public class FileProxyProteinSequenceCreator extends java.lang.Object implements SequenceCreatorInterface<AminoAcidCompound>
Constructor and Description |
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FileProxyProteinSequenceCreator(java.io.File file,
CompoundSet<AminoAcidCompound> compoundSet,
SequenceParserInterface sequenceParser)
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
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Modifier and Type | Method and Description |
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AbstractSequence<AminoAcidCompound> |
getSequence(java.util.List<AminoAcidCompound> list)
Not sure of use case and currently not supported
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AbstractSequence<AminoAcidCompound> |
getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader,
long index)
Should be able to extend the same concept to a remote URL call or database connection.
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AbstractSequence<AminoAcidCompound> |
getSequence(java.lang.String sequence,
long index)
Even though we are passing in the sequence we really only care about the length of the sequence and the offset
index in the fasta file.
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public FileProxyProteinSequenceCreator(java.io.File file, CompoundSet<AminoAcidCompound> compoundSet, SequenceParserInterface sequenceParser)
fastaFile
- compoundSet
- public AbstractSequence<AminoAcidCompound> getSequence(java.lang.String sequence, long index) throws CompoundNotFoundException, java.io.IOException
getSequence
in interface SequenceCreatorInterface<AminoAcidCompound>
sequence
- index
- CompoundNotFoundException
java.io.IOException
public AbstractSequence<AminoAcidCompound> getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
getSequence
in interface SequenceCreatorInterface<AminoAcidCompound>
proxyLoader
- index
- public AbstractSequence<AminoAcidCompound> getSequence(java.util.List<AminoAcidCompound> list)
getSequence
in interface SequenceCreatorInterface<AminoAcidCompound>
list
-