Class GffIOContext
The I/O context to use for GFF I/O.

Defined in <seqan/bam_io.h>
Signature template <typename TNameStore[, typename TNameStoreCache]> class GffIOContext;

Template Parameters

TNameStore The name store class.
TNameStoreCache The name store cache class, default: NameStoreCache<TNameStore>.

Member Function Overview

Interface Function Overview

Member Typedef Overview

Detailed Description


Creating a GffIOContext for a raw StringSet of CharString.

StringSet<CharString> nameStore;
NameStoreCache<StringSet<CharString> > nameStoreCache(nameStore);
GffIOContext<StringSet<CharString> > bamIOContext(nameStore, nameStoreCache);
// ...

Using a GffIOContext with a FragmentStore.

typedef FragmentStore<>::TContigNameStore         TNameStore;
typedef NameStoreCache<TNameStore>                TNameStoreCache;
FragmentStore<> store;
// Optionally, do something with store.
typedef GffIOContext<TNameStore, TNameStoreCache> TGffIOContext;
TGffIOContext bamIOContext(store.contigNameStore, store.contigNameStoreCache);
// ...

Member Functions Detail




Only the default constructor is provided.

Interface Functions Detail

TNameStore nameStore(context);

Return reference to name store from GffIOContext.


context The GffIOContext to query.


TNameStore Reference to the name store of the context (type TNameStore).

See Also

TNameStoreCache nameStoreCache(context);

Return reference to name store cache from GffIOContext.


context The GffIOContext to query.


TNameStoreCache A reference to the NameStoreCache of the context.

See Also

Member Typedef Detail

typedef (...) TNameStore;

The name store class.

See Also

typedef (...) TNameStoreCache;

The name store cache class.

See Also