Package opennlp.tools.formats

Class BioNLP2004NameSampleStream

java.lang.Object

opennlp.tools.formats.BioNLP2004NameSampleStream

All Implemented Interfaces:

AutoCloseable, ObjectStream<NameSample>

@Internal
public class BioNLP2004NameSampleStream
extends Object
implements ObjectStream<NameSample>

A sample stream for the training files of the BioNLP/NLPBA 2004 shared task.

The data contains five named entity types:

• DNA
• RNA
• protein
• cell_type
• cell_line

Data can be found on this website, or in this repository.

The BioNLP/NLPBA 2004 data were originally published here:

http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/ERtask/report.html,

yet this page was gone when last checked in December 2022.

It looks like this repo contains a copy of the data located on the original page: The BioNLP 2004 seems to be related to http://www.geniaproject.org/shared-tasks/bionlp-jnlpba-shared-task-2004

Note: Do not use this class, internal use only!

Field Summary

Fields

Modifier and Type	Field	Description
static int	GENERATE_CELLLINE_ENTITIES
static int	GENERATE_CELLTYPE_ENTITIES
static int	GENERATE_DNA_ENTITIES
static int	GENERATE_PROTEIN_ENTITIES
static int	GENERATE_RNA_ENTITIES

Constructor Summary

Constructors

Constructor	Description
BioNLP2004NameSampleStream(InputStreamFactory in, int types)	Initializes a BioNLP2004NameSampleStream.

Method Summary

Modifier and Type	Method	Description
void	close()	Closes the ObjectStream and releases all allocated resources.
NameSample	read()	Returns the next ObjectStream object.
void	reset()	Repositions the stream at the beginning and the previously seen object sequence will be repeated exactly.

Methods inherited from class java.lang.Object

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

Field Detail

GENERATE_DNA_ENTITIES

public static final int GENERATE_DNA_ENTITIES

See Also:

Constant Field Values

GENERATE_PROTEIN_ENTITIES

public static final int GENERATE_PROTEIN_ENTITIES

See Also:

Constant Field Values

GENERATE_CELLTYPE_ENTITIES

public static final int GENERATE_CELLTYPE_ENTITIES

See Also:

Constant Field Values

GENERATE_CELLLINE_ENTITIES

public static final int GENERATE_CELLLINE_ENTITIES

See Also:

Constant Field Values

GENERATE_RNA_ENTITIES

public static final int GENERATE_RNA_ENTITIES

See Also:

Constant Field Values

Constructor Detail

BioNLP2004NameSampleStream

public BioNLP2004NameSampleStream(InputStreamFactory in,
                                  int types)
                           throws IOException

Initializes a BioNLP2004NameSampleStream.

Parameters:

in - The InputStreamFactory to use.

types - The types to use.

Throws:

IOException - Thrown if IO errors occurred during initialization.

Method Detail

read

public NameSample read()
                throws IOException

Description copied from interface: ObjectStream

Returns the next ObjectStream object. Calling this method repeatedly until it returns null will return each object from the underlying source exactly once.

Specified by:

read in interface ObjectStream<NameSample>

Returns:

The next object or null to signal that the stream is exhausted.

Throws:

IOException - Thrown if there is an error during reading.

reset

public void reset()
           throws IOException,
                  UnsupportedOperationException

Description copied from interface: ObjectStream

Repositions the stream at the beginning and the previously seen object sequence will be repeated exactly. This method can be used to re-read the stream if multiple passes over the objects are required.

The implementation of this method is optional.

Specified by:

reset in interface ObjectStream<NameSample>

Throws:

IOException - Thrown if there is an error during resetting the stream.

UnsupportedOperationException - Thrown if the reset() is not supported. By default, this is the case.

close

public void close()
           throws IOException

Description copied from interface: ObjectStream

Closes the ObjectStream and releases all allocated resources. After close was called, it's not allowed to call ObjectStream.read() or ObjectStream.reset().

Specified by:

close in interface AutoCloseable

Specified by:

close in interface ObjectStream<NameSample>

Throws:

IOException - Thrown if there is an error during closing the stream.