Spec
ChainedSeedDescribes a seed with start and end position2 and diagonal upper and lower bounds.
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
-
void appendSeed(seed, diagonal);Adds a digional to a ChainedSeed. -
TReference back(seed);Returns a reference to the ChainedSeed diagonal. -
TIter begin(seed[, tag]);Returns an iterator to the beginning of the ChainedSeed's diagonals. -
TIter end(seed[, tag]);Returns an iterator to the end of the ChainedSeed's diagonals. -
TReference front(seed);Returns a reference to the first ChainedSeed diagonal. -
TSize length(seed);Returns the number of diagonals in the ChainedSeed. -
void truncateDiagonals(seed, first);Removes diagonals from the given first one to the end of the seed's diagonals.
Interface Functions Inherited From Seed
beginDiagonalbeginPositionHbeginPositionVendDiagonalendPositionHendPositionVextendSeedlowerDiagonalscoreseedSizesetBeginPositionHsetBeginPositionVsetEndPositionHsetEndPositionVsetLowerDiagonalsetScoresetUpperDiagonalupperDiagonal
Interface Functions Inherited From AssignableConcept
Interface Functions Inherited From ContainerConcept
Interface Metafunction Overview
-
Iterator<TChainedSeed[, Tag]>::Type;The type for iterating over the diagonals in a seed. -
Reference<TChainedSeed>::Type;Reference to the seed diagonal type. -
Value<TChainedSeed>::Type;The type of the diagonals in the ChainedSeed.
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!
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
Thread safety unknown!