org.biojava.bio.structure
Class DBRef

java.lang.Object
  extended by 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
DBRef()
           
 
Method Summary
 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)