e.position = 111;
e.metrics[0].SetValueInt8(9);
e.metrics[1].SetValueUInt8(10);
e.metrics[2].SetValueInt16(17);
e.metrics[3].SetValueUInt16(18);
e.metrics[4].SetValueInt32(33);
e.metrics[5].SetValueUInt32(34);
e.metrics[6].SetValueFloat(55.0f);
e.metrics[7].SetValueAscii("text");
e.metrics[8].SetValueText(L"ascii");
upd.UpdateMultiData(CopyNumberMultiDataType, 0, e, cols);
e.chr = 22;
e.position = 222;
e.metrics[0].SetValueInt8(10);
e.metrics[1].SetValueUInt8(11);
e.metrics[2].SetValueInt16(18);
e.metrics[3].SetValueUInt16(19);
e.metrics[4].SetValueInt32(34);
e.metrics[5].SetValueUInt32(35);
e.metrics[6].SetValueFloat(66.0f);
e.metrics[7].SetValueAscii("text2");
e.metrics[8].SetValueText(L"ascii2");
upd.UpdateMultiData(CopyNumberMultiDataType, 2, e, cols);
vector<ColumnInfo> cycols;
c.call = 11;
c.confidenceScore = 111.0f;
c.chr = 11;
c.startPosition = 11;
c.stopPosition = 22;
upd.UpdateMultiData(CytoMultiDataType, 0, c, cycols);
c.call = 2;
c.confidenceScore = 20.0f;
c.chr = 22;
c.startPosition = 22;
c.stopPosition = 33;
upd.UpdateMultiData(CytoMultiDataType, 1, c, cycols);
CHPMultiDataData data;
CHPMultiDataFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename(TEST3_FILE));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data));
CPPUNIT_ASSERT(data.GetEntryCount(CopyNumberMultiDataType) == 4);
CPPUNIT_ASSERT(data.GetEntryCount(CytoMultiDataType) == 2);
data.GetCopyNumberEntry(CopyNumberMultiDataType, 0, e);
CPPUNIT_ASSERT(e.name == "1");
CPPUNIT_ASSERT(e.chr == 11);
CPPUNIT_ASSERT(e.position == 111);
CPPUNIT_ASSERT(e.metrics[0].GetValueInt8() == 9);
CPPUNIT_ASSERT(e.metrics[1].GetValueUInt8() == 10);
CPPUNIT_ASSERT(e.metrics[2].GetValueInt16() == 17);
CPPUNIT_ASSERT(e.metrics[3].GetValueUInt16() == 18);
CPPUNIT_ASSERT(e.metrics[4].GetValueInt32() == 33);
CPPUNIT_ASSERT(e.metrics[5].GetValueUInt32() == 34);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.metrics[6].GetValueFloat(), 55.0f, 0.00001f);
CPPUNIT_ASSERT(e.metrics[7].GetValueAscii() == "text");
CPPUNIT_ASSERT(e.metrics[8].GetValueText() == L"ascii");
data.GetCopyNumberEntry(CopyNumberMultiDataType, 1, e);
CPPUNIT_ASSERT(e.name == "2");
CPPUNIT_ASSERT(e.chr == 2);
CPPUNIT_ASSERT(e.position == 20);
CPPUNIT_ASSERT(e.metrics[0].GetValueInt8() == 8);
CPPUNIT_ASSERT(e.metrics[1].GetValueUInt8() == 8);
CPPUNIT_ASSERT(e.metrics[2].GetValueInt16() == 16);
CPPUNIT_ASSERT(e.metrics[3].GetValueUInt16() == 16);
CPPUNIT_ASSERT(e.metrics[4].GetValueInt32() == 32);
CPPUNIT_ASSERT(e.metrics[5].GetValueUInt32() == 32);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.metrics[6].GetValueFloat(), 44.0f, 0.00001f);
CPPUNIT_ASSERT(e.metrics[7].GetValueAscii() == "ascii");
CPPUNIT_ASSERT(e.metrics[8].GetValueText() == L"text");
data.GetCopyNumberEntry(CopyNumberMultiDataType, 2, e);
CPPUNIT_ASSERT(e.name == "3");
CPPUNIT_ASSERT(e.chr == 22);
CPPUNIT_ASSERT(e.position == 222);
CPPUNIT_ASSERT(e.metrics[0].GetValueInt8() == 10);
CPPUNIT_ASSERT(e.metrics[1].GetValueUInt8() == 11);
CPPUNIT_ASSERT(e.metrics[2].GetValueInt16() == 18);
CPPUNIT_ASSERT(e.metrics[3].GetValueUInt16() == 19);
CPPUNIT_ASSERT(e.metrics[4].GetValueInt32() == 34);
CPPUNIT_ASSERT(e.metrics[5].GetValueUInt32() == 35);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.metrics[6].GetValueFloat(), 66.0f, 0.00001f);
CPPUNIT_ASSERT(e.metrics[7].GetValueAscii() == "text2");
CPPUNIT_ASSERT(e.metrics[8].GetValueText() == L"ascii2");
data.GetCopyNumberEntry(CopyNumberMultiDataType, 3, e);
CPPUNIT_ASSERT(e.name == "4");
CPPUNIT_ASSERT(e.chr == 4);
CPPUNIT_ASSERT(e.position == 40);
CPPUNIT_ASSERT(e.metrics[0].GetValueInt8() == 8);
CPPUNIT_ASSERT(e.metrics[1].GetValueUInt8() == 8);
CPPUNIT_ASSERT(e.metrics[2].GetValueInt16() == 16);
CPPUNIT_ASSERT(e.metrics[3].GetValueUInt16() == 16);
CPPUNIT_ASSERT(e.metrics[4].GetValueInt32() == 32);
CPPUNIT_ASSERT(e.metrics[5].GetValueUInt32() == 32);
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.metrics[6].GetValueFloat(), 44.0f, 0.00001f);
CPPUNIT_ASSERT(e.metrics[7].GetValueAscii() == "ascii");
CPPUNIT_ASSERT(e.metrics[8].GetValueText() == L"text");
data.GetCytoEntry(CytoMultiDataType, 0, c);
CPPUNIT_ASSERT(c.name == "1");
CPPUNIT_ASSERT(c.call == 11);
CPPUNIT_ASSERT(c.chr == 11);
CPPUNIT_ASSERT(c.startPosition == 11);
CPPUNIT_ASSERT(c.stopPosition == 22);
CPPUNIT_ASSERT_DOUBLES_EQUAL(c.confidenceScore, 111.0f, 0.00001f);
data.GetCytoEntry(CytoMultiDataType, 1, c);
CPPUNIT_ASSERT(c.name == "2");
CPPUNIT_ASSERT(c.chr == 22);
CPPUNIT_ASSERT(c.startPosition == 22);
CPPUNIT_ASSERT(c.stopPosition == 33);
CPPUNIT_ASSERT(c.call == 2);
CPPUNIT_ASSERT_DOUBLES_EQUAL(c.confidenceScore, 20.0f, 0.00001f);
}
