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// Author: Mark Chaisson
#ifndef _BLASR_REGION_ANNOTATION_HPP_
#define _BLASR_REGION_ANNOTATION_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/RegionTypeMap.hpp>
class HDFRegionTableReader;
class HDFRegionTableWriter;
class HDFRegionsWriter;
class RegionAnnotation
{
friend class HDFRegionTableReader;
friend class HDFRegionTableWriter;
friend class HDFRegionsWriter;
public:
static const int HOLENUMBERCOL = 0;
static const int REGIONTYPEINDEXCOL = 1;
static const int REGIONSTARTCOL = 2;
static const int REGIONENDCOL = 3;
static const int REGIONSCORECOL = 4;
static const int NCOLS = 5;
// Notice the discrepencies between Region and other hdf datasets!!
// Region annotation is defined as int32_t * 5, while
// holeNumber is defined as type UInt in other datasets (e.g., majorly ZMW),
// start and end are defined as type DNALength in other datasets.
int row[NCOLS];
public:
// FIXME: use regionType as a member varaible instead of regionTypeIndex
inline RegionAnnotation(UInt holeNumber = 0, int typeIndex = 0, int start = 0, int end = 0,
int score = -1);
inline bool operator<(const RegionAnnotation &rhs) const;
inline bool operator<(int holeNumber) const;
inline RegionAnnotation &operator=(const RegionAnnotation &rhs);
inline bool operator==(const RegionAnnotation &rhs) const;
inline int GetHoleNumber(void) const;
inline RegionAnnotation &SetHoleNumber(int holeNumber);
inline int GetTypeIndex(void) const;
inline std::string GetTypeString(const std::vector<RegionType> &types) const;
inline RegionAnnotation &SetTypeIndex(int typeIndex);
inline int GetStart(void) const;
inline RegionAnnotation &SetStart(int start);
inline int GetEnd(void) const;
inline RegionAnnotation &SetEnd(int end);
inline int GetScore(void) const;
inline RegionAnnotation &SetScore(int score);
public:
friend std::ostream &operator<<(std::ostream &os, const RegionAnnotation &ra);
};
inline bool compare_region_annotation_by_type(const RegionAnnotation &lhs,
const RegionAnnotation &rhs);
inline RegionAnnotation::RegionAnnotation(UInt holeNumber, int typeIndex, int start, int end,
int score)
{
SetHoleNumber(static_cast<int>(holeNumber));
SetTypeIndex(typeIndex);
SetStart(start);
SetEnd(end);
SetScore(score);
}
inline bool RegionAnnotation::operator<(const RegionAnnotation &rhs) const
{
if (GetHoleNumber() == rhs.GetHoleNumber())
if (GetStart() == rhs.GetStart()) {
if (GetEnd() == rhs.GetEnd())
return GetScore() < rhs.GetScore();
else
return GetEnd() > rhs.GetEnd();
} else {
return GetStart() < rhs.GetStart();
}
else
return GetHoleNumber() < rhs.GetHoleNumber();
}
inline bool RegionAnnotation::operator<(int holeNumber) const
{
return GetHoleNumber() < holeNumber;
}
inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs)
{
memcpy(row, rhs.row, sizeof(int) * NCOLS);
return *this;
}
inline bool RegionAnnotation::operator==(const RegionAnnotation &rhs) const
{
return (GetHoleNumber() == rhs.GetHoleNumber() and GetTypeIndex() == rhs.GetTypeIndex() and
GetStart() == rhs.GetStart() and GetEnd() == rhs.GetEnd() and
GetScore() == rhs.GetScore());
}
inline int RegionAnnotation::GetHoleNumber(void) const { return row[HOLENUMBERCOL]; }
inline RegionAnnotation &RegionAnnotation::SetHoleNumber(int holeNumber)
{
row[HOLENUMBERCOL] = holeNumber;
return *this;
}
inline int RegionAnnotation::GetTypeIndex(void) const { return row[REGIONTYPEINDEXCOL]; }
inline std::string RegionAnnotation::GetTypeString(const std::vector<RegionType> &typesTable) const
{
assert(GetTypeIndex() >= 0 and GetTypeIndex() < static_cast<int>(typesTable.size()));
return RegionTypeMap::ToString(typesTable[GetTypeIndex()]);
}
inline RegionAnnotation &RegionAnnotation::SetTypeIndex(int regionTypeIndex)
{
row[REGIONTYPEINDEXCOL] = regionTypeIndex;
return *this;
}
inline int RegionAnnotation::GetStart(void) const { return row[REGIONSTARTCOL]; }
inline RegionAnnotation &RegionAnnotation::SetStart(int start)
{
row[REGIONSTARTCOL] = start;
return *this;
}
inline int RegionAnnotation::GetEnd(void) const { return row[REGIONENDCOL]; }
inline RegionAnnotation &RegionAnnotation::SetEnd(int end)
{
row[REGIONENDCOL] = end;
return *this;
}
inline int RegionAnnotation::GetScore(void) const { return row[REGIONSCORECOL]; }
inline RegionAnnotation &RegionAnnotation::SetScore(int score)
{
row[REGIONSCORECOL] = score;
return *this;
}
inline bool compare_region_annotation_by_type(const RegionAnnotation &lhs,
const RegionAnnotation &rhs)
{
if (lhs.GetHoleNumber() == rhs.GetHoleNumber()) {
if (lhs.GetTypeIndex() == rhs.GetTypeIndex()) {
if (lhs.GetStart() == rhs.GetStart()) {
if (lhs.GetEnd() == rhs.GetEnd())
return lhs.GetScore() < rhs.GetScore();
else
return lhs.GetEnd() > rhs.GetEnd();
} else
return lhs.GetStart() < rhs.GetStart();
} else
return lhs.GetTypeIndex() < rhs.GetTypeIndex();
} else {
return lhs.GetHoleNumber() < rhs.GetHoleNumber();
}
}
#endif // _BLASR_REGION_ANNOTATION_HPP_
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