void CHPFileReaderTest::ReadCHPUniversalFileTest()
{
CHPData data;
CHPFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename("../data/CHP_universal_file"));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data));
CPPUNIT_ASSERT(data.GetFilename() == "../data/CHP_universal_file");
CPPUNIT_ASSERT(data.GetEntryCount() == 2);
CPPUNIT_ASSERT(data.GetBackgroundZoneCnt() == 2);
CHPUniversalEntry entry1;
data.GetEntry(0, entry1);
CPPUNIT_ASSERT(entry1.GetBackground() == 11.0f);
CHPUniversalEntry entry2;
data.GetEntry(1, entry2);
CPPUNIT_ASSERT(entry2.GetBackground() == 1.0f);
CHPBackgroundZone zone1;
data.GetBackgroundZone(0, zone1);
CPPUNIT_ASSERT(zone1.GetCenterX() == 11.0f);
CPPUNIT_ASSERT(zone1.GetCenterY() == 17.8f);
CPPUNIT_ASSERT(zone1.GetBackground() == 56.9f);
CPPUNIT_ASSERT(zone1.GetSmoothFactor() == 45.89f);
CHPBackgroundZone zone2;
data.GetBackgroundZone(1, zone2);
CPPUNIT_ASSERT(zone2.GetCenterX() == 1.0f);
CPPUNIT_ASSERT(zone2.GetCenterY() == 7.8f);
CPPUNIT_ASSERT(zone2.GetBackground() == 6.9f);
CPPUNIT_ASSERT(zone2.GetSmoothFactor() == 5.89f);
}
void CHPFileReaderTest::ReadCHPExpressionFileTest()
{
CHPData data;
CHPFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename("../data/CHP_expression_file"));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data));
CPPUNIT_ASSERT(data.GetFilename() == "../data/CHP_expression_file");
CPPUNIT_ASSERT(data.GetEntryCount() == 10);
CPPUNIT_ASSERT(data.GetBackgroundZoneCnt() == 2);
CHPExpressionEntry entry1;
data.GetEntry(0, entry1);
CPPUNIT_ASSERT(entry1.GetProbeSetName() == "probe set 1");
CPPUNIT_ASSERT(entry1.GetDetection() == 10);
CPPUNIT_ASSERT(entry1.GetDetectionPValue() == 11.0f);
float signal = entry1.GetSignal();
CPPUNIT_ASSERT(signal == 17.8f);
CPPUNIT_ASSERT(entry1.GetNumPairs() == 6);
CPPUNIT_ASSERT(entry1.GetNumPairsUsed() == 5);
CPPUNIT_ASSERT(entry1.GetChange() == 2);
float chgPVal = entry1.GetChangePValue();
CPPUNIT_ASSERT(chgPVal == 56.9f);
CPPUNIT_ASSERT(entry1.GetSigLogRatio() == 45.89f);
CPPUNIT_ASSERT(entry1.GetSigLogRatioLo() == 42.0f);
CPPUNIT_ASSERT(entry1.GetSigLogRatioHi() == 47.0f);
CPPUNIT_ASSERT(entry1.GetCommonPairs() == 2);
CHPExpressionEntry entry2;
data.GetEntry(1, entry2);
CPPUNIT_ASSERT(entry2.GetProbeSetName() == "probe set 2");
CPPUNIT_ASSERT(entry2.GetDetection() == 10);
CPPUNIT_ASSERT(entry2.GetDetectionPValue() == 1.0f);
CPPUNIT_ASSERT(entry2.GetSignal() == 7.8f);
CPPUNIT_ASSERT(entry2.GetNumPairs() == 6);
CPPUNIT_ASSERT(entry2.GetNumPairsUsed() == 5);
CPPUNIT_ASSERT(entry2.GetChange() == 2);
CPPUNIT_ASSERT(entry2.GetChangePValue() == 5.9f);
CPPUNIT_ASSERT(entry2.GetSigLogRatio() == 4.89f);
CPPUNIT_ASSERT(entry2.GetSigLogRatioLo() == 2.0f);
CPPUNIT_ASSERT(entry2.GetSigLogRatioHi() == 7.0f);
CPPUNIT_ASSERT(entry2.GetCommonPairs() == 2);
CHPBackgroundZone zone1;
data.GetBackgroundZone(0, zone1);
CPPUNIT_ASSERT(zone1.GetCenterX() == 11.0f);
CPPUNIT_ASSERT(zone1.GetCenterY() == 17.8f);
CPPUNIT_ASSERT(zone1.GetBackground() == 56.9f);
CPPUNIT_ASSERT(zone1.GetSmoothFactor() == 45.89f);
CHPBackgroundZone zone2;
data.GetBackgroundZone(1, zone2);
CPPUNIT_ASSERT(zone2.GetCenterX() == 1.0f);
CPPUNIT_ASSERT(zone2.GetCenterY() == 7.8f);
CPPUNIT_ASSERT(zone2.GetBackground() == 6.9f);
CPPUNIT_ASSERT(zone2.GetSmoothFactor() == 5.89f);
}
void CHPFileReaderTest::ReadCHPGenotypingFileTest()
{
CHPData data;
CHPFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename("../data/CHP_genotype_file"));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data));
CPPUNIT_ASSERT(data.GetFilename() == "../data/CHP_genotype_file");
CPPUNIT_ASSERT(data.GetEntryCount() == 2);
CPPUNIT_ASSERT(data.GetBackgroundZoneCnt() == 2);
CHPGenotypeEntry entry1;
data.GetEntry(0, entry1);
CPPUNIT_ASSERT(entry1.GetProbeSetName() == "probe set 1");
CPPUNIT_ASSERT(entry1.GetCall() == 1);
CPPUNIT_ASSERT(entry1.GetConfidence() == 11.0f);
float ras1 = entry1.GetRAS1();
CPPUNIT_ASSERT(ras1 == 17.8f);
CPPUNIT_ASSERT(entry1.GetRAS2() == 6.0f);
CPPUNIT_ASSERT(entry1.GetAACall() == 5.0f);
CPPUNIT_ASSERT(entry1.GetABCall() == 2.0f);
CPPUNIT_ASSERT(entry1.GetBBCall() == 56.9f);
CPPUNIT_ASSERT(entry1.GetNoCall() == 45.89f);
CHPGenotypeEntry entry2;
data.GetEntry(1, entry2);
CPPUNIT_ASSERT(entry2.GetProbeSetName() == "probe set 2");
CPPUNIT_ASSERT(entry2.GetCall() == 2);
CPPUNIT_ASSERT(entry2.GetConfidence() == 1.0f);
CPPUNIT_ASSERT(entry2.GetRAS1() == 7.8f);
CPPUNIT_ASSERT(entry2.GetRAS2() == 6.0f);
CPPUNIT_ASSERT(entry2.GetAACall() == 5.0f);
CPPUNIT_ASSERT(entry2.GetABCall() == 2.0f);
CPPUNIT_ASSERT(entry2.GetBBCall() == 5.9f);
CPPUNIT_ASSERT(entry2.GetNoCall() == 4.8f);
CHPBackgroundZone zone1;
data.GetBackgroundZone(0, zone1);
CPPUNIT_ASSERT(zone1.GetCenterX() == 11.0f);
CPPUNIT_ASSERT(zone1.GetCenterY() == 17.8f);
CPPUNIT_ASSERT(zone1.GetBackground() == 56.9f);
CPPUNIT_ASSERT(zone1.GetSmoothFactor() == 45.89f);
CHPBackgroundZone zone2;
data.GetBackgroundZone(1, zone2);
CPPUNIT_ASSERT(zone2.GetCenterX() == 1.0f);
CPPUNIT_ASSERT(zone2.GetCenterY() == 7.8f);
CPPUNIT_ASSERT(zone2.GetBackground() == 6.9f);
CPPUNIT_ASSERT(zone2.GetSmoothFactor() == 5.89f);
}
/*
* Check if the input file is a Calvin file.
*/
static bool IsCalvinCHPFile(const char *fileName)
{
CHPData data;
CHPFileReader reader;
reader.SetFilename(fileName);
try
{
reader.Read(data);
data.Clear();
return true;
}
catch (affymetrix_calvin_exceptions::CalvinException)
{
}
catch (...)
{
}
return false;
}
/*
* Open the files.
*/
bool CHPCompareGCOStoCalvin::OpenFiles(const char *gcosFile, const char *calvinFile)
{
gcos.SetFileName(gcosFile);
if (gcos.Read() == false)
{
differences = "Failed to read the GCOS file\r\n";
return false;
}
CHPFileReader reader;
try
{
reader.SetFilename(calvinFile);
reader.Read(calvin);
}
catch (...)
{
differences = "Failed to read the Calvin file\r\n";
return false;
}
return true;
}
/*
* Convert the file.
*/
bool CHPFileConvertToXDA::ConvertCalvinFile(const char *fileName, const char *newFile)
{
Clear();
// Read the input file.
CHPData inFile;
CHPFileReader reader;
reader.SetFilename(fileName);
try
{
reader.Read(inFile);
}
catch (...)
{
errorCode = UnableToOpenChpFile;
return false;
}
// Copy the input file object to the output file object.
CCHPFileWriter outFile;
outFile.SetFileName(newFile);
CHPConversionUtilities::Copy(inFile, outFile);
if (parentFileName.empty() == false)
{
// override the parent file name
// Attempt to remove the path.
string::size_type posBS = parentFileName.rfind('\\');
string::size_type posS = parentFileName.rfind('/');
if (posBS != -1)
{
outFile.SetParentCelFileName(parentFileName.substr(posBS+1).c_str());
}
else if (posS != -1)
{
outFile.SetParentCelFileName(parentFileName.substr(posS+1).c_str());
}
else
{
outFile.SetParentCelFileName(parentFileName.c_str());
}
}
// Override chip type if it was set in extra parameters
std::string chipType = GetChipTypeFromExtraParameters();
if (chipType.length() > 0)
{
outFile.GetHeader().SetChipType(chipType.c_str());
}
// Write the output file.
if (outFile.CreateNewFile() == false)
{
errorCode = UnableToWriteTheFile;
return false;
}
if (outFile.Save() == false)
{
errorCode = UnableToWriteTheFile;
return false;
}
return true;
}
void CHPFileReaderTest::ReadCHPReseqFileTest()
{
CHPData data;
CHPFileReader reader;
CPPUNIT_ASSERT_NO_THROW(reader.SetFilename("../data/CHP_reseq_file"));
CPPUNIT_ASSERT_NO_THROW(reader.Read(data));
CPPUNIT_ASSERT(data.GetFilename() == "../data/CHP_reseq_file");
CPPUNIT_ASSERT(data.GetEntryCount() == 5);
CPPUNIT_ASSERT(data.GetBackgroundZoneCnt() == 1);
CPPUNIT_ASSERT(data.GetForceCnt() == 2);
CPPUNIT_ASSERT(data.GetOrigCnt() == 3);
const double eps = 1e-5;
CHPReseqEntry e;
data.GetEntry(0, e);
CPPUNIT_ASSERT(e.call == 'a');
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.score, 1.0f, eps);
data.GetEntry(1, e);
CPPUNIT_ASSERT(e.call == 'c');
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.score, 2.0f, eps);
data.GetEntry(2, e);
CPPUNIT_ASSERT(e.call == 'g');
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.score, 3.0f, eps);
data.GetEntry(3, e);
CPPUNIT_ASSERT(e.call == 't');
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.score, 4.0f, eps);
data.GetEntry(4, e);
CPPUNIT_ASSERT(e.call == 'n');
CPPUNIT_ASSERT_DOUBLES_EQUAL(e.score, 5.0f, eps);
CHPReseqForceCall force;
data.GetForceCall(0, force);
CPPUNIT_ASSERT(force.position == 1);
CPPUNIT_ASSERT(force.call == 'a');
CPPUNIT_ASSERT(force.reason == CC_SATURATION_LEVEL_FORCE_CALL);
data.GetForceCall(1, force);
CPPUNIT_ASSERT(force.position == 2);
CPPUNIT_ASSERT(force.call == 'c');
CPPUNIT_ASSERT(force.reason == CC_WEAK_SIGNAL_THR_FORCE_CALL);
CHPReseqOrigCall orig;
data.GetOrigCall(0, orig);
CPPUNIT_ASSERT(orig.position == 3);
CPPUNIT_ASSERT(orig.call == 't');
data.GetOrigCall(1, orig);
CPPUNIT_ASSERT(orig.position == 4);
CPPUNIT_ASSERT(orig.call == 'a');
data.GetOrigCall(2, orig);
CPPUNIT_ASSERT(orig.position == 5);
CPPUNIT_ASSERT(orig.call == 'g');
}
