/usr/include/pbihdf/HDFRegionsWriter.hpp is in libpbihdf-dev 0~20151014+gitbe5d1bf-2.
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//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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// SUCH DAMAGE.
// Author: Yuan Li
#ifndef _HDF_REGIONS_WRITER_HPP_
#define _HDF_REGIONS_WRITER_HPP_
#include <string>
#include "Enumerations.h"
#include "reads/RegionTable.hpp"
#include "HDFFile.hpp"
#include "HDFArray.hpp"
#include "HDF2DArray.hpp"
#include "HDFAtom.hpp"
#include "HDFWriterBase.hpp"
using namespace H5;
using namespace std;
class HDFRegionsWriter: public HDFWriterBase {
public:
/// \name Constructor and destructor
/// \{
/// \param[in] filename, hdf file name
/// \param[in] parentGroup, parent hdf group in hirarchy
HDFRegionsWriter(const std::string & filename,
HDFGroup & parentGroup,
const std::vector<std::string> & regionTypes = PacBio::AttributeValues::Regions::regiontypes);
~HDFRegionsWriter(void);
/// \}
private:
/// \name Private variables for hdf IO.
/// \{
HDFGroup & parentGroup_; //< parent hdf group
/// A vector of strings of region types for RegionTypeIndex to look up. Order matters!
std::vector<std::string> regionTypes_;
HDF2DArray<int> regionsArray_; //< HDF2DArray for writing regions to hdf
int curRow_; //< which row to write
static const int NCOLS = 5; //< number of columns in Regions table.
/// \brief Write attributes of the 'regions' group
bool WriteAttributes(void);
/// \}
public:
/// \name Method to write region annotations.
/// \{
/// \brief Append a vector of region annotations to 'regions'
/// \param[in] annotations - region annotations to append.
/// \returns true if succeeded.
bool Write(const std::vector<RegionAnnotation> &annotations);
/// \brief Append a region annotation to 'regions'
/// \param[in] annotation - region annotation to append
/// \returns true if succeeded.
bool Write(const RegionAnnotation &annotation);
void Flush(void);
void Close(void);
};
#endif
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