org.biojava.nbio.core.sequence.io.embl

Class EmblReference

java.lang.Object

org.biojava.nbio.core.sequence.io.embl.EmblReference

public class EmblReference
extends Object

This class contains the processed data of embl file that contains the referenceNumber, referenceComment, referencePosition referenceCrossReference, referenceGroup, referenceAuthor referenceTitle, referenceLocation

Since:

5.0.0

Author:

Noor Aldeen Al Mbaidin

Constructor Summary

Constructors

Constructor and Description
EmblReference()

Method Summary

Modifier and Type	Method and Description
EmblReference	copyEmblReference(EmblReference emblReference) return copy of EmblReference
String	getReferenceAuthor() The RA (Reference Author) lines list the authors of the paper (or other work) cited.
String	getReferenceComment() The RC (Reference Comment) linetype is an optional linetype which appears if The reference has a comment.
String	getReferenceCrossReference() The RX (reference cross-reference) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.
String	getReferenceGroup() The RG (Reference Group) lines list the working groups/consortia that produced the record.
String	getReferenceLocation() The RL (Reference Location) line contains the conventional citation information for the reference.
String	getReferenceNumber() The RN (Reference Number) line gives a unique number to each reference Citation within an entry.
String	getReferencePosition() The RP (Reference Position) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.
String	getReferenceTitle() The RT (Reference Title) lines give the title of the paper (or other work) as exactly as is possible given the limitations of computer character sets.
void	setReferenceAuthor(String referenceAuthor)
void	setReferenceComment(String referenceComment)
void	setReferenceCrossReference(String referenceCrossReference)
void	setReferenceGroup(String referenceGroup)
void	setReferenceLocation(String referenceLocation)
void	setReferenceNumber(String referenceNumber)
void	setReferencePosition(String referencePosition)
void	setReferenceTitle(String referenceTitle)

Methods inherited from class java.lang.Object

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

Constructor Detail

EmblReference

public EmblReference()

Method Detail

getReferenceNumber

public String getReferenceNumber()

The RN (Reference Number) line gives a unique number to each reference Citation within an entry. This number is used to designate the reference in comments and in the feature table.

Returns:

referenceNumber

setReferenceNumber

public void setReferenceNumber(String referenceNumber)

getReferenceComment

public String getReferenceComment()

The RC (Reference Comment) linetype is an optional linetype which appears if The reference has a comment.

Returns:

String

setReferenceComment

public void setReferenceComment(String referenceComment)

getReferencePosition

public String getReferencePosition()

The RP (Reference Position) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.

Returns:

String

setReferencePosition

public void setReferencePosition(String referencePosition)

getReferenceCrossReference

public String getReferenceCrossReference()

The RX (reference cross-reference) linetype is an optional linetype which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.

Returns:

String

setReferenceCrossReference

public void setReferenceCrossReference(String referenceCrossReference)

getReferenceGroup

public String getReferenceGroup()

The RG (Reference Group) lines list the working groups/consortia that produced the record.

Returns:

String

setReferenceGroup

public void setReferenceGroup(String referenceGroup)

getReferenceAuthor

public String getReferenceAuthor()

The RA (Reference Author) lines list the authors of the paper (or other work) cited. All of the authors are included, and are listed in the order given in the paper.

Returns:

String

setReferenceAuthor

public void setReferenceAuthor(String referenceAuthor)

getReferenceTitle

public String getReferenceTitle()

The RT (Reference Title) lines give the title of the paper (or other work) as exactly as is possible given the limitations of computer character sets.

Returns:

String

setReferenceTitle

public void setReferenceTitle(String referenceTitle)

getReferenceLocation

public String getReferenceLocation()

The RL (Reference Location) line contains the conventional citation information for the reference.

Returns:

String

setReferenceLocation

public void setReferenceLocation(String referenceLocation)

copyEmblReference

public EmblReference copyEmblReference(EmblReference emblReference)

return copy of EmblReference

Parameters:

emblReference -

Returns:

EmblReference