org.jbei.ice.lib.entry.sequence.composers.formatters

Class GenbankFormatter

java.lang.Object

org.jbei.ice.lib.entry.sequence.composers.formatters.AbstractFormatter

org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter

All Implemented Interfaces:

IFormatter

public class GenbankFormatter
extends AbstractFormatter

Formatter for the Genbank file format.

Author:

Zinovii Dmytriv, Timothy Ham

Field Summary

Fields inherited from class org.jbei.ice.lib.entry.sequence.composers.formatters.AbstractFormatter

DEFAULT_NAMESPACE

Constructor Summary

Constructors

Constructor and Description
GenbankFormatter(String name) Constructor using only the name.
GenbankFormatter(String name, String accessionNumber, int version, double seqVersion) Constructor using the complete header fields.

Method Summary

Modifier and Type	Method and Description
void	format(Sequence sequence, OutputStream outputStream) Interface method to take a Sequence object and output the formatted file to the OutputStream.
protected org.biojavax.RichAnnotation	getAnnotations(SequenceFeature sequenceFeature) Convert SequenceFeature into a RichAnnotation.
boolean	getCircular()
protected String	getDefaultFeatureSource() Return the default feature source for a Genbank file.
String	getDescription()
String	getDivision()
protected String	getFeatureType(SequenceFeature sequenceFeature) Retrieve feature type from given SequenceFeature.
String	getIdentifier()
protected org.biojavax.bio.seq.RichLocation.Strand	getStrand(SequenceFeature sequenceFeature) Get the strand of the SequenceFeature feature.
void	setCircular(boolean value)
void	setDescription(String description)
void	setDivision(String division)
void	setIdentifier(String identifier)

Methods inherited from class org.jbei.ice.lib.entry.sequence.composers.formatters.AbstractFormatter

getNamespace

Methods inherited from class java.lang.Object

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

Constructor Detail

GenbankFormatter

public GenbankFormatter(String name)

Constructor using only the name.

Parameters:

name -

GenbankFormatter

public GenbankFormatter(String name,
                        String accessionNumber,
                        int version,
                        double seqVersion)

Constructor using the complete header fields.

Parameters:

name -

accessionNumber -

version -

seqVersion -

Method Detail

getCircular

public boolean getCircular()

setCircular

public void setCircular(boolean value)

getDescription

public String getDescription()

setDescription

public void setDescription(String description)

getDivision

public String getDivision()

setDivision

public void setDivision(String division)

getIdentifier

public String getIdentifier()

setIdentifier

public void setIdentifier(String identifier)

format

public void format(Sequence sequence,
                   OutputStream outputStream)
            throws FormatterException,
                   IOException

Description copied from interface: IFormatter

Interface method to take a Sequence object and output the formatted file to the OutputStream.

Specified by:

format in interface IFormatter

Overrides:

format in class AbstractFormatter

Throws:

FormatterException

IOException

getStrand

protected org.biojavax.bio.seq.RichLocation.Strand getStrand(SequenceFeature sequenceFeature)

Get the strand of the SequenceFeature feature.

Parameters:

sequenceFeature -

Returns:

Strand of the feature.

getAnnotations

protected org.biojavax.RichAnnotation getAnnotations(SequenceFeature sequenceFeature)

Convert SequenceFeature into a RichAnnotation.

Parameters:

sequenceFeature -

Returns:

RichAnnotation object.

getFeatureType

protected String getFeatureType(SequenceFeature sequenceFeature)

Retrieve feature type from given SequenceFeature. Populate it with "misc_feature" if undefined.

Parameters:

sequenceFeature -

Returns:

Genbank Feature type.

getDefaultFeatureSource

protected String getDefaultFeatureSource()

Return the default feature source for a Genbank file.

Returns:

Returns "org.jbei".