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#ifndef _BLASR_HDF_ALN_GROUP_HPP_
#define _BLASR_HDF_ALN_GROUP_HPP_
#include <hdf/HDFArray.h>
#include <hdf/HDFGroup.h>
class HDFAlnGroup
{
public:
HDFGroup alnGroup;
HDFArray<unsigned int> idArray;
HDFStringArray pathArray;
void Initialize(HDFGroup &parent)
{
alnGroup.Initialize(parent.group, "AlnGroup");
idArray.Initialize(alnGroup.group, "ID");
}
void Read(AlnGroup &aln)
{
// Seem to write data in this HDFAlnGroup obj to AlnGroup & aln
int idNElem = idArray.arrayLength;
int pathNElem = pathArray.arrayLength;
if (idNElem > 0) {
aln.id.resize(idNElem);
idArray.Read(0, idNElem);
aln.path.resize(pathNElem);
unsigned int i;
for (i = 0; i < pathNElem; i++) {
pathArray.Read(i, i + 1, &aln.path[i]);
}
}
}
int AddPath(std::string &path)
{
int id;
pathArray.Write(&path, 1);
id = pathArray.size();
idArray.Write(&id, 1);
return id;
}
~HDFAlnGroup() { alnGroup.Close(); }
};
#endif
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