Package org.biojava.nbio.core.sequence.io

Class GenbankReader<S extends AbstractSequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.core.sequence.io.GenbankReader<S,C>

public class GenbankReader<S extends AbstractSequence<C>,C extends Compound>
extends Object

Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files

Constructor Summary

Constructors

Constructor	Description
GenbankReader(File file, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.
GenbankReader(InputStream is, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator)	If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads.

Method Summary

Modifier and Type	Method	Description
void	close()
boolean	isClosed()
LinkedHashMap<String,S>	process()	The parsing is done in this method. This method will return all the available Genbank records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap. You don't need to call close() after calling this method.
LinkedHashMap<String,S>	process(int max)	This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open. Subsequent calls to the same method continue parsing the rest of the file. This is particularly useful when dealing with very big data files, (e.g.

Methods inherited from class java.lang.Object

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

Constructor Detail

GenbankReader

public GenbankReader(InputStream is,
                     SequenceHeaderParserInterface<S,C> headerParser,
                     SequenceCreatorInterface<C> sequenceCreator)

If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about local file offsets for quick reads. InputStream does not give you the name of the stream to access quickly via file seek. A seek in an InputStream is forced to read all the data so you don't gain anything.

Parameters:

is -

headerParser -

sequenceCreator -

GenbankReader

public GenbankReader(File file,
                     SequenceHeaderParserInterface<S,C> headerParser,
                     SequenceCreatorInterface<C> sequenceCreator)
              throws FileNotFoundException

If you are going to use the FileProxyProteinSequenceCreator then you need to use this constructor because we need details about the location of the file.

Parameters:

file -

headerParser -

sequenceCreator -

Throws:

FileNotFoundException - if the file does not exist, is a directory rather than a regular file, or for some other reason cannot be opened for reading.

SecurityException - if a security manager exists and its checkRead method denies read access to the file.

Method Detail

isClosed

public boolean isClosed()

process

public LinkedHashMap<String,S> process()
                                      throws IOException,
                                             CompoundNotFoundException

The parsing is done in this method.
This method will return all the available Genbank records in the File or InputStream, closes the underlying resource, and return the results in LinkedHashMap.
You don't need to call close() after calling this method.

Returns:

HashMap containing all the parsed Genbank records present, starting current fileIndex onwards.

Throws:

IOException

CompoundNotFoundException

OutOfMemoryError - if the input resource is larger than the allocated heap.

See Also:

process(int)

process

public LinkedHashMap<String,S> process(int max)
                                      throws IOException,
                                             CompoundNotFoundException

This method tries to parse maximum max records from the open File or InputStream, and leaves the underlying resource open.
Subsequent calls to the same method continue parsing the rest of the file.
This is particularly useful when dealing with very big data files, (e.g. NCBI nr database), which can't fit into memory and will take long time before the first result is available.
N.B.

• This method can't be called after calling its NO-ARGUMENT twin.
• remember to close the underlying resource when you are done.

Parameters:

max - maximum number of records to return.

Returns:

HashMap containing maximum max parsed Genbank records present, starting current fileIndex onwards.

Throws:

IOException

CompoundNotFoundException

Since:

3.0.6

See Also:

process()

close

public void close()