java.lang.Object

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

org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator

All Implemented Interfaces:: SequenceCreatorInterface<AminoAcidCompound>

public class CasePreservingProteinSequenceCreator extends ProteinSequenceCreator

A sequence creator which preserves the case of its input string in the user collection of the returned ProteinSequence.

The user collection will be the same length as the resulting ProteinSequence. Each object can be cast to a Boolean. If true, the corresponding position in the input file was uppercase.

Example

CasePreservingProteinSequenceCreator creator =
    new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet());
AbstractSequence seq = creator.getSequence("aaAA",0);
System.out.println(seq.getSequenceAsString()); //"AAAA"
System.out.println(seq.getUserCollection()); //"[false, false, true, true]"

Constructor Summary

Constructors

Constructor

Description

CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
Method Summary

Modifier and Type

Method

Description

AbstractSequence<AminoAcidCompound>

getSequence(String sequence, long index)

AbstractSequence<AminoAcidCompound>

getSequence(List<AminoAcidCompound> list)

Assumes all compounds were uppercase

AbstractSequence<AminoAcidCompound>

getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)

static void

main(String[] args)

static void

setLowercaseToNull(ProteinSequence seq, Object[] out)

Takes a ProteinSequence which was created by a CasePreservingProteinSequenceCreator.

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

Constructor Details
- CasePreservingProteinSequenceCreator
  
  public CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
Method Details
- getSequence
  
  public AbstractSequence<AminoAcidCompound> getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
  Specified by:
  
  getSequence in interface SequenceCreatorInterface<AminoAcidCompound>
  
  Overrides:
  
  getSequence in class ProteinSequenceCreator
  
  index - not used in this implementation
  
  Returns:
  
  See Also:
  
  ProteinSequenceCreator.getSequence(org.biojava.nbio.core.sequence.template.ProxySequenceReader, long)
- getSequence
  
  public AbstractSequence<AminoAcidCompound> getSequence(String sequence, long index) throws CompoundNotFoundException
  
  Specified by:
  
  getSequence in interface SequenceCreatorInterface<AminoAcidCompound>
  
  Overrides:
  
  getSequence in class ProteinSequenceCreator
  
  index - not used in this implementation
  
  Returns:
  
  Throws:
  
  CompoundNotFoundException
- getSequence
  
  public AbstractSequence<AminoAcidCompound> getSequence(List<AminoAcidCompound> list)
  
  Assumes all compounds were uppercase
  Specified by:
  
  getSequence in interface SequenceCreatorInterface<AminoAcidCompound>
  
  Overrides:
  
  getSequence in class ProteinSequenceCreator
  
  Returns:
  
  See Also:
  
  ProteinSequenceCreator.getSequence(java.util.List)
- main
  
  public static void main(String[] args) throws Exception
  
  Throws:
  
  Exception
- setLowercaseToNull
  
  public static void setLowercaseToNull(ProteinSequence seq, Object[] out)
  
  Takes a ProteinSequence which was created by a CasePreservingProteinSequenceCreator. Uses the case info stored in the user collection to modify the output array.
  Sets elements of the output array which correspond to lowercase letters to null.
  
  Parameters:
  
  seq - Input sequence with case stored as the user collection
  
  out -

Class CasePreservingProteinSequenceCreator

Example

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

CasePreservingProteinSequenceCreator

Method Details

getSequence

getSequence

getSequence

main

setLowercaseToNull