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// Author: Yuan Li
#include <hdf/HDFWriterBase.hpp>
HDFWriterBase::~HDFWriterBase(void) {}
std::vector<std::string> HDFWriterBase::Errors(void) const { return errors_; }
void HDFWriterBase::CopyObject(HDFFile &src, const char *path)
{
H5Ocopy(src.hdfFile.getId(), path, outfile_.hdfFile.getId(), path, H5P_DEFAULT, H5P_DEFAULT);
}
void HDFWriterBase::WriteScanData(const ScanData &scanData)
{
// sanity check chemistry meta data.
SanityCheckChemistry(scanData.BindingKit(), scanData.SequencingKit());
HDFScanDataWriter writer(outfile_.rootGroup);
writer.Write(scanData);
}
bool HDFWriterBase::WriteFakeDataSets() { return true; }
void HDFWriterBase::Flush() {}
bool HDFWriterBase::WriteOneZmw(const SMRTSequence &, const std::vector<RegionAnnotation> &)
{
// XXX: unused variables
return true;
}
bool HDFWriterBase::AddChildGroup(HDFGroup &parentGroup, HDFGroup &childGroup,
const std::string &childGroupName)
{
parentGroup.AddGroup(childGroupName);
if (childGroup.Initialize(parentGroup, childGroupName) == 0) {
FAILED_TO_CREATE_GROUP_ERROR(childGroupName);
return false;
}
return true;
}
template <>
bool HDFWriterBase::AddAttribute(HDFData &group, const std::string &attributeName,
const std::vector<std::string> &attributeValues)
{
try {
HDFAtom<std::vector<std::string> > attributeAtom;
attributeAtom.Create(group.dataset, std::string(attributeName), attributeValues);
attributeAtom.Close();
} catch (H5::Exception &e) {
FAILED_TO_CREATE_ATTRIBUTE_ERROR(attributeName);
return false;
}
return true;
}
template <>
bool HDFWriterBase::AddAttribute(HDFGroup &group, const std::string &attributeName,
const std::vector<std::string> &attributeValues)
{
try {
HDFAtom<std::vector<std::string> > attributeAtom;
attributeAtom.Create(group.group, std::string(attributeName), attributeValues);
attributeAtom.Close();
} catch (H5::Exception &e) {
FAILED_TO_CREATE_ATTRIBUTE_ERROR(attributeName);
return false;
}
return true;
}
void HDFWriterBase::SanityCheckChemistry(const std::string &bindingKit,
const std::string &sequencingKit)
{
if (bindingKit.empty()) {
AddErrorMessage("Binding kit must be specified.");
}
if (sequencingKit.empty()) {
AddErrorMessage("Sequencing kit must be specified.");
}
}
void HDFWriterBase::AddErrorMessage(const std::string &errmsg) { errors_.push_back(errmsg); }
void HDFWriterBase::FAILED_TO_CREATE_GROUP_ERROR(const std::string &groupName)
{
std::stringstream ss;
ss << "Failed to create group " << groupName << " in " << filename_;
AddErrorMessage(ss.str());
}
void HDFWriterBase::FAILED_TO_CREATE_ATTRIBUTE_ERROR(const std::string &attributeName)
{
std::stringstream ss;
ss << "Failed to create attribute " << attributeName << " in " << filename_;
AddErrorMessage(ss.str());
}
void HDFWriterBase::PARENT_GROUP_NOT_INITIALIZED_ERROR(const std::string &groupName)
{
std::stringstream ss;
ss << "Parent hdf group of " << groupName << " in file " << filename_ << " is not initialized.";
AddErrorMessage(ss.str());
}
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