ProteinSequenceCreator

java.lang.Object
- org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

All Implemented Interfaces:

SequenceCreatorInterface<AminoAcidCompound>

Direct Known Subclasses:

CasePreservingProteinSequenceCreator
```
public class ProteinSequenceCreator
extends java.lang.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)

Constructors
Constructor	Description
`ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`AbstractSequence<AminoAcidCompound>`	`getSequence(java.lang.String sequence, long index)`
`AbstractSequence<AminoAcidCompound>`	`getSequence(java.util.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 Detail

ProteinSequenceCreator

public ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)

Parameters:: compoundSet -

Method Detail

getSequence

public AbstractSequence<AminoAcidCompound> getSequence(java.lang.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(java.util.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:

Class ProteinSequenceCreator

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ProteinSequenceCreator

Method Detail

getSequence

getSequence

getSequence