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BamMultiMerger_p.h
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BamMultiMerger_p.h
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// ***************************************************************************
// BamMultiMerger_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides merging functionality for BamMultiReader. At this point, supports
// sorting results by (refId, position) or by read name.
// ***************************************************************************
#ifndef BAMMULTIMERGER_P_H
#define BAMMULTIMERGER_P_H
#include "api/api_global.h"
// -------------
// W A R N I N G
// -------------
//
// This file is not part of the BamTools API. It exists purely as an
// implementation detail. This header file may change from version to version
// without notice, or even be removed.
//
// We mean it.
#include <deque>
#include <functional>
#include <set>
#include <string>
#include "api/BamAlignment.h"
#include "api/BamReader.h"
#include "api/algorithms/Sort.h"
namespace BamTools {
namespace Internal {
struct API_NO_EXPORT MergeItem
{
// data members
BamReader* Reader;
BamAlignment* Alignment;
// ctors & dtor
MergeItem(BamReader* reader = 0, BamAlignment* alignment = 0)
: Reader(reader)
, Alignment(alignment)
{}
};
template <typename Compare>
struct API_NO_EXPORT MergeItemSorter
{
public:
MergeItemSorter(const Compare& comp = Compare())
: m_comp(comp)
{}
bool operator()(const MergeItem& lhs, const MergeItem& rhs) const
{
const BamAlignment& l = *lhs.Alignment;
const BamAlignment& r = *rhs.Alignment;
return m_comp(l, r);
}
private:
Compare m_comp;
};
// pure ABC so we can just work polymorphically with any specific merger implementation
class API_NO_EXPORT IMultiMerger
{
public:
IMultiMerger() {}
virtual ~IMultiMerger() {}
public:
virtual void Add(MergeItem item) = 0;
virtual void Clear() = 0;
virtual const MergeItem& First() const = 0;
virtual bool IsEmpty() const = 0;
virtual void Remove(BamReader* reader) = 0;
virtual int Size() const = 0;
virtual MergeItem TakeFirst() = 0;
};
// general merger
template <typename Compare>
class API_NO_EXPORT MultiMerger : public IMultiMerger
{
public:
typedef Compare CompareType;
typedef MergeItemSorter<CompareType> MergeType;
public:
explicit MultiMerger(const Compare& comp = Compare())
: IMultiMerger()
, m_data(MergeType(comp))
{}
public:
void Add(MergeItem item);
void Clear();
const MergeItem& First() const;
bool IsEmpty() const;
void Remove(BamReader* reader);
int Size() const;
MergeItem TakeFirst();
private:
typedef MergeItem ValueType;
typedef std::multiset<ValueType, MergeType> ContainerType;
typedef typename ContainerType::iterator DataIterator;
typedef typename ContainerType::const_iterator DataConstIterator;
ContainerType m_data;
};
template <typename Compare>
void MultiMerger<Compare>::Add(MergeItem item)
{
// N.B. - any future custom Compare types must define this method
// see algorithms/Sort.h
if (CompareType::UsesCharData()) {
item.Alignment->BuildCharData();
}
m_data.insert(item);
}
template <typename Compare>
void MultiMerger<Compare>::Clear()
{
m_data.clear();
}
template <typename Compare>
const MergeItem& MultiMerger<Compare>::First() const
{
const ValueType& entry = (*m_data.begin());
return entry;
}
template <typename Compare>
bool MultiMerger<Compare>::IsEmpty() const
{
return m_data.empty();
}
template <typename Compare>
void MultiMerger<Compare>::Remove(BamReader* reader)
{
if (reader == 0) {
return;
}
const std::string& filenameToRemove = reader->GetFilename();
// iterate over readers in cache
DataIterator dataIter = m_data.begin();
DataIterator dataEnd = m_data.end();
for (; dataIter != dataEnd; ++dataIter) {
const MergeItem& item = (*dataIter);
const BamReader* itemReader = item.Reader;
if (itemReader == 0) {
continue;
}
// remove iterator on match
if (itemReader->GetFilename() == filenameToRemove) {
m_data.erase(dataIter);
return;
}
}
}
template <typename Compare>
int MultiMerger<Compare>::Size() const
{
return m_data.size();
}
template <typename Compare>
MergeItem MultiMerger<Compare>::TakeFirst()
{
DataIterator firstIter = m_data.begin();
MergeItem firstItem = (*firstIter);
m_data.erase(firstIter);
return firstItem;
}
// unsorted "merger"
template <>
class API_NO_EXPORT MultiMerger<Algorithms::Sort::Unsorted> : public IMultiMerger
{
public:
explicit MultiMerger(const Algorithms::Sort::Unsorted& = Algorithms::Sort::Unsorted())
: IMultiMerger()
{}
public:
void Add(MergeItem item);
void Clear();
const MergeItem& First() const;
bool IsEmpty() const;
void Remove(BamReader* reader);
int Size() const;
MergeItem TakeFirst();
private:
typedef MergeItem ValueType;
typedef std::deque<ValueType> ContainerType;
typedef ContainerType::iterator DataIterator;
typedef ContainerType::const_iterator DataConstIterator;
ContainerType m_data;
};
inline void MultiMerger<Algorithms::Sort::Unsorted>::Add(MergeItem item)
{
m_data.push_back(item);
}
inline void MultiMerger<Algorithms::Sort::Unsorted>::Clear()
{
m_data.clear();
}
inline const MergeItem& MultiMerger<Algorithms::Sort::Unsorted>::First() const
{
return m_data.front();
}
inline bool MultiMerger<Algorithms::Sort::Unsorted>::IsEmpty() const
{
return m_data.empty();
}
inline void MultiMerger<Algorithms::Sort::Unsorted>::Remove(BamReader* reader)
{
if (reader == 0) {
return;
}
const std::string filenameToRemove = reader->GetFilename();
// iterate over readers in cache
DataIterator dataIter = m_data.begin();
DataIterator dataEnd = m_data.end();
for (; dataIter != dataEnd; ++dataIter) {
const MergeItem& item = (*dataIter);
const BamReader* itemReader = item.Reader;
if (itemReader == 0) {
continue;
}
// remove iterator on match
if (itemReader->GetFilename() == filenameToRemove) {
m_data.erase(dataIter);
return;
}
}
}
inline int MultiMerger<Algorithms::Sort::Unsorted>::Size() const
{
return m_data.size();
}
inline MergeItem MultiMerger<Algorithms::Sort::Unsorted>::TakeFirst()
{
MergeItem firstItem = m_data.front();
m_data.pop_front();
return firstItem;
}
} // namespace Internal
} // namespace BamTools
#endif // BAMMULTIMERGER_P_H