SequenceCreatorInterface<NucleotideCompound>
public class FileProxyDNASequenceCreator extends java.lang.Object implements SequenceCreatorInterface<NucleotideCompound>
Constructor | Description |
---|---|
FileProxyDNASequenceCreator(java.io.File file,
CompoundSet<NucleotideCompound> compoundSet,
SequenceParserInterface sequenceParser) |
Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
|
Modifier and Type | Method | Description |
---|---|---|
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.
|
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.
|
public FileProxyDNASequenceCreator(java.io.File file, CompoundSet<NucleotideCompound> compoundSet, SequenceParserInterface sequenceParser)
fastaFile
- compoundSet
- public AbstractSequence<NucleotideCompound> getSequence(java.lang.String sequence, long index) throws CompoundNotFoundException, java.io.IOException
getSequence
in interface SequenceCreatorInterface<NucleotideCompound>
sequence
- index
- CompoundNotFoundException
java.io.IOException
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
-