ProteinSequenceCreator

java.lang.Object

org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

All Implemented Interfaces:: SequenceCreatorInterface<AminoAcidCompound>

Direct Known Subclasses:: CasePreservingProteinSequenceCreator

public class ProteinSequenceCreator extends Object implements SequenceCreatorInterface<AminoAcidCompound>

Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.

Author:: Scooter Willis

Constructor Summary

Constructors

Constructor

Description

ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
Method Summary

Modifier and Type

Method

Description

AbstractSequence<AminoAcidCompound>

getSequence(String sequence, long index)

AbstractSequence<AminoAcidCompound>

getSequence(List<AminoAcidCompound> list)

AbstractSequence<AminoAcidCompound>

getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)

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

Constructor Details
- ProteinSequenceCreator
  
  public ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
  
  Parameters:
  
  compoundSet -
Method Details
- getSequence
  
  public AbstractSequence<AminoAcidCompound> getSequence(String sequence, long index) throws CompoundNotFoundException
  
  Specified by:
  
  getSequence in interface SequenceCreatorInterface<AminoAcidCompound>
  
  Parameters:
  
  sequence -
  
  index - not used in this implementation
  
  Returns:
  
  Throws:
  
  CompoundNotFoundException
- getSequence
  
  public AbstractSequence<AminoAcidCompound> getSequence(List<AminoAcidCompound> list)
  
  Specified by:
  
  getSequence in interface SequenceCreatorInterface<AminoAcidCompound>
  
  Parameters:
  
  list -
  
  Returns:
- getSequence
  
  public AbstractSequence<AminoAcidCompound> getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
  
  Specified by:
  
  getSequence in interface SequenceCreatorInterface<AminoAcidCompound>
  
  Parameters:
  
  proxyLoader -
  
  index - not used in this implementation
  
  Returns: