Constructor Summary

Method Summary

• 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()

• 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:

  getChainName()

• 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)