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 |
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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. |
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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
beginDiagonal
beginPositionH
beginPositionV
endDiagonal
endPositionH
endPositionV
extendSeed
lowerDiagonal
score
seedSize
setBeginPositionH
setBeginPositionV
setEndPositionH
setEndPositionV
setLowerDiagonal
setScore
setUpperDiagonal
upperDiagonal
Interface Functions Inherited From AssignableConcept
Interface Functions Inherited From ContainerConcept
Interface Metafunction Overview
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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). |
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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. |
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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. |
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Returns
TReference |
Reference to the last ChainedSeed diagonal. TReference is the reference type of seed. |
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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. |
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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. |
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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. |
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Returns
TReference |
Reference to first ChainedSeed diagonal. TReference is the reference type of seed. |
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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. |
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Returns
TSize |
The number of diagonals in the ChainedSeed. TSize is the Size type of seed |
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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. |
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first
|
An iterator into the ChainedSeed, as returned by Iterator. |
Data Races
Thread safety unknown!