## org.biojava.bio.structure
Class DBRef

    java.lang.Object
      org.biojava.bio.structure.DBRef

All Implemented Interfaces:
  PDBRecord

    public class DBRef

extends Object
implements PDBRecord

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

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)`