public class GenbankProxySequenceReader<C extends Compound> extends StringProxySequenceReader<C> implements FeaturesKeyWordInterface, DatabaseReferenceInterface, FeatureRetriever
Constructor and Description |
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GenbankProxySequenceReader(java.lang.String genbankDirectoryCache,
java.lang.String accessionID,
CompoundSet<C> compoundSet) |
Modifier and Type | Method and Description |
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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) |
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