Package org.biojava.nbio.structure

Class DBRef

java.lang.Object
org.biojava.nbio.structure.DBRef
All Implemented Interfaces:
Serializable, 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
See Also:

  • Constructor Summary

    Constructors
    Constructor
    Description
    DBRef()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    String
    getChainName()
    The name 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
    setChainName(String chainName)
    The name 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 Details

  • Method Details

    • getId

      public Long getId()
      Get the ID used by Hibernate.
      Returns:
      the ID used by Hibernate
      See Also:

    • setId

      public void setId(Long id)
      Set the ID used by Hibernate.
      Parameters:
      id - the id assigned by Hibernate
      See Also:

    • setParent

      public void setParent(Structure s)
      Set the structure object that this DBRef relates to.
      Parameters:
      s - a structure object
      See Also:

    • getParent

      public Structure getParent()
      Get the structure object that this DBRef relates to.
      Returns:
      s a structure object
      See Also:

    • 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

      public void setIdCode(String idCode)
      Set the idCode for this entry.
      Parameters:
      idCode - the idCode for this entry
      See Also:

    • getChainName

      public String getChainName()
      The name of the corresponding chain.
      Returns:
      chainName the name of the corresponding chain.

    • setChainName

      public void setChainName(String chainName)
      The name of the corresponding chain.
      Parameters:
      chainName - the name of the corresponding chain
      See Also:

    • 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

      public void setDatabase(String database)
      Specifies the database value.
      Parameters:
      database - the database
      See Also:

    • getDbAccession

      public String getDbAccession()
      Sequence database accession code.
      Returns:
      the dbAccession
      See Also:

    • setDbAccession

      public void setDbAccession(String dbAccession)
      Sequence database accession code.
      Parameters:
      dbAccession - the dbAccession
      See Also:

    • getDbIdCode

      public String getDbIdCode()
      Sequence database identification code.
      Returns:
      the dbIdCode
      See Also:

    • setDbIdCode

      public void setDbIdCode(String dbIdCode)
      Sequence database identification code.
      Parameters:
      dbIdCode - identification code
      See Also:

    • getDbSeqBegin

      public int getDbSeqBegin()
      Initial sequence number of the database seqment.
      Returns:
      position
      See Also:

    • setDbSeqBegin

      public void setDbSeqBegin(int dbSeqBegin)
      Initial sequence number of the database seqment.
      Parameters:
      dbSeqBegin - a sequence position
      See Also:

    • getDbSeqEnd

      public int getDbSeqEnd()
      Ending sequence position of the database segment.
      Returns:
      dbSeqEnd
      See Also:

    • setDbSeqEnd

      public void setDbSeqEnd(int dbSeqEnd)
      The begin of the sequence position in the database
      Parameters:
      dbSeqEnd - sequence position
      See Also:

    • getIdbnsBegin

      public char getIdbnsBegin()
      Insertion code of initial residue of the segment, if PDB is the reference.
      Returns:
      idbnsBegin isnertion code
      See Also:

    • 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:

    • 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

      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:

    • getInsertBegin

      public char getInsertBegin()
      Initial insertion code of the PDB sequence segment.
      Returns:
      insertBegin
      See Also:

    • setInsertBegin

      public void setInsertBegin(char insertBegin)
      Initial insertion code of the PDB sequence segment.
      Parameters:
      insertBegin -
      See Also:

    • getInsertEnd

      public char getInsertEnd()
      Ending insertion code of the PDB sequence segment.
      Returns:
      insertEnd insertion code
      See Also:

    • setInsertEnd

      public void setInsertEnd(char insertEnd)
      Ending insertion code of the PDB sequence segment.
      Parameters:
      insertEnd - insertEnd
      See Also:

    • getSeqBegin

      public int getSeqBegin()
      Initial sequence number of the PDB sequence segment.
      Returns:
      start seq. position
      See Also:

    • setSeqBegin

      public void setSeqBegin(int seqbegin)
      Initial sequence number of the PDB sequence segment.
      Parameters:
      seqbegin - start seq. position
      See Also:

    • getSeqEnd

      public int getSeqEnd()
      Ending sequence number of the PDB sequence segment.
      Returns:
      sequence end position
      See Also:

    • setSeqEnd

      public void setSeqEnd(int seqEnd)
      Ending sequence number of the PDB sequence segment.
      Parameters:
      seqEnd - sequence end position
      See Also: