DBRef

java.lang.Object
- org.biojava.nbio.structure.DBRef

All Implemented Interfaces:

java.io.Serializable, PDBRecord
```
public class DBRef
extends java.lang.Object
implements PDBRecord, java.io.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()

Constructors
Constructor and Description
`DBRef()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.lang.String`	`getChainId()` The chain ID of the corresponding chain.
`java.lang.String`	`getDatabase()` The database of the db-ref.
`java.lang.String`	`getDbAccession()` Sequence database accession code.
`java.lang.String`	`getDbIdCode()` Sequence database identification code.
`int`	`getDbSeqBegin()` Initial sequence number of the database seqment.
`int`	`getDbSeqEnd()` Ending sequence position of the database segment.
`java.lang.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.
`java.lang.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(java.lang.String chainId)` The chain ID of the corresponding chain.
`void`	`setDatabase(java.lang.String database)` Specifies the database value.
`void`	`setDbAccession(java.lang.String dbAccession)` Sequence database accession code.
`void`	`setDbIdCode(java.lang.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(java.lang.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(java.lang.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.
`java.lang.String`	`toPDB()` Convert the DBRef object to a DBREF record as it is used in PDB files
`void`	`toPDB(java.lang.StringBuffer buf)` Append the PDB representation of this DBRef to the provided StringBuffer
`java.lang.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 java.lang.Long getId()
```
    Get the ID used by Hibernate.
    
    Returns:
    
    the ID used by Hibernate
    
    See Also:
    
    setId(Long)
  - setId
```
public void setId(java.lang.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 java.lang.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(java.lang.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 java.lang.String toString()
```
    String representation of a DBRef.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    a String
  - getIdCode
```
public java.lang.String getIdCode()
```
    get the idCode for this entry
    
    Returns:
    
    the idCode
    
    See Also:
    
    setIdCode(String)
  - setIdCode
```
public void setIdCode(java.lang.String idCode)
```
    Set the idCode for this entry.
    
    Parameters:
    
    idCode - the idCode for this entry
    
    See Also:
    
    getIdCode()
  - getChainId
```
public java.lang.String getChainId()
```
    The chain ID of the corresponding chain.
    
    Returns:
    
    chainId the ID of the corresponding chain.
  - setChainId
```
public void setChainId(java.lang.String chainId)
```
    The chain ID of the corresponding chain.
    
    Parameters:
    
    chainId - the ID of the corresponding chain
    
    See Also:
    
    getChainId()
  - getDatabase
```
public java.lang.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(java.lang.String database)
```
    Specifies the database value.
    
    Parameters:
    
    database - the database
    
    See Also:
    
    getDatabase()
  - getDbAccession
```
public java.lang.String getDbAccession()
```
    Sequence database accession code.
    
    Returns:
    
    the dbAccession
    
    See Also:
    
    setDbAccession(String)
  - setDbAccession
```
public void setDbAccession(java.lang.String dbAccession)
```
    Sequence database accession code.
    
    Parameters:
    
    dbAccession - the dbAccession
    
    See Also:
    
    getDbAccession()
  - getDbIdCode
```
public java.lang.String getDbIdCode()
```
    Sequence database identification code.
    
    Returns:
    
    the dbIdCode
    
    See Also:
    
    setDbIdCode(String)
  - setDbIdCode
```
public void setDbIdCode(java.lang.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)

Class DBRef

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

DBRef

Method Detail

getId

setId

setParent

getParent

toPDB

toPDB

toString

getIdCode

setIdCode

getChainId

setChainId

getDatabase

setDatabase

getDbAccession

setDbAccession

getDbIdCode

setDbIdCode

getDbSeqBegin

setDbSeqBegin

getDbSeqEnd

setDbSeqEnd

getIdbnsBegin

setIdbnsBegin

getIdbnsEnd

setIdbnsEnd

getInsertBegin

setInsertBegin

getInsertEnd

setInsertEnd

getSeqBegin

setSeqBegin

getSeqEnd

setSeqEnd