org.biojava3.core.sequence.io
Class CasePreservingProteinSequenceCreator

java.lang.Object
  extended by org.biojava3.core.sequence.io.ProteinSequenceCreator
      extended by org.biojava3.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
CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
           
 
Method Summary
 AbstractSequence<AminoAcidCompound> getSequence(List<AminoAcidCompound> list)
          Assumes all compounds were uppercase
 AbstractSequence<AminoAcidCompound> getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
           
 AbstractSequence<AminoAcidCompound> getSequence(String sequence, 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 Detail

CasePreservingProteinSequenceCreator

public CasePreservingProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)
Method Detail

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.biojava3.core.sequence.template.ProxySequenceReader, long)

getSequence

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

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)

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 -