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// Author: Yuan Li
#include "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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