Class BedIOContext
The I/O context to use for BED I/O.

Defined in <seqan/bed_io.h>
Signature template <typename TNameStore, typename TNameStoreCache = NameStoreCache<TNameStore> > class BedIOContext;

Template Parameters

TNameStore The name store class.
TNameStoreCache The name store cache class.

Member Function Overview

Interface Function Overview

Member Typedef Overview

Detailed Description

Examples

Creating a BedIOContext for a raw StringSet of CharString.

StringSet<CharString> nameStore;
NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
BedIOContext<StringSet<CharString> > bedIOContext(nameStore, nameStoreCache);
// ...

Using a BedIOContext with a FragmentStore.

typedef FragmentStore<>::TContigNameStore         TNameStore;
typedef NameStoreCache<TNameStore>                TNameStoreCache;
FragmentStore<> store;
// Optionally, do something with store.
typedef BedIOContext<TNameStore, TNameStoreCache> TBedIOContext;
TBedIOContext bedIOContext(store.contigNameStore, store.contigNameStoreCache);
// ...

Member Functions Detail

BedIOContext::BedIOContext();

Constructor.

Interface Functions Detail

TNameStore nameStore(context);

Return reference to name store from BedIOContext.

Parameters

context The BedIOContext to query.

Returns

TNameStoreCache A reference to the name store.

See Also

TNameStoreCache nameStoreCache(context);

Return reference to name store cache from BedIOContext.

Parameters

context The BedIOContext to query.

Returns

TNameStoreCache A reference to the name store cache.

See Also

Member Typedef Detail

typedef (...) BedIOContext::TNameStoreCache;

The name store class.

See Also

typedef (...) BedIOContext::TNameStoreCache;

The name store cache class.

See Also