Spec ChainedSeed
Describes a seed with start and end position2 and diagonal upper and lower bounds.

Extends Seed
Implements ContainerConcept
All Extended Seed
All Impl'd AssignableConcept, ContainerConcept, DestructibleConcept
Defined in <seqan/seeds.h>
Signature template <[typename TConfig]> class Seed<ChainedSeed, TConfig>;

Template Parameters

TConfig The configuration to use for the chained seed specialization. Defaults to DefaultSeedConfig.

Member Function Overview

Member Functions Inherited From AssignableConcept

Interface Function Overview

Interface Functions Inherited From Seed

Interface Functions Inherited From AssignableConcept

Interface Functions Inherited From ContainerConcept

Interface Metafunction Overview

Interface Metafunctions Inherited From Seed

Interface Metafunctions Inherited From ContainerConcept

Detailed Description

Diagonals are stored as SeedDiagonal objects.

Member Functions Detail

Seed::Seed(); Seed::Seed(beginPosH, beginPosV, length);

Constructor

Parameters

beginPosH Begin position in dat abase (horizontal).
beginPosV Begin position in query (vertical).
length The length of the seed.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Interface Functions Detail

void appendSeed(seed, diagonal);

Adds a digional to a ChainedSeed.

Parameters

seed The ChainedSeed to which the digonal should be added.
diagonal The SeedDiagional to add to seed.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TReference back(seed);

Returns a reference to the ChainedSeed diagonal.

Parameters

seed The ChainedSeed to query.

Returns

TReference Reference to the last ChainedSeed diagonal. TReference is the reference type of seed.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TIter begin(seed[, tag]);

Returns an iterator to the beginning of the ChainedSeed's diagonals.

Parameters

seed The ChainedSeed to the begin iterator for.
tag A tag for selecting the type of the iterator, one of Standard and Rooted.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TIter end(seed[, tag]);

Returns an iterator to the end of the ChainedSeed's diagonals.

Parameters

seed The ChainedSeed to the end iterator for.
tag A tag for selecting the type of the iterator, one of Standard and Rooted.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TReference front(seed);

Returns a reference to the first ChainedSeed diagonal.

Parameters

seed The ChainedSeed to query.

Returns

TReference Reference to first ChainedSeed diagonal. TReference is the reference type of seed.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TSize length(seed);

Returns the number of diagonals in the ChainedSeed.

Parameters

seed The ChainedSeed to query for its number of diagonals.

Returns

TSize The number of diagonals in the ChainedSeed. TSize is the Size type of seed

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

void truncateDiagonals(seed, first);

Removes diagonals from the given first one to the end of the seed's diagonals.

Parameters

seed The ChainedSeed to truncate diagonals from.
first An iterator into the ChainedSeed, as returned by Iterator.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Interface Metafunctions Detail

Iterator<TChainedSeed[, Tag]>::Type;

The type for iterating over the diagonals in a seed.

Template Parameters

TChainedSeed The seed to query for the diagonal iterator type.
Tag The tag to select the iterator with. One of Standard and Rooted.

Returns

Type Reference to the contained seeds.

Reference<TChainedSeed>::Type;

Reference to the seed diagonal type.

Template Parameters

TChainedSeed The seed to query for the reference to diagonal values.

Returns

Type Reference to the contained seeds.

Value<TChainedSeed>::Type;

The type of the diagonals in the ChainedSeed.

Template Parameters

TChainedSeed The seed to query for its diagonal object type.

Returns

Type The resulting diagonal seed.