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java.lang.Objectorg.biojava.bio.structure.DBRef
public class DBRef
A class to represent database cross references. This is just a simple bean that contains the infor from one DBREF line
Constructor Summary | |
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DBRef()
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Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public DBRef()
Method Detail |
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public Long getId()
setId(Long)
public void setId(Long id)
id
- the id assigned by HibernategetId()
public void setParent(Structure s)
s
- a structure objectgetParent()
public Structure getParent()
setParent(Structure)
public String toPDB()
toPDB
in interface PDBRecord
public void toPDB(StringBuffer buf)
toPDB
in interface PDBRecord
buf
- the StringBuffer to write to.public String toString()
toString
in class Object
public String getIdCode()
setIdCode(String)
public void setIdCode(String idCode)
idCode
- the idCode for this entrygetIdCode()
public Character getChainId()
setChainId(Character)
public void setChainId(Character chainId)
chainId
- the ID of the corresponding chaingetChainId()
public String getDatabase()
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
setDatabase(String)
public void setDatabase(String database)
database
- the databasegetDatabase()
public String getDbAccession()
setDbAccession(String)
public void setDbAccession(String dbAccession)
dbAccession
- the dbAccessiongetDbAccession()
public String getDbIdCode()
setDbIdCode(String)
public void setDbIdCode(String dbIdCode)
dbIdCode
- identification codegetDbIdCode()
public int getDbSeqBegin()
setDbSeqBegin(int)
public void setDbSeqBegin(int dbSeqBegin)
dbSeqBegin
- a sequence positiongetDbSeqBegin()
public int getDbSeqEnd()
setDbSeqEnd(int)
public void setDbSeqEnd(int dbSeqEnd)
dbSeqEnd
- sequence positiongetDbSeqEnd()
public char getIdbnsBegin()
setIdbnsBegin(char)
public void setIdbnsBegin(char idbnsBegin)
idbnsBegin
- insertion codegetIdbnsBegin()
public char getIdbnsEnd()
setIdbnsEnd(char)
public void setIdbnsEnd(char idbnsEnd)
idbnsEnd
- the insertion codesetIdbnsEnd(char)
public char getInsertBegin()
setInsertBegin(char)
public void setInsertBegin(char insertBegin)
insertBegin
- getInsertBegin()
public char getInsertEnd()
setInsertEnd(char)
public void setInsertEnd(char insertEnd)
insertEnd
- insertEndgetInsertEnd()
public int getSeqBegin()
setSeqBegin(int)
public void setSeqBegin(int seqbegin)
seqbegin
- start seq. positiongetSeqBegin()
public int getSeqEnd()
getSeqEnd()
public void setSeqEnd(int seqEnd)
seqEnd
- sequence end positionsetSeqEnd(int)
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