Package org.biojava.nbio.core.sequence.io

Class CasePreservingProteinSequenceCreator

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 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.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 -