void TestFileGenerator::WriteSmallCelFileWithAPartialDatHeaderTest()
{
CelFileData data("small_cel_file_partial_datheader");
// Write
ParameterNameValueType nvt;
GenericDataHeader datHdr;
datHdr.SetFileId(AffymetrixGuid::GenerateNewGuid());
datHdr.SetFileTypeId("affymetrix-calvin-scan-acquisition");
datHdr.SetFileCreationTime(L"2004-07-01T13:14:15Z");
nvt.SetName(L"affymetrix-partial-dat-header");
std::wstring datHeaderString = L" small_cel_file_partial_datheader:CLS=25 RWS=25 XIN=1 YIN=1 VE=0 0 05/19/05 02:45:59 ScannerID: ScannerTyp \x14 \x14 Hg-Small.1sq \x14 \x14 \x14 \x14 \x14 570 \x14 45.200001 \x14 0.340000 \x14 1.0900 \x14 3";
nvt.SetValueText(datHeaderString);
datHdr.AddNameValParam(nvt);
nvt.SetName(L"affymetrix-max-pixel-intensity");
nvt.SetValueUInt16(46001);
datHdr.AddNameValParam(nvt);
nvt.SetName(L"affymetrix-min-pixel-intensity");
nvt.SetValueUInt16(1);
datHdr.AddNameValParam(nvt);
// Add DAT GenericDataHeader as parent.
data.GetFileHeader()->GetGenericDataHdr()->AddParent(datHdr);
WriteRemaingSmallCelFileWithGridParameters(data);
}
void CHPQuantificationDataTest::test_AlgParams()
{
ParameterNameValueTypeList params;
ParameterNameValueType param;
CHPQuantificationData data;
param.SetName(L"n1");
param.SetValueText(L"v1");
params.push_back(param);
param.SetName(L"n2");
param.SetValueText(L"v2");
params.push_back(param);
data.AddAlgParams(params);
ParameterNameValueTypeList params_out = data.GetAlgParams();
CPPUNIT_ASSERT(params_out.size() == 2);
ParameterNameValueTypeList::iterator it = params_out.begin();
param = *it;
CPPUNIT_ASSERT(param.GetName() == L"n1");
CPPUNIT_ASSERT(param.GetValueText() == L"v1");
++it;
param = *it;
CPPUNIT_ASSERT(param.GetName() == L"n2");
CPPUNIT_ASSERT(param.GetValueText() == L"v2");
}
void TestFileGenerator::AddStandardGenericDataHeader(GenericDataHeader& gdh)
{
// Fill the GenericDataHeader.
gdh.SetFileTypeId(SCAN_ACQUISITION_DATA_TYPE);
gdh.SetFileId("test-dat-guid");
gdh.SetFileCreationTime(L"2004-07-04T11:12:13Z");
gdh.SetLocale(L"en-US");
ParameterNameValueType nvt;
nvt.SetName(ARRAY_TYPE_PARAM_NAME);
nvt.SetValueText(L"Hg-U133A");
gdh.AddNameValParam(nvt);
nvt.SetName(ARRAY_BARCODE_PARAM_NAME);
nvt.SetValueText(L"Barcode");
gdh.AddNameValParam(nvt);
nvt.SetName(L"Parameter1");
nvt.SetValueText(L"Value1");
gdh.AddNameValParam(nvt);
GenericDataHeader gdhParent;
gdhParent.SetFileTypeId(ARRAY_TYPE_IDENTIFIER);
gdhParent.SetFileId("test-array-guid");
gdhParent.SetFileCreationTime(L"2004-07-01T13:14:15Z");
gdhParent.SetLocale(L"en-US");
nvt.SetName(ARRAY_TYPE_PARAM_NAME);
nvt.SetValueText(L"Hg-U133A");
gdhParent.AddNameValParam(nvt);
nvt.SetName(ARRAY_LOT_PARAM_NAME);
nvt.SetValueText(L"Thanks alot");
gdhParent.AddNameValParam(nvt);
gdh.AddParent(gdhParent);
}
void CHPMultiDataDataTest::test_SumParams()
{
ParameterNameValueTypeList params;
ParameterNameValueType param;
CHPMultiDataData data;
param.SetName(L"n1");
param.SetValueText(L"v1");
params.push_back(param);
param.SetName(L"n2");
param.SetValueText(L"v2");
params.push_back(param);
data.AddSummaryParams(params);
ParameterNameValueTypeList params_out = data.GetSummaryParams();
CPPUNIT_ASSERT(params_out.size() == 2);
ParameterNameValueTypeList::iterator it = params_out.begin();
param = *it;
CPPUNIT_ASSERT(param.GetName() == L"n1");
CPPUNIT_ASSERT(param.GetValueText() == L"v1");
++it;
param = *it;
CPPUNIT_ASSERT(param.GetName() == L"n2");
CPPUNIT_ASSERT(param.GetValueText() == L"v2");
}
void TestFileGenerator::WriteSmallCelFileNoStdev()
{
CelFileData data("small_cel_file_no_stdev");
data.SetIntensityCount(25);
data.SetStdDevCount(0);
data.SetPixelCount(25);
data.SetOutlierCount(2);
data.SetMaskCount(3);
data.SetRows(5);
data.SetCols(5);
data.SetArrayType(L"Hg-small");
data.SetAlgorithmName(L"Feature Extraction");
ParameterNameValueType nvt;
nvt.SetName(L"percentile");
nvt.SetValueFloat(0.75f);
data.AddAlgorithmParameter(nvt);
nvt.SetName(L"outlierlow");
nvt.SetValueFloat(1.004f);
data.AddAlgorithmParameter(nvt);
CelFileWriter* writer = new CelFileWriter(data);
FloatVector vInten;
Int16Vector vPixels;
for (int i=0; i<25; ++i)
{
vInten.push_back(100.0f*i);
vPixels.push_back(25);
}
// Do some writing
writer->WriteIntensities(vInten);
writer->WritePixels(vPixels);
// XYCoordVector
XYCoordVector outlier;
XYCoord xy(0,0);
outlier.push_back(xy);
xy.xCoord = 1;
xy.yCoord = 2;
outlier.push_back(xy);
writer->WriteOutlierCoords(outlier);
XYCoordVector masked;
xy.xCoord = 1;
xy.yCoord = 0;
masked.push_back(xy);
xy.xCoord = 2;
xy.yCoord = 1;
masked.push_back(xy);
xy.xCoord = 3;
xy.yCoord = 2;
masked.push_back(xy);
writer->WriteMaskCoords(masked);
delete writer;
}
void TestFileGenerator::WriteOutGenericDATDataFileNoGrid()
{
GenericDataHeader gdh;
AddStandardGenericDataHeader(gdh);
// Fill the DataGroupHeader
DataGroupHeader dch;
dch.SetName(L"First Data Cube");
// Fill the DataSetHeader
DataSetHeader dph;
dph.SetName(L"acquired data");
ParameterNameValueType nvt;
nvt.SetName(L"Scanner");
nvt.SetValueText(L"M10");
dph.AddNameValParam(nvt);
nvt.SetName(L"Pixel Size");
nvt.SetValueFloat(0.051f);
dph.AddNameValParam(nvt);
dph.AddColumn(UShortColumn(L"Pixel"));
int32_t rows = 100;
dph.SetRowCnt(rows);
dch.AddDataSetHdr(dph);
// Set the FileHeader
FileHeader fh;
fh.SetFilename("test.file.data_dat");
fh.SetGenericDataHdr(gdh);
fh.AddDataGroupHdr(dch);
// Create the generic file writer
GenericFileWriter gfWriter(&fh);
gfWriter.WriteHeader();
DataGroupWriterIt dcwBegin, dcwEnd;
gfWriter.GetDataGroupWriters(dcwBegin, dcwEnd);
DataGroupWriter d = *dcwBegin;
dcwBegin->WriteHeader();
DataSetWriterIt dpwBegin, dpwEnd;
dcwBegin->GetDataSetWriters(dpwBegin, dpwEnd);
dpwBegin->WriteHeader();
// Write out the data
for( int32_t i=0; i < rows; ++i )
{
u_int16_t value = (u_int16_t)(i*10+i);
dpwBegin->Write(value);
}
dpwBegin->UpdateNextDataSetOffset();
dcwBegin->Close();
}
void DATFileUpdaterTest::AddParameters(DATData& data)
{
ParameterNameValueType nvt;
nvt.SetName(L"Santa Clara");
nvt.SetValueUInt8(56);
data.AddGridAlignmentAlgorithmParameter(nvt);
nvt.SetName(L"San Mateo");
nvt.SetValueFloat(4.56f);
data.AddGridAlignmentAlgorithmParameter(nvt);
}
/*
* Save the program information to the AGCC file.
*/
void MAS5CHPUtils::StoreProgramInfo()
{
ParameterNameValueType p;
p.SetName(PROGRAM_NAME);
p.SetValueText(programName);
cc_data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(p);
p.SetName(PROGRAM_ID);
p.SetValueText(programId);
cc_data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(p);
p.SetName(PROGRAM_COMPANY);
p.SetValueText(programCompany);
cc_data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(p);
}
void DataGroupHeaderTest::FindDataSetHeaderTest()
{
// Create DataSetHeaders
DataSetHeader dph1;
dph1.SetName(L"pixel intensity");
ParameterNameValueType param;
param.SetName(L"Scanner");
param.SetValueText(L"M10");
dph1.AddNameValParam(param);
dph1.AddUShortColumn(L"");
dph1.SetRowCnt(1);
DataSetHeader dph2;
dph2.SetName(L"grid coordinates");
param.SetName(L"Corner Pattern");
param.SetValueText(L"Checkerboard");
dph2.AddNameValParam(param);
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.AddUShortColumn(L"");
dph2.SetRowCnt(1);
header->AddDataSetHdr(dph1);
header->AddDataSetHdr(dph2);
const DataSetHeader* dph = header->FindDataSetHeader(L"none");
CPPUNIT_ASSERT(0 == dph);
dph = header->FindDataSetHeader(dph1.GetName());
CPPUNIT_ASSERT(0 != dph);
CPPUNIT_ASSERT(dph->GetName() == dph1.GetName());
dph = header->FindDataSetHeader(dph2.GetName());
CPPUNIT_ASSERT(0 != dph);
CPPUNIT_ASSERT(dph->GetName() == dph2.GetName());
}
/*
* Store the start index and count of probe sets for the given chromosome.
*/
void CopyNumberResultWriter::SetChromosomeProbeSetIndexInformation(u_int8_t chr, int startIndex, int count)
{
ostringstream str;
str << (int) chr;
wstring schr = StringUtils::ConvertMBSToWCS(str.str());
ParameterNameValueType param;
param.SetName(schr + L":start");
param.SetValueInt32(startIndex);
chrStartStop.push_back(param);
param.SetName(schr + L":count");
param.SetValueInt32(count);
chrStartStop.push_back(param);
param.SetName(schr + L":display");
param.SetValueAscii(ChromosomeToString(chr));
chrStartStop.push_back(param);
}
void TestFileGenerator::WriteCelFileWithADataSetWithZeroRows()
{
CelFileData data("small_cel_file_with_dataset_of_zero_rows");
data.SetIntensityCount(25);
data.SetStdDevCount(25);
data.SetPixelCount(25);
data.SetOutlierCount(0);
data.SetMaskCount(0);
data.SetRows(5);
data.SetCols(5);
data.SetArrayType(L"Hg-small");
data.SetAlgorithmName(L"Feature Extraction");
ParameterNameValueType nvt;
nvt.SetName(L"percentile");
nvt.SetValueFloat(0.75f);
data.AddAlgorithmParameter(nvt);
nvt.SetName(L"outlierlow");
nvt.SetValueFloat(1.004f);
data.AddAlgorithmParameter(nvt);
CelFileWriter* writer = new CelFileWriter(data);
FloatVector vInten;
FloatVector vStdev;
Int16Vector vPixels;
for (int i=0; i<25; ++i)
{
vInten.push_back(100.0f*i);
vStdev.push_back(.123f);
vPixels.push_back(25);
}
// Do some writing
writer->WriteIntensities(vInten);
writer->WriteStdDevs(vStdev);
writer->WritePixels(vPixels);
XYCoordVector outlier;
writer->WriteOutlierCoords(outlier);
XYCoordVector masked;
writer->WriteMaskCoords(masked);
delete writer;
}
void CHPQuantificationData::SetWStringToGenericHdr(const std::wstring& name, const std::wstring value, int32_t reserve)
{
ParameterNameValueType paramType;
paramType.SetName(name);
paramType.SetValueText(value, reserve);
GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
hdr->AddNameValParam(paramType);
}
void CHPData::SetFloatToGenericHdr(const std::wstring& name, float value)
{
ParameterNameValueType paramType;
paramType.SetName(name);
paramType.SetValueFloat(value);
GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
hdr->AddNameValParam(paramType);
}
void CDFData::SetUInt32ToGenericHdr(const std::wstring& name, u_int32_t value)
{
ParameterNameValueType paramType;
paramType.SetName(name);
paramType.SetValueUInt32(value);
GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
hdr->AddNameValParam(paramType);
}
void CDFData::SetRefSequence(const std::string &seq)
{
GenericDataHeader* gPtr = genericData.Header().GetGenericDataHdr();
ParameterNameValueType paramType;
paramType.SetName(CDF_REFSEQ_PARAM);
paramType.SetValueAscii(seq);
gPtr->AddNameValParam(paramType);
}
ParameterNameValueType CHPData::GetChipSum(const std::wstring& tag)
{
std::wstring name = CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S + tag;
ParameterNameValueType paramType;
GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
hdr->FindNameValParam(name, paramType);
ParameterNameValueType type = paramType;
type.SetName(tag);
return type;
}
void TestFileGenerator::WriteSmallDatFileWithGridAndSubgridsAndParameters()
{
std::string filename = "small_DAT_file_with_subgrids_and_parameters";
WriteDatFile(filename, L"Hg-small", 4, 5, true);
DATData data(filename);
AddGridAndSubgrids(data, 2.5, 10);
ParameterNameValueType nvt;
nvt.SetName(L"Zip Code");
nvt.SetValueInt32(95051);
data.AddGridAlignmentAlgorithmParameter(nvt);
nvt.SetName(L"County");
nvt.SetValueText(L"Santa Clara");
data.AddGridAlignmentAlgorithmParameter(nvt);
DATFileUpdater update(data);
update.Update();
}
ParameterNameValueType CHPData::GetAlgParam(const std::wstring& tag)
{
std::wstring name = ALGORITHM_PARAM_NAME_PREFIX_S + tag;
ParameterNameValueType paramType;
GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
hdr->FindNameValParam(name, paramType);
ParameterNameValueType type = paramType;
type.SetName(tag);
return type;
}
void CHPMultiDataData::AddAppMetaInfo(const ParameterNameValueTypeList& params)
{
ParameterNameValueType param;
GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); ++it)
{
param = *it;
param.SetName(APPLICATION_META_INFO_PREFIX_S + param.GetName());
hdr->AddNameValParam(param);
}
}
void CHPMultiDataData::AddAlgParams(const ParameterNameValueTypeList& params)
{
ParameterNameValueType param;
GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); it++)
{
param = *it;
param.SetName(ALGORITHM_PARAM_NAME_PREFIX_S + param.GetName());
hdr->AddNameValParam(param);
}
}
void CHPQuantificationData::AddSummaryParams(const ParameterNameValueTypeList& params)
{
ParameterNameValueType param;
GenericDataHeader* hdr = genericData.Header().GetGenericDataHdr();
for (ParameterNameValueTypeList::const_iterator it=params.begin(); it != params.end(); it++)
{
param = *it;
param.SetName(CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S + param.GetName());
hdr->AddNameValParam(param);
}
}
void TestFileGenerator::WriteSmallCelFileNoOutlierNoMask()
{
CelFileData data("small_cel_file_no_outlier_no_mask");
data.SetIntensityCount(10);
data.SetStdDevCount(10);
data.SetPixelCount(10);
data.SetOutlierCount(0);
data.SetMaskCount(0);
data.SetRows(2);
data.SetCols(5);
data.SetArrayType(L"Hg-small");
data.SetAlgorithmName(L"Feature Extraction");
ParameterNameValueType nvt;
nvt.SetName(L"percentile");
nvt.SetValueFloat(0.75f);
data.AddAlgorithmParameter(nvt);
nvt.SetName(L"outlierlow");
nvt.SetValueFloat(1.004f);
data.AddAlgorithmParameter(nvt);
CelFileWriter* writer = new CelFileWriter(data);
FloatVector vInten;
FloatVector vStdev;
Int16Vector vPixels;
for (int i=0; i<10; ++i)
{
vInten.push_back(100.0f*i);
vStdev.push_back(.5*i);
vPixels.push_back(25);
}
// Do some writing
writer->WriteIntensities(vInten);
writer->WriteStdDevs(vStdev);
writer->WritePixels(vPixels);
delete writer;
}
bool DataSetHeader::FindNameValParam(const std::wstring& name, ParameterNameValueType& result) const
{
ParameterNameValueType t;
t.SetName(name);
t.SetValueText(L"");
ParameterNameValueTypeConstIt found = FindNameValParam(t);
if (found != nameValParams.end())
{
result = *found;
return true;
}
return false;
}
void TestFileGenerator::WriteSmallDatFileWithReservedStringParameters()
{
int32_t rows = 4;
int32_t cols = 5;
int32_t pixelCount = rows*cols;
DATData data("small_dat_file_with_reserved_string_parameters");
data.SetPixelCount(pixelCount);
data.SetStatsCount(1);
data.SetArrayType(L"Hg_small");
data.SetPixelSize(0.71f);
data.SetScannerType(L"M10");
data.SetScannerID(L"main");
DateTime dt = DateTime::Parse(L"2005-12-25T11:12:13Z");
data.SetScanDate(dt);
data.SetRows(rows);
data.SetCols(cols);
std::string arrayId = "smellsliketeenspirit";
data.SetArrayId(arrayId);
ParameterNameValueType nvt;
nvt.SetName(L"fixedlen");
nvt.SetValueText(L"twenty-five", 25);
data.GetFileHeader()->GetGenericDataHdr()->AddNameValParam(nvt);
DATFileWriter writer(data);
Uint16Vector pixels;
pixels.reserve(pixelCount);
u_int16_t inten = 10;
for (int32_t i=0; i<pixelCount; ++i, ++inten)
{
if (inten > 46000)
{
inten = 0;
}
pixels.push_back(inten);
}
Uint16Vector stats;
stats.push_back(pixels[0]); // min
stats.push_back(pixels[19]); // max
writer.WriteStats(stats);
writer.WritePixels(pixels);
}
void TestFileGenerator::WriteSmallCelFileWithAFullDatHeaderTest() // Files converted from GCOS will have a full DatHeader
{
CelFileData data("small_cel_file_full_datheader");
// Write
ParameterNameValueType nvt;
GenericDataHeader datHdr;
datHdr.SetFileId(AffymetrixGuid::GenerateNewGuid());
datHdr.SetFileTypeId("affymetrix-calvin-scan-acquisition");
datHdr.SetFileCreationTime(L"2004-07-01T13:14:15Z");
nvt.SetName(L"affymetrix-dat-header");
std::wstring datHeaderString = L"[45..56789] small_cel_file_full_datheader:CLS=25 RWS=25 XIN=1 YIN=1 VE=0 0 05/19/05 02:45:59 ScannerID: ScannerTyp \x14 \x14 Hg-Small.1sq \x14 \x14 \x14 \x14 \x14 570 \x14 45.200001 \x14 0.340000 \x14 1.0900 \x14 3";
nvt.SetValueText(datHeaderString);
datHdr.AddNameValParam(nvt);
// Add DAT GenericDataHeader as parent.
data.GetFileHeader()->GetGenericDataHdr()->AddParent(datHdr);
WriteRemaingSmallCelFileWithGridParameters(data);
}
ParameterNameValueTypeList CHPQuantificationData::GetSummaryParams()
{
ParameterNameValueTypeList nvt;
ParameterNameValueTypeIt begin, end;
ParameterNameValueType param;
genericData.Header().GetGenericDataHdr()->GetNameValIterators(begin, end);
while(begin != end)
{
std::wstring key = begin->GetName();
if(key.compare(0, CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S.size(),CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S) == 0)
{
param = *begin;
key.erase(0, CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S.size());
param.SetName(key);
nvt.push_back(param);
}
begin++;
}
return nvt;
}
ParameterNameValueTypeVector CHPData::GetAlgParams()
{
ParameterNameValueTypeVector nvt;
ParameterNameValueTypeIt begin, end;
ParameterNameValueType param;
genericData.Header().GetGenericDataHdr()->GetNameValIterators(begin, end);
while(begin != end)
{
std::wstring key = begin->GetName();
if(key.compare(0, ALGORITHM_PARAM_NAME_PREFIX_S.size(),ALGORITHM_PARAM_NAME_PREFIX_S) == 0)
{
param = *begin;
key.erase(0, ALGORITHM_PARAM_NAME_PREFIX_S.size());
param.SetName(key);
nvt.push_back(param);
}
begin++;
}
return nvt;
}
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile2()
{
CHPMultiDataData data(TEST2_FILE);
vector<ColumnInfo> cols;
ParameterNameValueType nv;
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);
ProbeSetMultiDataGenotypeData e;
data.SetEntryCount(GenotypeMultiDataType, 4, 10, cols);
CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data);
nv.SetName(L"byte");
nv.SetValueInt8(8);
e.metrics.push_back(nv);
nv.SetName(L"ubyte");
nv.SetValueUInt8(8);
e.metrics.push_back(nv);
nv.SetName(L"short");
nv.SetValueInt16(16);
e.metrics.push_back(nv);
nv.SetName(L"ushort");
nv.SetValueUInt16(16);
e.metrics.push_back(nv);
nv.SetName(L"int");
nv.SetValueInt32(32);
e.metrics.push_back(nv);
nv.SetName(L"uint");
nv.SetValueUInt32(32);
e.metrics.push_back(nv);
nv.SetName(L"float");
nv.SetValueFloat(44.0f);
e.metrics.push_back(nv);
nv.SetName(L"ascii");
nv.SetValueAscii("ascii");
e.metrics.push_back(nv);
nv.SetName(L"text");
nv.SetValueText(L"text");
e.metrics.push_back(nv);
writer->SeekToDataSet(GenotypeMultiDataType);
e.name = "1";
e.call = 1;
e.confidence = 10.0f;
writer->WriteEntry(e);
e.name = "2";
e.call = 2;
e.confidence = 20.0f;
writer->WriteEntry(e);
e.name = "3";
e.call = 3;
e.confidence = 30.0f;
writer->WriteEntry(e);
e.name = "4";
e.call = 4;
e.confidence = 40.0f;
writer->WriteEntry(e);
delete writer;
}
/**
* Get set up for a run of reporting probesets. Often used to open file
* streams and print headers to files etc.
*
* @param qMethod - Quantification method to be used.
* @param layout - Where the probesets, probes, etc are on the chip.
*
* @return true if success, false otherwise.
*/
bool QuantMethodExprCCCHPReport::prepare(QuantMethod &qMethod, const IntensityMart &iMart)
{
QuantExprMethod *eMethod = dynamic_cast<QuantExprMethod *>(&qMethod);
if (eMethod == NULL) { Err::errAbort("Can only use a QuantMethodExprReport with a QuantExprMethod."); }
setupFileNames(iMart);
int nfiles = m_CHPFileNames.size();
// Make sure our output directory exists.
if (!Fs::isWriteableDir(m_Prefix.c_str()) &&
(Fs::mkdirPath(m_Prefix, false) != APT_OK)) {
APT_ERR_ABORT("Can't make or write to directory: " + m_Prefix);
}
removeAllChps();
// Get CEL file GUIDs
///@todo This be computed by the engine and passed in via AnalysisInfo
m_celGuids.resize(nfiles);
std::string tmp_unc_name;
for (int chip=0; chip<nfiles; chip++) {
FusionCELData cel;
try {
tmp_unc_name=Fs::convertToUncPath(m_CELFileNames[chip]);
cel.SetFileName(tmp_unc_name.c_str());
if (!cel.ReadHeader()) {
Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name));
}
GenericData *gdata = cel.GetGenericData();
if (gdata != NULL) {
m_celGuids[chip] = gdata->Header().GetGenericDataHdr()->GetFileId();
}
cel.Close();
}
catch (...) {
Err::errAbort("Unable to read CEL file " + tmp_unc_name);
}
}
int maxProbeSetNameLength = 0;
for (int i=0; i<m_Info.m_ProbesetNames.size(); i++) {
int len = (int)strlen(m_Info.m_ProbesetNames.at(i));
if (m_Info.m_ProbesetDisplayNames.size() > 0 && m_Info.m_ProbesetDisplayNames.at(i) != NULL)
len = (int)strlen(m_Info.m_ProbesetDisplayNames.at(i));
maxProbeSetNameLength = Max(maxProbeSetNameLength, len);
}
// Prepare headers for all CHP files.
wstring algName = StringUtils::ConvertMBSToWCS(m_Info.m_AlgName);
wstring algVersion = StringUtils::ConvertMBSToWCS(m_Info.m_AlgVersion);
wstring chipType = StringUtils::ConvertMBSToWCS(m_Info.m_ChipType);
// For each chip, precreate all probeset signal entries (default to 0.0).
Verbose::out(1,"QuantMethodExprCCCHPReport: Creating temporary files for CHP output");
for (int chip=0; chip<nfiles; chip++) {
try {
ParameterNameValueType param;
// Create tmp chp file
std::string tmp_chp_name=m_CHPFileNames[chip] + ".tmp";
CHPQuantificationData *data = new CHPQuantificationData(tmp_chp_name);
m_TmpChpFiles.push_back(tmp_chp_name);
// set parent header
FusionCELData cel;
try {
tmp_unc_name=Fs::convertToUncPath(m_CELFileNames[chip]);
cel.SetFileName(tmp_unc_name.c_str());
if (!cel.ReadHeader()) {
Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name));
}
GenericData *gdata = cel.GetGenericData();
if (gdata != NULL) {
data->GetFileHeader()->GetGenericDataHdr()->AddParent(*gdata->Header().GetGenericDataHdr());
}
cel.Close();
}
catch (...) {
Err::errAbort("Unable to read CEL file: "+FS_QUOTE_PATH(tmp_unc_name));
}
data->SetEntryCount(m_Info.m_NumProbeSets, maxProbeSetNameLength);
data->SetAlgName(algName);
data->SetAlgVersion(algVersion);
data->SetArrayType(chipType);
param.SetName(L"program-name");
param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramName));
data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
param.SetName(L"program-version");
param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramVersion));
data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
param.SetName(L"program-company");
param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ProgramCompany));
data->GetGenericData().Header().GetGenericDataHdr()->AddNameValParam(param);
// Add algorithm parameters to list.
ParameterNameValueTypeList paramList;
assert(m_Info.m_ParamNames.size() == m_Info.m_ParamValues.size());
for (int i=0; i<m_Info.m_ParamNames.size(); i++) {
if (m_Info.m_ParamValues[i].length() > 0) {
param.SetName(StringUtils::ConvertMBSToWCS(m_Info.m_ParamNames[i]));
param.SetValueText(StringUtils::ConvertMBSToWCS(m_Info.m_ParamValues[i]));
paramList.push_back(param);
}
}
// Add list of all CEL GUIDs in batch
///@todo should this be computed by the engine and passed in via AnalysisInfo?
string prefix = "apt-opt-";
for (int chip=0; chip<m_CHPFileNames.size(); chip++) {
if (m_celGuids[chip].empty() == false) {
string paramName = prefix + "cel-guid-" + ToStr(chip+1);
param.SetName(StringUtils::ConvertMBSToWCS(paramName));
param.SetValueText(StringUtils::ConvertMBSToWCS(m_celGuids[chip]));
paramList.push_back(param);
}
}
data->AddAlgParams(paramList);
// Add the run report parameters to the list
ParameterNameValueTypeList summaryParamList;
std::string blankStr(256, ' ');
for (int source=0; source<m_ChipSummaries.size(); source++) {
ChipSummary::metricDefVec_t metricDefs = m_ChipSummaries[source]->getMetricDefs();
for (int i = 0; i < metricDefs.size(); i++) {
param.SetName(StringUtils::ConvertMBSToWCS(metricDefs[i].m_name));
if (metricDefs[i].m_type == ChipSummary::Metric::Double) {
param.SetValueFloat(-1.0);
}
else if (metricDefs[i].m_type == ChipSummary::Metric::Integer) {
param.SetValueInt32(-1);
}
else if (metricDefs[i].m_type == ChipSummary::Metric::String) {
param.SetValueAscii(blankStr);
}
else {
Err::errAbort("QuantMethodExprCCCHPReport: Unable to handle unknown type: " +
ToStr(metricDefs[i].m_type) );
}
summaryParamList.push_back(param);
}
}
data->AddSummaryParams(summaryParamList);
ProbeSetQuantificationData entry;
CHPQuantificationFileWriter writer(*data);
writer.SeekToDataSet(); // seek to data table location
for (int index=0; index<m_Info.m_ProbesetNames.size(); index++) {
if (m_Info.m_ProbesetDisplayNames.size() > 0 && m_Info.m_ProbesetDisplayNames[index] != NULL)
entry.name = m_Info.m_ProbesetDisplayNames[index];
else
entry.name = m_Info.m_ProbesetNames[index];
entry.quantification = 0.0f;
writer.WriteEntry(entry);
}
delete data;
}
catch (...) {
Err::errAbort("QuantMethodExprCHPReport::prepare() - Unable to write header and/or precreate signal entries to file: " + m_CHPFileNames[chip] + ".tmp");
}
}
// initialize expression signal buffer writer
m_ExpressionQuantificationBufferWriter.Initialize(&m_TmpChpFiles);
return true;
}
void CalvinCHPMultiDataFileUpdaterTest::CreateReferenceFile3()
{
CHPMultiDataData data(TEST3_FILE);
vector<ColumnInfo> cols;
ParameterNameValueType nv;
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);
ProbeSetMultiDataCopyNumberData e;
ProbeSetMultiDataCytoRegionData c;
data.SetEntryCount(CopyNumberMultiDataType, 4, 10, cols);
data.SetEntryCount(CytoMultiDataType, 2, 10);
CHPMultiDataFileWriter *writer = new CHPMultiDataFileWriter(data);
nv.SetName(L"byte");
nv.SetValueInt8(8);
e.metrics.push_back(nv);
nv.SetName(L"ubyte");
nv.SetValueUInt8(8);
e.metrics.push_back(nv);
nv.SetName(L"short");
nv.SetValueInt16(16);
e.metrics.push_back(nv);
nv.SetName(L"ushort");
nv.SetValueUInt16(16);
e.metrics.push_back(nv);
nv.SetName(L"int");
nv.SetValueInt32(32);
e.metrics.push_back(nv);
nv.SetName(L"uint");
nv.SetValueUInt32(32);
e.metrics.push_back(nv);
nv.SetName(L"float");
nv.SetValueFloat(44.0f);
e.metrics.push_back(nv);
nv.SetName(L"ascii");
nv.SetValueAscii("ascii");
e.metrics.push_back(nv);
nv.SetName(L"text");
nv.SetValueText(L"text");
e.metrics.push_back(nv);
writer->SeekToDataSet(CopyNumberMultiDataType);
e.name = "1";
e.chr = 1;
e.position = 10;
writer->WriteEntry(e);
e.name = "2";
e.chr = 2;
e.position = 20;
writer->WriteEntry(e);
e.name = "3";
e.chr = 3;
e.position = 30;
writer->WriteEntry(e);
e.name = "4";
e.chr = 4;
e.position = 40;
writer->WriteEntry(e);
writer->SeekToDataSet(CytoMultiDataType);
c.name = "1";
c.chr= 1;
c.startPosition = 1;
c.stopPosition = 2;
c.call = 1;
c.confidenceScore = 10.0f;
writer->WriteEntry(c);
c.name = "2";
c.chr= 2;
c.startPosition = 2;
c.stopPosition = 3;
c.call = 2;
c.confidenceScore = 20.0f;
writer->WriteEntry(c);
delete writer;
}
