org.biojava.bio.structure

Class DBRef

java.lang.Object

org.biojava.bio.structure.DBRef

All Implemented Interfaces:

Serializable, PDBRecord

public class DBRef
extends Object
implements PDBRecord, Serializable

A class to represent database cross references. This is just a simple bean that contains the infor from one DBREF line

Since:

4:56:14 PM

Version:

%I% %G%

Author:

Andreas Prlic

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
DBRef()

Method Summary

Methods

Modifier and Type	Method and Description
Character	getChainId() The chain ID of the corresponding chain.
String	getDatabase() The database of the db-ref.
String	getDbAccession() Sequence database accession code.
String	getDbIdCode() Sequence database identification code.
int	getDbSeqBegin() Initial sequence number of the database seqment.
int	getDbSeqEnd() Ending sequence position of the database segment.
Long	getId() Get the ID used by Hibernate.
char	getIdbnsBegin() Insertion code of initial residue of the segment, if PDB is the reference.
char	getIdbnsEnd() Insertion code of the ending residue of the segment, if PDB is the reference.
String	getIdCode() get the idCode for this entry
char	getInsertBegin() Initial insertion code of the PDB sequence segment.
char	getInsertEnd() Ending insertion code of the PDB sequence segment.
Structure	getParent() Get the structure object that this DBRef relates to.
int	getSeqBegin() Initial sequence number of the PDB sequence segment.
int	getSeqEnd() Ending sequence number of the PDB sequence segment.
void	setChainId(Character chainId) The chain ID of the corresponding chain.
void	setDatabase(String database) Specifies the database value.
void	setDbAccession(String dbAccession) Sequence database accession code.
void	setDbIdCode(String dbIdCode) Sequence database identification code.
void	setDbSeqBegin(int dbSeqBegin) Initial sequence number of the database seqment.
void	setDbSeqEnd(int dbSeqEnd) The begin of the sequence position in the database
void	setId(Long id) Set the ID used by Hibernate.
void	setIdbnsBegin(char idbnsBegin) Insertion code of initial residue of the segment, if PDB is the reference.
void	setIdbnsEnd(char idbnsEnd) Insertion code of the ending residue of the segment, if PDB is the reference.
void	setIdCode(String idCode) Set the idCode for this entry.
void	setInsertBegin(char insertBegin) Initial insertion code of the PDB sequence segment.
void	setInsertEnd(char insertEnd) Ending insertion code of the PDB sequence segment.
void	setParent(Structure s) Set the structure object that this DBRef relates to.
void	setSeqBegin(int seqbegin) Initial sequence number of the PDB sequence segment.
void	setSeqEnd(int seqEnd) Ending sequence number of the PDB sequence segment.
String	toPDB() Convert the DBRef object to a DBREF record as it is used in PDB files
void	toPDB(StringBuffer buf) Append the PDB representation of this DBRef to the provided StringBuffer
String	toString() String representation of a DBRef.

Methods inherited from class java.lang.Object

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

Constructor Detail

DBRef

public DBRef()

Method Detail

getId

public Long getId()

Get the ID used by Hibernate.

Returns:

the ID used by Hibernate

See Also:

setId(Long)

setId

public void setId(Long id)

Set the ID used by Hibernate.

Parameters:

id - the id assigned by Hibernate

See Also:

getId()

setParent

public void setParent(Structure s)

Set the structure object that this DBRef relates to.

Parameters:

s - a structure object

See Also:

getParent()

getParent

public Structure getParent()

Get the structure object that this DBRef relates to.

Returns:

s a structure object

See Also:

setParent(Structure)

toPDB

public String toPDB()

Convert the DBRef object to a DBREF record as it is used in PDB files

Specified by:

toPDB in interface PDBRecord

Returns:

a PDB - DBREF formatted line

toPDB

public void toPDB(StringBuffer buf)

Append the PDB representation of this DBRef to the provided StringBuffer

Specified by:

toPDB in interface PDBRecord

Parameters:

buf - the StringBuffer to write to.

toString

public String toString()

String representation of a DBRef.

Overrides:

toString in class Object

Returns:

a String

getIdCode

public String getIdCode()

get the idCode for this entry

Returns:

the idCode

See Also:

setIdCode(String)

setIdCode

public void setIdCode(String idCode)

Set the idCode for this entry.

Parameters:

idCode - the idCode for this entry

See Also:

getIdCode()

getChainId

public Character getChainId()

The chain ID of the corresponding chain.

Returns:

chainId the ID of the corresponding chain.

See Also:

setChainId(Character)

setChainId

public void setChainId(Character chainId)

The chain ID of the corresponding chain.

Parameters:

chainId - the ID of the corresponding chain

See Also:

getChainId()

getDatabase

public String getDatabase()

The database of the db-ref. uses the abbreviation as provided in the PDB files:

   Database name                         database
                                     (code in columns 27 - 32)
    ----------------------------------------------------------
    GenBank                               GB
    Protein Data Bank                     PDB
    Protein Identification Resource       PIR
    SWISS-PROT                            SWS
    TREMBL                                TREMBL
    UNIPROT                               UNP
    

Returns:

name of database of this DBRef

See Also:

setDatabase(String)

setDatabase

public void setDatabase(String database)

Specifies the database value.

Parameters:

database - the database

See Also:

getDatabase()

getDbAccession

public String getDbAccession()

Sequence database accession code.

Returns:

the dbAccession

See Also:

setDbAccession(String)

setDbAccession

public void setDbAccession(String dbAccession)

Sequence database accession code.

Parameters:

dbAccession - the dbAccession

See Also:

getDbAccession()

getDbIdCode

public String getDbIdCode()

Sequence database identification code.

Returns:

the dbIdCode

See Also:

setDbIdCode(String)

setDbIdCode

public void setDbIdCode(String dbIdCode)

Sequence database identification code.

Parameters:

dbIdCode - identification code

See Also:

getDbIdCode()

getDbSeqBegin

public int getDbSeqBegin()

Initial sequence number of the database seqment.

Returns:

position

See Also:

setDbSeqBegin(int)

setDbSeqBegin

public void setDbSeqBegin(int dbSeqBegin)

Initial sequence number of the database seqment.

Parameters:

dbSeqBegin - a sequence position

See Also:

getDbSeqBegin()

getDbSeqEnd

public int getDbSeqEnd()

Ending sequence position of the database segment.

Returns:

dbSeqEnd

See Also:

setDbSeqEnd(int)

setDbSeqEnd

public void setDbSeqEnd(int dbSeqEnd)

The begin of the sequence position in the database

Parameters:

dbSeqEnd - sequence position

See Also:

getDbSeqEnd()

getIdbnsBegin

public char getIdbnsBegin()

Insertion code of initial residue of the segment, if PDB is the reference.

Returns:

idbnsBegin isnertion code

See Also:

setIdbnsBegin(char)

setIdbnsBegin

public void setIdbnsBegin(char idbnsBegin)

Insertion code of initial residue of the segment, if PDB is the reference.

Parameters:

idbnsBegin - insertion code

See Also:

getIdbnsBegin()

getIdbnsEnd

public char getIdbnsEnd()

Insertion code of the ending residue of the segment, if PDB is the reference.

Returns:

idbnsEnd insertion code

See Also:

setIdbnsEnd(char)

setIdbnsEnd

public void setIdbnsEnd(char idbnsEnd)

Insertion code of the ending residue of the segment, if PDB is the reference.

Parameters:

idbnsEnd - the insertion code

See Also:

setIdbnsEnd(char)

getInsertBegin

public char getInsertBegin()

Initial insertion code of the PDB sequence segment.

Returns:

insertBegin

See Also:

setInsertBegin(char)

setInsertBegin

public void setInsertBegin(char insertBegin)

Initial insertion code of the PDB sequence segment.

Parameters:

insertBegin -

See Also:

getInsertBegin()

getInsertEnd

public char getInsertEnd()

Ending insertion code of the PDB sequence segment.

Returns:

insertEnd insertion code

See Also:

setInsertEnd(char)

setInsertEnd

public void setInsertEnd(char insertEnd)

Ending insertion code of the PDB sequence segment.

Parameters:

insertEnd - insertEnd

See Also:

getInsertEnd()

getSeqBegin

public int getSeqBegin()

Initial sequence number of the PDB sequence segment.

Returns:

start seq. position

See Also:

setSeqBegin(int)

setSeqBegin

public void setSeqBegin(int seqbegin)

Initial sequence number of the PDB sequence segment.

Parameters:

seqbegin - start seq. position

See Also:

getSeqBegin()

getSeqEnd

public int getSeqEnd()

Ending sequence number of the PDB sequence segment.

Returns:

sequence end position

See Also:

getSeqEnd()

setSeqEnd

public void setSeqEnd(int seqEnd)

Ending sequence number of the PDB sequence segment.

Parameters:

seqEnd - sequence end position

See Also:

setSeqEnd(int)