uk.ac.ebi.intenz.tools.sib.sptr_enzyme

Class EnzymeCrossReference

java.lang.Object

uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference

All Implemented Interfaces:

Serializable, uk.ac.ebi.interfaces.CrossReference, uk.ac.ebi.interfaces.sptr.SPTRCrossReference

public class EnzymeCrossReference
extends Object
implements uk.ac.ebi.interfaces.sptr.SPTRCrossReference, Serializable

This class implements the SPTRCrossReference interface.

Version:

preliminary - $Revision: 1.2 $ $Date: 2008/01/28 11:43:22 $

Author:

Michael Darsow

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	MIM Constant for database cross reference to MIM Disease Database.
static String	PROSITE Constant for database cross reference to PROSITE.
static String	SWISSPROT Constant for database cross reference to SwissProt.

Fields inherited from interface uk.ac.ebi.interfaces.sptr.SPTRCrossReference

PROPERTY_ADDITION, PROPERTY_DESCRIPTION, PROPERTY_EMBL_MT_GENOMIC_DNA, PROPERTY_EMBL_MT_GENOMIC_RNA, PROPERTY_EMBL_MT_MRNA, PROPERTY_EMBL_MT_OTHER_DNA, PROPERTY_EMBL_MT_OTHER_RNA, PROPERTY_EMBL_MT_UNASSIGNED_DNA, PROPERTY_EMBL_MT_UNASSIGNED_RNA, PROPERTY_EMBL_MT_UNKNOWN, PROPERTY_EMBL_MT_VIRAL_CRNA, PROPERTY_EMBL_PRE_RNA, PROPERTY_HIT_FALSE_NEG, PROPERTY_HIT_FALSE_POS, PROPERTY_HIT_PARTIAL, PROPERTY_HIT_TRUE_POS, PROPERTY_HIT_UNKNOWN, PROPERTY_PDB_CHAINS, PROPERTY_PDB_METHOD, PROPERTY_PDB_METHOD_EM, PROPERTY_PDB_METHOD_FIBER, PROPERTY_PDB_METHOD_IR, PROPERTY_PDB_METHOD_MODEL, PROPERTY_PDB_METHOD_NEUTRON, PROPERTY_PDB_METHOD_NMR, PROPERTY_PDB_METHOD_XRAY, PROPERTY_PDB_RESOLUTION, PROPERTY_VALUE_UNKNOWN, QUATERNARY_PROPERTY, SECONDARY_PROPERTY, TERTIARY_PROPERTY

Constructor Summary

Constructors

Constructor and Description
EnzymeCrossReference(String databaseName) Creates an EnzymeCrossReference instance to the given database.

Method Summary

Methods

Modifier and Type	Method and Description
String	getAccessionNumber() Returns the accession number of this EnzymeCrossReference.
String	getDatabaseName() Returns the name of the database this EnzymeCrossReference refers to.
String	getPropertyValue(int property) Returns the value of the property.
boolean	hasProperty(int property) Indicates if a cross reference property is set.
void	setAccessionNumber(String accessionNumber) Sets the accession number of this EnzymeCrossReference.
void	setPropertyValue(int property, String value) Sets a property and value of this EnzymeCrossReference.

Methods inherited from class java.lang.Object

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

Field Detail

SWISSPROT

public static final String SWISSPROT

Constant for database cross reference to SwissProt.

See Also:

Constant Field Values

PROSITE

public static final String PROSITE

Constant for database cross reference to PROSITE.

See Also:

Constant Field Values

MIM

public static final String MIM

Constant for database cross reference to MIM Disease Database.

See Also:

Constant Field Values

Constructor Detail

EnzymeCrossReference

public EnzymeCrossReference(String databaseName)

Creates an EnzymeCrossReference instance to the given database. Possible database name constants are:

• SwissProt
• PROSITE
• MIM Disease Database

Parameters:

databaseName - The name of database of this cross reference.

Method Detail

setAccessionNumber

public void setAccessionNumber(String accessionNumber)

Sets the accession number of this EnzymeCrossReference.

Cross references are found in the DR/PR/DI lines on the marked positions, where the data base name is marked red (if existing) and the accession number green. DR lines are SwissProt, PR lines are PROSITE and DI lines are MIM cross references. DR lines contain between 1 and 3 cross references.

 DR   O66503; RIR1_AQUAE; P42491, RIR1_ASFB7;  P26685, RIR1_ASFM2;
 PR   PROSITE; PDOC00084;
 DI   Guanidinoacetate methyltransferase deficiency; MIM:601240.
 

Specified by:

setAccessionNumber in interface uk.ac.ebi.interfaces.CrossReference

Specified by:

setAccessionNumber in interface uk.ac.ebi.interfaces.sptr.SPTRCrossReference

Parameters:

accessionNumber - The accession number.

getAccessionNumber

public String getAccessionNumber()

Returns the accession number of this EnzymeCrossReference.

Cross references are found in the DR/PR/DI lines on the marked positions, where the data base name is marked red (if existing) and the accession number green. DR lines are SwissProt, PR lines are PROSITE and DI lines are MIM cross references. DR lines contain between 1 and 3 cross references.

 DR   O66503; RIR1_AQUAE; P42491, RIR1_ASFB7;  P26685, RIR1_ASFM2;
 PR   PROSITE; PDOC00084;
 DI   Guanidinoacetate methyltransferase deficiency; MIM:601240.
 

Specified by:

getAccessionNumber in interface uk.ac.ebi.interfaces.CrossReference

Specified by:

getAccessionNumber in interface uk.ac.ebi.interfaces.sptr.SPTRCrossReference

Returns:

The accession number of this EnzymeCrossReference.

setPropertyValue

public void setPropertyValue(int property,
                    String value)

Sets a property and value of this EnzymeCrossReference. Properties of Enzyme cross references are always descriptions.

Specified by:

setPropertyValue in interface uk.ac.ebi.interfaces.sptr.SPTRCrossReference

Parameters:

property - The property.

value - The value of the property.

Throws:

IllegalArgumentException - if the property is not a valid property.

hasProperty

public boolean hasProperty(int property)

Indicates if a cross reference property is set.

Specified by:

hasProperty in interface uk.ac.ebi.interfaces.sptr.SPTRCrossReference

Parameters:

property - The property.

Returns:

true, if the property is set, false if it is not.

getPropertyValue

public String getPropertyValue(int property)

Returns the value of the property.

Specified by:

getPropertyValue in interface uk.ac.ebi.interfaces.sptr.SPTRCrossReference

Parameters:

property - The property.

Returns:

The value of the property.

getDatabaseName

public String getDatabaseName()

Returns the name of the database this EnzymeCrossReference refers to.

Specified by:

getDatabaseName in interface uk.ac.ebi.interfaces.CrossReference

Specified by:

getDatabaseName in interface uk.ac.ebi.interfaces.sptr.SPTRCrossReference

Returns:

The name of the database this EnzymeCrossReference refers to.