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

All Implemented Interfaces:: Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

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

An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String is also valid but will require a CompoundSet). The idea is to represent large runs of a single compound without the memory footprint of storing these compounds e.g. a run of 10KB of Ns in a DNASequence.

Author:: ayates

Constructor Summary

Constructors

Constructor

Description

SingleCompoundSequenceReader(C compound, CompoundSet<C> compoundSet, int length)

Build the object with a compound rather than a String

SingleCompoundSequenceReader(String compound, CompoundSet<C> compoundSet, int length)

Public constructor to be used with String based constructor
Method Summary

Modifier and Type

Method

Description

int

countCompounds(C... compounds)

Delegates to SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])

boolean

equals(Object o)

AccessionID

getAccession()

Unsupoorted

List<C>

getAsList()

Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)

C

getCompoundAt(int position)

Always returns the compound given at construction

CompoundSet<C>

getCompoundSet()

Returns the compound set given at construction

int

getIndexOf(C compound)

Returns 1 if the given compound is equal to the one given during construction; otherwise will return -1.

SequenceView<C>

getInverse()

Does the right thing to get the inverse of the current Sequence.

int

getLastIndexOf(C compound)

Returns the length of the Sequence if the given compound was equal to the one given during construction.

int

getLength()

Returns the length given during construction

String

getSequenceAsString()

Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)

SequenceView<C>

getSubSequence(Integer start, Integer end)

Creates a SequenceProxyView for the given coordinates

int

hashCode()

Iterator<C>

iterator()

Returns an instance of SequenceMixin.SequenceIterator

void

setCompoundSet(CompoundSet<C> compoundSet)

Unsupported

void

setContents(String sequence)

Unsupported

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Constructor Details
- SingleCompoundSequenceReader
  
  public SingleCompoundSequenceReader(String compound, CompoundSet<C> compoundSet, int length)
  
  Public constructor to be used with String based constructor
- SingleCompoundSequenceReader
  
  public SingleCompoundSequenceReader(C compound, CompoundSet<C> compoundSet, int length)
  
  Build the object with a compound rather than a String
Method Details
- setCompoundSet
  
  public void setCompoundSet(CompoundSet<C> compoundSet)
  
  Unsupported
  
  Specified by:
  
  setCompoundSet in interface SequenceReader<C extends Compound>
- setContents
  
  public void setContents(String sequence) throws CompoundNotFoundException
  
  Unsupported
  
  Specified by:
  
  setContents in interface SequenceReader<C extends Compound>
  
  Throws:
  
  CompoundNotFoundException
- getLength
  
  public int getLength()
  
  Returns the length given during construction
  
  Specified by:
  
  getLength in interface Sequence<C extends Compound>
- getCompoundAt
  
  public C getCompoundAt(int position)
  
  Always returns the compound given at construction
  
  Specified by:
  
  getCompoundAt in interface Sequence<C extends Compound>
  
  Parameters:
  
  position - Biological index (1 to n)
  
  Returns:
  
  Compound at the specified position
- getIndexOf
  
  public int getIndexOf(C compound)
  
  Returns 1 if the given compound is equal to the one given during construction; otherwise will return -1.
  
  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)
  
  Returns the length of the Sequence if the given compound was equal to the one given during construction. Otherwise returns -1
  
  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()
  
  Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)
  
  Specified by:
  
  getSequenceAsString in interface Sequence<C extends Compound>
- getAsList
  
  public List<C> getAsList()
  
  Delegates to SequenceMixin.toList(org.biojava.nbio.core.sequence.template.Sequence)
  
  Specified by:
  
  getAsList in interface Sequence<C extends Compound>
- getSubSequence
  
  public SequenceView<C> getSubSequence(Integer start, Integer end)
  
  Creates a SequenceProxyView for the given coordinates
  
  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
- getCompoundSet
  
  public CompoundSet<C> getCompoundSet()
  
  Returns the compound set given at construction
  
  Specified by:
  
  getCompoundSet in interface Sequence<C extends Compound>
- getAccession
  
  public AccessionID getAccession()
  
  Unsupoorted
  
  Specified by:
  
  getAccession in interface Accessioned
- countCompounds
  
  public int countCompounds(C... compounds)
  
  Delegates to SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[])
  
  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
- iterator
  
  public Iterator<C> iterator()
  
  Returns an instance of SequenceMixin.SequenceIterator
  
  Specified by:
  
  iterator in interface Iterable<C extends Compound>
- 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>
- hashCode
  
  public int hashCode()
  
  Overrides:
  
  hashCode in class Object
- equals
  
  public boolean equals(Object o)
  
  Overrides:
  
  equals in class Object

Class SingleCompoundSequenceReader<C extends Compound>

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Constructor Details

SingleCompoundSequenceReader

SingleCompoundSequenceReader

Method Details

setCompoundSet

setContents

getLength

getCompoundAt

getIndexOf

getLastIndexOf

getSequenceAsString

getAsList

getSubSequence

getCompoundSet

getAccession

countCompounds

iterator

getInverse

hashCode

equals