org.biojava.nbio.core.sequence.loader

Class GenbankProxySequenceReader<C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.loader.StringProxySequenceReader<C>

org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader<C>

All Implemented Interfaces:

Iterable<C>, DatabaseReferenceInterface, FeatureRetriever, FeaturesKeyWordInterface, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

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

Author:

Karl Nicholas , Jacek Grzebyta

Constructor Summary

Constructors

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

Method Summary

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

Methods inherited from class org.biojava.nbio.core.sequence.loader.StringProxySequenceReader

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

GenbankProxySequenceReader

public GenbankProxySequenceReader(String genbankDirectoryCache,
                                  String accessionID,
                                  CompoundSet<C> compoundSet)
                           throws IOException,
                                  InterruptedException,
                                  CompoundNotFoundException

Throws:

InterruptedException

IOException

CompoundNotFoundException

Method Detail

getGenbankDirectoryCache

public String getGenbankDirectoryCache()

Local directory cache of Genbank that can be downloaded

Returns:

the uniprotDirectoryCache

setGenbankDirectoryCache

public void setGenbankDirectoryCache(String genbankDirectoryCache)

Parameters:

genbankDirectoryCache -

getHeader

public String getHeader()

getHeaderParser

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

getFeatures

public HashMap<String,ArrayList<AbstractFeature>> getFeatures()

Specified by:

getFeatures in interface FeatureRetriever

getDatabaseReferences

public LinkedHashMap<String,ArrayList<DBReferenceInfo>> getDatabaseReferences()

Specified by:

getDatabaseReferences in interface DatabaseReferenceInterface

getKeyWords

public ArrayList<String> getKeyWords()

Specified by:

getKeyWords in interface FeaturesKeyWordInterface

Returns:

main

public static void main(String[] args)
                 throws Throwable

Throws:

Throwable