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// Author: Mark Chaisson
#ifndef _BLASR_REGION_TABLE_HPP_
#define _BLASR_REGION_TABLE_HPP_
#include <cassert>
#include <cstring>
#include <iostream>
#include <map>
#include <ostream>
#include <string>
#include <vector>
#include <pbdata/Enumerations.h>
#include <pbdata/PacBioDefs.h>
#include <pbdata/Types.h>
#include <pbdata/reads/RegionAnnotation.hpp>
#include <pbdata/reads/RegionAnnotations.hpp>
class RegionTable
{
private:
/// RegionTable reading from h5 file 'Regions' dataset.
/// \name member variables
/// \{
/// Map zmw hole number to zmw RegionAnnotations.
std::map<UInt, RegionAnnotations> map_;
/// \}
/// \name Region table attributes.
std::vector<std::string> columnNames;
std::vector<std::string> regionTypes;
std::vector<std::string> regionDescriptions;
std::vector<std::string> regionSources;
std::vector<RegionType> regionTypeEnums;
/// \}
public:
/// \name Constructor & destructor & reset
/// \{
RegionTable() {}
~RegionTable() {}
/// Clears member variables in region table.
/// \returns *this
RegionTable& Reset();
/// \}
// Different region tables have different ways of encoding regions.
// This maps from the way they are encoded in the rgn table to a
// standard encoding.
//
/// \name Accessor functions to region table attributes.
/// \{
/// \returns *default PacBio* region types (order matters).
static std::vector<RegionType> DefaultRegionTypes(void);
/// \returns RegionType enums (order matters).
std::vector<RegionType> RegionTypeEnums(void) const;
/// \returns RegionType strings in order
std::vector<std::string> RegionTypes(void) const;
/// \returns column names.
std::vector<std::string> ColumnNames(void) const;
/// \returns region descriptions.
std::vector<std::string> RegionDescriptions(void) const;
/// \returns region sources.
std::vector<std::string> RegionSources(void) const;
/// Construct map_ (holeNumber --> RegionAnnotations) from table.
/// \params[in] region table containing region annotations of all zmws
/// \params[in] ordered region type strings, which maps region types
/// to region type indice.
RegionTable& ConstructTable(std::vector<RegionAnnotation>& table,
const std::vector<std::string>& regionTypeStrs);
/// Note that the ORDER of region types does matter.
/// Set region types (order matters).
RegionTable& RegionTypes(const std::vector<std::string>& in);
/// Set column names, e.g.,
/// {"HoleNumber", "TypeIndex", "Start", "End", "Score"}
RegionTable& ColumnNames(const std::vector<std::string>& in);
/// Set region descriptions. e.g.,
/// {"desc of holenumber", "desc of index", "desc of start", "desc of end", "desc of score"}
RegionTable& RegionDescriptions(const std::vector<std::string>& in);
/// Set region sources, e.g.,
/// {"source of holenumber", "source of index", "source of start", "source of end", "source of score"}
RegionTable& RegionSources(const std::vector<std::string>& in);
/// \}
/// \name Assessor functions to zmw region annotations.
/// \{
/// \returns Whether or not this region table has regions of a zmw.
bool HasHoleNumber(const UInt holeNumber) const;
/// Get zmw region annotaions given its hole number.
/// Note that HasHoleNumber must be called first.
/// \returns RegionAnnotations of a zmw.
RegionAnnotations operator[](const UInt holeNumber) const;
/// \}
};
#endif // _BLASR_REGION_TABLE_HPP_
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