org.biojava3.core.sequence.io
Class ProteinSequenceCreator

java.lang.Object
  extended by org.biojava3.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
ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
           
 
Method Summary
 AbstractSequence<AminoAcidCompound> getSequence(List<AminoAcidCompound> list)
           
 AbstractSequence<AminoAcidCompound> getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
           
 AbstractSequence<AminoAcidCompound> getSequence(String sequence, long index)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ProteinSequenceCreator

public ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
Parameters:
compoundSet -
Method Detail

getSequence

public AbstractSequence<AminoAcidCompound> getSequence(String sequence,
                                                       long index)
Specified by:
getSequence in interface SequenceCreatorInterface<AminoAcidCompound>
Parameters:
sequence -
index - not used in this implementation
Returns:

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: