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// Author: Yuan Li
#include "HDFRegionsWriter.hpp"
HDFRegionsWriter::HDFRegionsWriter(const std::string & filename,
HDFGroup & parentGroup,
const std::vector<std::string> & regionTypes)
: HDFWriterBase(filename)
, parentGroup_(parentGroup)
, regionTypes_(regionTypes)
, curRow_(0)
{
// Initialize the 'regions' group.
regionsArray_.Initialize(parentGroup_, PacBio::GroupNames::regions, RegionAnnotation::NCOLS);
}
HDFRegionsWriter::~HDFRegionsWriter(void)
{
WriteAttributes();
Close();
}
bool HDFRegionsWriter::WriteAttributes(void)
{
if (curRow_ > 0) {
AddAttribute<std::vector<std::string>>(regionsArray_, PacBio::AttributeNames::Regions::columnnames, PacBio::AttributeValues::Regions::columnnames);
AddAttribute<std::vector<std::string>>(regionsArray_, PacBio::AttributeNames::Regions::regiontypes, regionTypes_);
AddAttribute<std::vector<std::string>>(regionsArray_, PacBio::AttributeNames::Regions::regiondescriptions, PacBio::AttributeValues::Regions::regiondescriptions);
AddAttribute<std::vector<std::string>>(regionsArray_, PacBio::AttributeNames::Regions::regionsources, PacBio::AttributeValues::Regions::regionsources);
return true;
} else {
AddErrorMessage("Could not write attributes when Regions group is empty.");
return false;
}
}
bool HDFRegionsWriter::Write(const std::vector<RegionAnnotation> &annotations) {
for (auto annotation: annotations)
if (not Write(annotation))
return false;
return true;
}
bool HDFRegionsWriter::Write(const RegionAnnotation &annotation) {
try {
regionsArray_.WriteRow(annotation.row, HDFRegionsWriter::NCOLS);
}
catch (H5::Exception &e) {
std::ostringstream sout;
sout << "Failed to write region annotation "
<< annotation.GetHoleNumber();
AddErrorMessage(sout.str());
return false;
}
++curRow_;
return true;
}
void HDFRegionsWriter::Flush(void) {
regionsArray_.Flush();
}
void HDFRegionsWriter::Close(void) {
Flush();
regionsArray_.Close();
}
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