java.lang.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
Constructor | Description |
---|---|
GenbankProxySequenceReader(java.lang.String genbankDirectoryCache,
java.lang.String accessionID,
CompoundSet<C> compoundSet) |
Modifier and Type | Method | Description |
---|---|---|
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>> |
getDatabaseReferences() |
|
java.util.HashMap<java.lang.String,java.util.ArrayList<AbstractFeature>> |
getFeatures() |
|
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) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
countCompounds, getAccession, getAsList, getCompoundAt, getCompoundSet, getIndexOf, getInverse, getLastIndexOf, getLength, getSequenceAsString, getSequenceAsString, getSubSequence, iterator, setCompoundSet, setContents, setContents, toString
public GenbankProxySequenceReader(java.lang.String genbankDirectoryCache, java.lang.String accessionID, CompoundSet<C> compoundSet) throws java.io.IOException, java.lang.InterruptedException, CompoundNotFoundException
java.lang.InterruptedException
java.io.IOException
CompoundNotFoundException
public java.lang.String getGenbankDirectoryCache()
public void setGenbankDirectoryCache(java.lang.String genbankDirectoryCache)
genbankDirectoryCache
- public java.lang.String getHeader()
public GenericGenbankHeaderParser<AbstractSequence<C>,C> getHeaderParser()
public java.util.HashMap<java.lang.String,java.util.ArrayList<AbstractFeature>> getFeatures()
getFeatures
in interface FeatureRetriever
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<DBReferenceInfo>> getDatabaseReferences()
getDatabaseReferences
in interface DatabaseReferenceInterface
public java.util.ArrayList<java.lang.String> getKeyWords()
getKeyWords
in interface FeaturesKeyWordInterface
public static void main(java.lang.String[] args) throws java.lang.Throwable
java.lang.Throwable