cgatools::reference::RangeAnnotationStore< Derived, TValue > Class Template Reference

Front end to IntervalTree based on reference ranges that allows to load annotations from a file. More...

#include <RangeAnnotationStore.hpp>

List of all members.

Public Types
typedef DataStore::QueryResultType	QueryResultType
Public Member Functions
	RangeAnnotationStore (const reference::CrrFile &crr)
const util::DelimitedFileMetadata &	getMetadata () const
	Returns metadata of the source delimited file.
void	intersect (const reference::Range &range, std::vector< QueryResultType > &result) const
	Fills the vector with iterators that point to the ranges intersecting a given range.
Protected Types
typedef RangeAnnotationStore < Derived, TValue >	Base
	Typedef for this class to simplify constructor invocation in descendants.
Protected Member Functions
void	load (const std::string &fn)
	Load data from the file with a given name.
void	bindRangeColumns (util::DelimitedFile &df, reference::Range &range, const std::string &chrColName="chromosome", const std::string &begColName="begin", const std::string &endColName="end")
	Utility function that the implementation of the derived class can call from bindColumns to add the parsers for the columns that correspond to range data.

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Detailed Description

template<typename Derived, typename TValue>
class cgatools::reference::RangeAnnotationStore< Derived, TValue >

Front end to IntervalTree based on reference ranges that allows to load annotations from a file.

To build your own annotation store, derive from this class and provide an implementation for bindColumns method to associate column names to fields of the TValue structure. See class RepMaskStore in VarFileCombine.cpp for an example.

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Member Function Documentation

template<typename Derived, typename TValue>

void cgatools::reference::RangeAnnotationStore< Derived, TValue >::bindRangeColumns	(	util::DelimitedFile &	df,
		reference::Range &	range,
		const std::string &	chrColName = "chromosome",
		const std::string &	begColName = "begin",
		const std::string &	endColName = "end"
	)			[inline, protected]

Utility function that the implementation of the derived class can call from bindColumns to add the parsers for the columns that correspond to range data.

template<typename Derived, typename TValue>

void cgatools::reference::RangeAnnotationStore< Derived, TValue >::intersect	(	const reference::Range &	range,
		std::vector< QueryResultType > &	result
	)			const [inline]

Fills the vector with iterators that point to the ranges intersecting a given range.

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The documentation for this class was generated from the following file:

• RangeAnnotationStore.hpp