org.biojava.nbio.core.sequence.storage

Class JoiningSequenceReader<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.storage.JoiningSequenceReader<C>

Type Parameters:

C - Tyoe of compound to hold

All Implemented Interfaces:

Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

public class JoiningSequenceReader<C extends Compound>
extends Object
implements ProxySequenceReader<C>

This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence. The code takes in any number of sequences, records the minimum and maximum bounds each sequence covers with respect to 1 position indexing and then binary searches these when a position is requested. Because of this 0 length Sequences are excluded during construction. Performance is not as good as if you are using a flat sequence however the speed of lookup is more than adaquate for most situations. Using the iterator gives the best performance as this does not rely on the binary search mechanism instead iterating through each sequence in turn.

Author:

ayates

Constructor Summary

Constructors

Constructor and Description
JoiningSequenceReader(CompoundSet<C> compoundSet, List<Sequence<C>> sequences)
JoiningSequenceReader(CompoundSet<C> compoundSet, Sequence<C>... sequences)
JoiningSequenceReader(List<Sequence<C>> sequences) Allows creation of the store from List>.
JoiningSequenceReader(Sequence<C>... sequences) Allows creation of the store from Vargs Sequence objects.

Method Summary

Modifier and Type	Method and Description
int	countCompounds(C... compounds) Returns the number of times we found a compound in the Sequence
AccessionID	getAccession() Returns the AccessionID this location is currently bound with
List<C>	getAsList() Returns the Sequence as a List of compounds
C	getCompoundAt(int position) Returns the Compound at the given biological index
CompoundSet<C>	getCompoundSet() Gets the compound set used to back this Sequence
int	getIndexOf(C compound) Scans through the Sequence looking for the first occurrence of the given compound
SequenceView<C>	getInverse() Does the right thing to get the inverse of the current Sequence.
int	getLastIndexOf(C compound) Scans through the Sequence looking for the last occurrence of the given compound
int	getLength() Returns the length of the Sequence
String	getSequenceAsString() Returns the String representation of the Sequence
SequenceView<C>	getSubSequence(Integer start, Integer end) Returns a portion of the sequence from the different positions.
Iterator<C>	iterator() Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to
void	setCompoundSet(CompoundSet<C> compoundSet)
void	setContents(String sequence)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

JoiningSequenceReader

public JoiningSequenceReader(Sequence<C>... sequences)

Allows creation of the store from Vargs Sequence objects. CompoundSet defaults to the first element of the array (assuming there are elements available during construction otherwise we will throw an illegal state exception).

JoiningSequenceReader

public JoiningSequenceReader(List<Sequence<C>> sequences)

Allows creation of the store from List>. CompoundSet defaults to the first element of the List (assuming there are elements available during construction otherwise we will throw an illegal state exception).

JoiningSequenceReader

public JoiningSequenceReader(CompoundSet<C> compoundSet,
                             Sequence<C>... sequences)

JoiningSequenceReader

public JoiningSequenceReader(CompoundSet<C> compoundSet,
                             List<Sequence<C>> sequences)

Method Detail

getCompoundAt

public C getCompoundAt(int position)

Description copied from interface: Sequence

Returns the Compound at the given biological index

Specified by:

getCompoundAt in interface Sequence<C extends Compound>

Parameters:

position - Biological index (1 to n)

Returns:

Compound at the specified position

getCompoundSet

public CompoundSet<C> getCompoundSet()

Description copied from interface: Sequence

Gets the compound set used to back this Sequence

Specified by:

getCompoundSet in interface Sequence<C extends Compound>

getLength

public int getLength()

Description copied from interface: Sequence

Returns the length of the Sequence

Specified by:

getLength in interface Sequence<C extends Compound>

iterator

public Iterator<C> iterator()

Iterator implementation which attempts to move through the 2D structure attempting to skip onto the next sequence as & when it is asked to

Specified by:

iterator in interface Iterable<C extends Compound>

setCompoundSet

public void setCompoundSet(CompoundSet<C> compoundSet)

Specified by:

setCompoundSet in interface SequenceReader<C extends Compound>

setContents

public void setContents(String sequence)
                 throws CompoundNotFoundException

Specified by:

setContents in interface SequenceReader<C extends Compound>

Throws:

CompoundNotFoundException

countCompounds

public int countCompounds(C... compounds)

Description copied from interface: Sequence

Returns the number of times we found a compound in the Sequence

Specified by:

countCompounds in interface Sequence<C extends Compound>

Parameters:

compounds - Vargs of the compounds to count

Returns:

Number of times a compound was found

getAccession

public AccessionID getAccession()
                         throws UnsupportedOperationException

Description copied from interface: Accessioned

Returns the AccessionID this location is currently bound with

Specified by:

getAccession in interface Accessioned

Throws:

UnsupportedOperationException

getAsList

public List<C> getAsList()

Description copied from interface: Sequence

Returns the Sequence as a List of compounds

Specified by:

getAsList in interface Sequence<C extends Compound>

getIndexOf

public int getIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the first occurrence of the given compound

Specified by:

getIndexOf in interface Sequence<C extends Compound>

Parameters:

compound - Compounds to look for

Returns:

Index of the first position of the compound in the sequence (1 to n)

getLastIndexOf

public int getLastIndexOf(C compound)

Description copied from interface: Sequence

Scans through the Sequence looking for the last occurrence of the given compound

Specified by:

getLastIndexOf in interface Sequence<C extends Compound>

Parameters:

compound - Compounds to look for

Returns:

Index of the last position of the compound in the sequence (1 to n)

getSequenceAsString

public String getSequenceAsString()

Description copied from interface: Sequence

Returns the String representation of the Sequence

Specified by:

getSequenceAsString in interface Sequence<C extends Compound>

getSubSequence

public SequenceView<C> getSubSequence(Integer start,
                                      Integer end)

Description copied from interface: Sequence

Returns a portion of the sequence from the different positions. This is indexed from 1

Specified by:

getSubSequence in interface Sequence<C extends Compound>

Parameters:

start - Biological index start; must be greater than 0

end - Biological end; must be less than length + 1

Returns:

A SequenceView of the offset

getInverse

public SequenceView<C> getInverse()

Description copied from interface: Sequence

Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.

Specified by:

getInverse in interface Sequence<C extends Compound>