org.biojava3.core.sequence.io
public class FileProxyDNASequenceCreator extends java.lang.Object implements SequenceCreatorInterface<NucleotideCompound>
Constructor and Description |
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FileProxyDNASequenceCreator(java.io.File fastaFile,
CompoundSet<NucleotideCompound> compoundSet)
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<NucleotideCompound> |
getSequence(java.util.List<NucleotideCompound> list)
Not sure of use case and currently not supported
|
AbstractSequence<NucleotideCompound> |
getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader,
long index)
Should be able to extend the same concept to a remote URL call or database connection.
|
AbstractSequence<NucleotideCompound> |
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 FileProxyDNASequenceCreator(java.io.File fastaFile, CompoundSet<NucleotideCompound> compoundSet)
fastaFile
- compoundSet
- public AbstractSequence<NucleotideCompound> getSequence(java.lang.String sequence, long index)
getSequence
in interface SequenceCreatorInterface<NucleotideCompound>
sequence
- index
- public AbstractSequence<NucleotideCompound> getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
getSequence
in interface SequenceCreatorInterface<NucleotideCompound>
proxyLoader
- index
- public AbstractSequence<NucleotideCompound> getSequence(java.util.List<NucleotideCompound> list)
getSequence
in interface SequenceCreatorInterface<NucleotideCompound>
list
-