void CCHPFileWriter::InitializeForWriting(affxcdf::CCDFFileData &cdf, bool allocateMemory)
{
InitializeForWriting(
cdf.GetHeader().GetRows(),
cdf.GetHeader().GetCols(),
cdf.GetHeader().GetNumProbeSets(),
cdf.GetChipType().c_str(),
cdf.GetProbeSetType(0),
allocateMemory);
}
void FusionCdfFileTest::testQCObjects(affxcdf::CCDFFileData &gcosCdf, affymetrix_fusion_io::FusionCDFData &fusionCdf)
{
affxcdf::CCDFQCProbeSetInformation gcosSet;
affxcdf::CCDFQCProbeInformation gcosCel;
affymetrix_fusion_io::FusionCDFQCProbeSetInformation fusionSet;
affymetrix_fusion_io::FusionCDFQCProbeInformation fusionCel;
CPPUNIT_ASSERT(gcosCdf.GetHeader().GetCols() == fusionCdf.GetHeader().GetCols());
CPPUNIT_ASSERT(gcosCdf.GetHeader().GetRows() == fusionCdf.GetHeader().GetRows());
CPPUNIT_ASSERT(gcosCdf.GetHeader().GetNumQCProbeSets() == fusionCdf.GetHeader().GetNumQCProbeSets());
CPPUNIT_ASSERT(gcosCdf.GetChipType() == fusionCdf.GetChipType());
CPPUNIT_ASSERT(gcosCdf.GetFileName() == fusionCdf.GetFileName());
int nps = gcosCdf.GetHeader().GetNumQCProbeSets();
for (int ips=0; ips<nps; ips++)
{
gcosCdf.GetQCProbeSetInformation(ips, gcosSet);
fusionCdf.GetQCProbeSetInformation(ips, fusionSet);
CPPUNIT_ASSERT(gcosSet.GetQCProbeSetType() == fusionSet.GetQCProbeSetType());
CPPUNIT_ASSERT(gcosSet.GetNumCells() == fusionSet.GetNumCells());
int nc = gcosSet.GetNumCells();
for (int ic=0; ic<nc; ic++)
{
gcosSet.GetProbeInformation(ic, gcosCel);
fusionSet.GetProbeInformation(ic, fusionCel);
CPPUNIT_ASSERT(gcosCel.GetX() == fusionCel.GetX());
CPPUNIT_ASSERT(gcosCel.GetY() == fusionCel.GetY());
CPPUNIT_ASSERT(gcosCel.GetPLen() == fusionCel.GetPLen());
CPPUNIT_ASSERT(gcosCel.IsPerfectMatchProbe() == fusionCel.IsPerfectMatchProbe());
CPPUNIT_ASSERT(gcosCel.IsBackgroundProbe() == fusionCel.IsBackgroundProbe());
}
}
}
void FusionCdfFileTest::testRegObjects(affxcdf::CCDFFileData &gcosCdf, affymetrix_fusion_io::FusionCDFData &fusionCdf)
{
affxcdf::CCDFFileHeader &gcosHeader = gcosCdf.GetHeader();
affxcdf::CCDFProbeSetInformation gcosSet;
affxcdf::CCDFProbeGroupInformation gcosGroup;
affxcdf::CCDFProbeInformation gcosCel;
affymetrix_fusion_io::FusionCDFFileHeader &fusionHeader = fusionCdf.GetHeader();
affymetrix_fusion_io::FusionCDFProbeSetInformation fusionSet;
affymetrix_fusion_io::FusionCDFProbeGroupInformation fusionGroup;
affymetrix_fusion_io::FusionCDFProbeInformation fusionCel;
CPPUNIT_ASSERT(gcosHeader.GetCols() == fusionHeader.GetCols());
CPPUNIT_ASSERT(gcosHeader.GetRows() == fusionHeader.GetRows());
CPPUNIT_ASSERT(gcosHeader.GetNumProbeSets() == fusionHeader.GetNumProbeSets());
CPPUNIT_ASSERT(gcosHeader.GetNumQCProbeSets() == fusionHeader.GetNumQCProbeSets());
CPPUNIT_ASSERT(gcosHeader.GetReference() == fusionHeader.GetReference());
CPPUNIT_ASSERT(gcosCdf.GetChipType() == fusionCdf.GetChipType());
CPPUNIT_ASSERT(gcosCdf.GetFileName() == fusionCdf.GetFileName());
int nps = gcosHeader.GetNumProbeSets();
for (int ips=0; ips<nps; ips++)
{
CPPUNIT_ASSERT(gcosCdf.GetProbeSetName(ips) == fusionCdf.GetProbeSetName(ips));
CPPUNIT_ASSERT(gcosCdf.GetProbeSetType(ips) == fusionCdf.GetProbeSetType(ips));
}
for (int ips=0; ips<nps; ips++)
{
gcosCdf.GetProbeSetInformation(ips, gcosSet);
fusionCdf.GetProbeSetInformation(ips, fusionSet);
CPPUNIT_ASSERT(gcosSet.GetNumLists() == fusionSet.GetNumLists());
CPPUNIT_ASSERT(gcosSet.GetNumGroups() == fusionSet.GetNumGroups());
CPPUNIT_ASSERT(gcosSet.GetNumCells() == fusionSet.GetNumCells());
CPPUNIT_ASSERT(gcosSet.GetNumCellsPerList() == fusionSet.GetNumCellsPerList());
CPPUNIT_ASSERT(gcosSet.GetProbeSetNumber() == fusionSet.GetProbeSetNumber());
CPPUNIT_ASSERT(gcosSet.GetProbeSetType() == fusionSet.GetProbeSetType());
CPPUNIT_ASSERT(gcosSet.GetDirection() == fusionSet.GetDirection());
int ng = gcosSet.GetNumGroups();
for (int ig=0; ig<ng; ig++)
{
gcosSet.GetGroupInformation(ig, gcosGroup);
fusionSet.GetGroupInformation(ig, fusionGroup);
CPPUNIT_ASSERT(gcosGroup.GetDirection() == fusionGroup.GetDirection());
CPPUNIT_ASSERT(gcosGroup.GetNumLists() == fusionGroup.GetNumLists());
CPPUNIT_ASSERT(gcosGroup.GetNumCells() == fusionGroup.GetNumCells());
CPPUNIT_ASSERT(gcosGroup.GetNumCellsPerList() == fusionGroup.GetNumCellsPerList());
CPPUNIT_ASSERT(gcosGroup.GetStart() == fusionGroup.GetStart());
CPPUNIT_ASSERT(gcosGroup.GetStop() == fusionGroup.GetStop());
CPPUNIT_ASSERT(gcosGroup.GetName() == fusionGroup.GetName());
CPPUNIT_ASSERT(gcosGroup.GetAlleleCode() == fusionGroup.GetAlleleCode());
CPPUNIT_ASSERT(gcosGroup.GetWobbleSituation() == fusionGroup.GetWobbleSituation());
CPPUNIT_ASSERT(gcosGroup.GetChannel() == fusionGroup.GetChannel());
CPPUNIT_ASSERT(gcosGroup.GetRepType() == fusionGroup.GetRepType());
int nc=gcosGroup.GetNumCells();
for (int ic=0; ic<nc; ic++)
{
gcosGroup.GetCell(ic, gcosCel);
fusionGroup.GetCell(ic, fusionCel);
CPPUNIT_ASSERT(gcosCel.GetX() == fusionCel.GetX());
CPPUNIT_ASSERT(gcosCel.GetY() == fusionCel.GetY());
CPPUNIT_ASSERT(gcosCel.GetListIndex() == fusionCel.GetListIndex());
CPPUNIT_ASSERT(gcosCel.GetExpos() == fusionCel.GetExpos());
CPPUNIT_ASSERT(gcosCel.GetPBase() == fusionCel.GetPBase());
CPPUNIT_ASSERT(gcosCel.GetTBase() == fusionCel.GetTBase());
CPPUNIT_ASSERT(gcosCel.GetProbeLength() == fusionCel.GetProbeLength());
CPPUNIT_ASSERT(gcosCel.GetProbeGrouping() == fusionCel.GetProbeGrouping());
}
}
}
}