org.biojava3.core.sequence.loader

Class GenbankProxySequenceReader<C extends Compound>

java.lang.Object

org.biojava3.core.sequence.loader.StringProxySequenceReader<C>

org.biojava3.core.sequence.loader.GenbankProxySequenceReader<C>

All Implemented Interfaces:

java.lang.Iterable<C>, DatabaseReferenceInterface, FeaturesKeyWordInterface, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

public class GenbankProxySequenceReader<C extends Compound>
extends StringProxySequenceReader<C>
implements FeaturesKeyWordInterface, DatabaseReferenceInterface

Constructor Summary

Constructors

Constructor and Description
GenbankProxySequenceReader(java.lang.String genbankDirectoryCache, java.lang.String accessionID, CompoundSet<C> compoundSet)

Method Summary

Methods

Modifier and Type	Method and Description
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>>	getDatabaseReferences()
java.lang.String	getGenbankDirectoryCache() Local directory cache of Genbank that can be downloaded
java.lang.String	getHeader()
GenericGenbankHeaderParser<AbstractSequence<C>,C>	getHeaderParser()
java.util.ArrayList<java.lang.String>	getKeyWords()
static void	main(java.lang.String[] args)
void	setGenbankDirectoryCache(java.lang.String genbankDirectoryCache)

Methods inherited from class org.biojava3.core.sequence.loader.StringProxySequenceReader

countCompounds, getAccession, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSequenceAsString, getSubSequence, iterator, setCompoundSet, setContents, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

GenbankProxySequenceReader

public GenbankProxySequenceReader(java.lang.String genbankDirectoryCache,
                          java.lang.String accessionID,
                          CompoundSet<C> compoundSet)
                           throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

getGenbankDirectoryCache

public java.lang.String getGenbankDirectoryCache()

Local directory cache of Genbank that can be downloaded

Returns:

the uniprotDirectoryCache

setGenbankDirectoryCache

public void setGenbankDirectoryCache(java.lang.String genbankDirectoryCache)

Parameters:

aGenbankDirectoryCache - the GenbankDirectoryCache to set

getHeader

public java.lang.String getHeader()

getHeaderParser

public GenericGenbankHeaderParser<AbstractSequence<C>,C> getHeaderParser()

getDatabaseReferences

public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>> getDatabaseReferences()
                                                                                                     throws java.lang.Exception

Specified by:

getDatabaseReferences in interface DatabaseReferenceInterface

Throws:

java.lang.Exception

getKeyWords

public java.util.ArrayList<java.lang.String> getKeyWords()
                                                  throws java.lang.Exception

Specified by:

getKeyWords in interface FeaturesKeyWordInterface

Returns:

Throws:

java.lang.Exception

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Throws:

java.lang.Exception