com.milaboratory.core.sequence.provider

Class CachedSequenceProvider<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.sequence.provider.CachedSequenceProvider<S>

All Implemented Interfaces:

SequenceProvider<S>

public final class CachedSequenceProvider<S extends Sequence<S>>
extends Object
implements SequenceProvider<S>

Constructor Summary

Constructors

Constructor and Description
CachedSequenceProvider(Alphabet<S> alphabet) Cached sequence provider without underlying sequence provider, with automatically inferred provider size.
CachedSequenceProvider(Alphabet<S> alphabet, int size) Cached sequence provider without underlying sequence provider, with fixed provider size.
CachedSequenceProvider(Alphabet<S> alphabet, int size, String missingErrorMessage) Cached sequence provider without underlying sequence provider, with fixed provider size.
CachedSequenceProvider(Alphabet<S> alphabet, SequenceProvider<S> provider) Cached sequence provider wrapping specified sequence provider.
CachedSequenceProvider(Alphabet<S> alphabet, String missingErrorMessage) Cached sequence provider without underlying sequence provider, with automatically inferred provider size.

Method Summary

Methods

Modifier and Type	Method and Description
Map.Entry<Range,S>	ensureEntry(Range range)
Set<Map.Entry<Range,S>>	entrySet()
S	getRegion(Range range) Retrieves specified region of the sequence.
void	setRegion(Range range, S seq)
int	size() Returns the length of the sequence this object represents.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CachedSequenceProvider

public CachedSequenceProvider(Alphabet<S> alphabet,
                      SequenceProvider<S> provider)

Cached sequence provider wrapping specified sequence provider.

Parameters:

alphabet - alphabet

provider - provider to cache sequences from

CachedSequenceProvider

public CachedSequenceProvider(Alphabet<S> alphabet,
                      String missingErrorMessage)

Cached sequence provider without underlying sequence provider, with automatically inferred provider size.

Parameters:

alphabet - alphabet

missingErrorMessage - error message for missing sequence

CachedSequenceProvider

public CachedSequenceProvider(Alphabet<S> alphabet,
                      int size,
                      String missingErrorMessage)

Cached sequence provider without underlying sequence provider, with fixed provider size.

Parameters:

alphabet - alphabet

size - size

missingErrorMessage - error message for missing sequence

CachedSequenceProvider

public CachedSequenceProvider(Alphabet<S> alphabet,
                      int size)

Cached sequence provider without underlying sequence provider, with fixed provider size.

Parameters:

alphabet - alphabet

size - size

CachedSequenceProvider

public CachedSequenceProvider(Alphabet<S> alphabet)

Cached sequence provider without underlying sequence provider, with automatically inferred provider size.

Parameters:

alphabet - alphabet

Method Detail

ensureEntry

public Map.Entry<Range,S> ensureEntry(Range range)

entrySet

public Set<Map.Entry<Range,S>> entrySet()

size

public int size()

Description copied from interface: SequenceProvider

Returns the length of the sequence this object represents.

Specified by:

size in interface SequenceProvider<S extends Sequence<S>>

Returns:

length of the sequence this object represents

getRegion

public S getRegion(Range range)

Description copied from interface: SequenceProvider

Retrieves specified region of the sequence.

Specified by:

getRegion in interface SequenceProvider<S extends Sequence<S>>

Parameters:

range - range of the sequence to be retrieved

Returns:

sequence

setRegion

public void setRegion(Range range,
             S seq)