CHPFileWriter::CHPFileWriter(CHPData &p)
{
writer = new GenericFileWriter(p.GetFileHeader());
entryPos = 0;
bgZonePos = 0;
forcePos = 0;
origPos = 0;
maxProbeSetName = p.GetMaxProbeSetName();
WriteHeaders();
}
void CHPFileReader::Read(CHPData& data)
{
data.Clear();
GenericFileReader reader;
if (fileName.empty())
{
fileName = data.GetFilename();
}
reader.SetFilename(fileName);
reader.ReadHeader(data.GetGenericData());
}
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);
}
/*
* 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;
}
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);
}
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');
}
