Package org.biojava.nbio.structure
Class DBRef
- java.lang.Object
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- org.biojava.nbio.structure.DBRef
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- 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:
- Serialized Form
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Constructor Summary
Constructors Constructor Description DBRef()
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Method Summary
All Methods Instance Methods Concrete Methods 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 entrychar
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 databasevoid
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 filesvoid
toPDB(StringBuffer buf)
Append the PDB representation of this DBRef to the provided StringBufferString
toString()
String representation of a DBRef.
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Constructor Detail
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DBRef
public DBRef()
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Method Detail
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getId
public Long getId()
Get the ID used by Hibernate.- Returns:
- the ID used by Hibernate
- See Also:
setId(Long)
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setId
public void setId(Long id)
Set the ID used by Hibernate.- Parameters:
id
- the id assigned by Hibernate- See Also:
getId()
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setParent
public void setParent(Structure s)
Set the structure object that this DBRef relates to.- Parameters:
s
- a structure object- See Also:
getParent()
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getParent
public Structure getParent()
Get the structure object that this DBRef relates to.- Returns:
- s a structure object
- See Also:
setParent(Structure)
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toPDB
public void toPDB(StringBuffer buf)
Append the PDB representation of this DBRef to the provided StringBuffer
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getIdCode
public String getIdCode()
get the idCode for this entry- Returns:
- the idCode
- See Also:
setIdCode(String)
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setIdCode
public void setIdCode(String idCode)
Set the idCode for this entry.- Parameters:
idCode
- the idCode for this entry- See Also:
getIdCode()
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getChainName
public String getChainName()
The name of the corresponding chain.- Returns:
- chainName the name of the corresponding chain.
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setChainName
public void setChainName(String chainName)
The name of the corresponding chain.- Parameters:
chainName
- the name of the corresponding chain- See Also:
getChainName()
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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)
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setDatabase
public void setDatabase(String database)
Specifies the database value.- Parameters:
database
- the database- See Also:
getDatabase()
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getDbAccession
public String getDbAccession()
Sequence database accession code.- Returns:
- the dbAccession
- See Also:
setDbAccession(String)
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setDbAccession
public void setDbAccession(String dbAccession)
Sequence database accession code.- Parameters:
dbAccession
- the dbAccession- See Also:
getDbAccession()
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getDbIdCode
public String getDbIdCode()
Sequence database identification code.- Returns:
- the dbIdCode
- See Also:
setDbIdCode(String)
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setDbIdCode
public void setDbIdCode(String dbIdCode)
Sequence database identification code.- Parameters:
dbIdCode
- identification code- See Also:
getDbIdCode()
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getDbSeqBegin
public int getDbSeqBegin()
Initial sequence number of the database seqment.- Returns:
- position
- See Also:
setDbSeqBegin(int)
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setDbSeqBegin
public void setDbSeqBegin(int dbSeqBegin)
Initial sequence number of the database seqment.- Parameters:
dbSeqBegin
- a sequence position- See Also:
getDbSeqBegin()
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getDbSeqEnd
public int getDbSeqEnd()
Ending sequence position of the database segment.- Returns:
- dbSeqEnd
- See Also:
setDbSeqEnd(int)
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setDbSeqEnd
public void setDbSeqEnd(int dbSeqEnd)
The begin of the sequence position in the database- Parameters:
dbSeqEnd
- sequence position- See Also:
getDbSeqEnd()
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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)
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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()
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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)
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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)
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getInsertBegin
public char getInsertBegin()
Initial insertion code of the PDB sequence segment.- Returns:
- insertBegin
- See Also:
setInsertBegin(char)
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setInsertBegin
public void setInsertBegin(char insertBegin)
Initial insertion code of the PDB sequence segment.- Parameters:
insertBegin
-- See Also:
getInsertBegin()
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getInsertEnd
public char getInsertEnd()
Ending insertion code of the PDB sequence segment.- Returns:
- insertEnd insertion code
- See Also:
setInsertEnd(char)
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setInsertEnd
public void setInsertEnd(char insertEnd)
Ending insertion code of the PDB sequence segment.- Parameters:
insertEnd
- insertEnd- See Also:
getInsertEnd()
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getSeqBegin
public int getSeqBegin()
Initial sequence number of the PDB sequence segment.- Returns:
- start seq. position
- See Also:
setSeqBegin(int)
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setSeqBegin
public void setSeqBegin(int seqbegin)
Initial sequence number of the PDB sequence segment.- Parameters:
seqbegin
- start seq. position- See Also:
getSeqBegin()
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getSeqEnd
public int getSeqEnd()
Ending sequence number of the PDB sequence segment.- Returns:
- sequence end position
- See Also:
getSeqEnd()
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setSeqEnd
public void setSeqEnd(int seqEnd)
Ending sequence number of the PDB sequence segment.- Parameters:
seqEnd
- sequence end position- See Also:
setSeqEnd(int)
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