GenbankProxySequenceReader

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 <github:karlnicholas>, Jacek Grzebyta <github:jgrzebyta>

Constructor Summary

Constructors

Constructor

Description

GenbankProxySequenceReader(String genbankDirectoryCache, String accessionID, CompoundSet<C> compoundSet)
Method Summary

Modifier and Type

Method

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 Details
- GenbankProxySequenceReader
  
  public GenbankProxySequenceReader(String genbankDirectoryCache, String accessionID, CompoundSet<C> compoundSet) throws IOException, InterruptedException, CompoundNotFoundException
  
  Throws:
  
  InterruptedException
  
  IOException
  
  CompoundNotFoundException
Method Details
- 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