Package org.rcsb.cif.model.generated

Class StructRefSeq

java.lang.Object

org.rcsb.cif.model.BaseCategory

org.rcsb.cif.model.generated.StructRefSeq

All Implemented Interfaces:

Category

@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class StructRefSeq
extends BaseCategory

Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry.

Field Summary

Fields inherited from class org.rcsb.cif.model.BaseCategory

isText, textFields

Constructor Summary

Constructors

Constructor	Description
StructRefSeq(String name)
StructRefSeq(String name, int rowCount, Object[] encodedColumns)
StructRefSeq(String name, Map<String,Column> columns)

Method Summary

Modifier and Type	Method	Description
StrColumn	getAlignId()	The value of _struct_ref_seq.align_id must uniquely identify a record in the STRUCT_REF_SEQ list.
IntColumn	getDbAlignBeg()	The sequence position in the referenced database entry at which the alignment begins.
IntColumn	getDbAlignEnd()	The sequence position in the referenced database entry at which the alignment ends.
StrColumn	getDetails()	A description of special aspects of the sequence alignment.
StrColumn	getPdbxAuthSeqAlignBeg()	Initial position in the PDB sequence segment.
StrColumn	getPdbxAuthSeqAlignEnd()	Ending position in the PDB sequence segment
StrColumn	getPdbxDbAccession()	Accession code of the reference database.
StrColumn	getPdbxDbAlignBegInsCode()	Initial insertion code of the sequence segment of the reference database.
StrColumn	getPdbxDbAlignEndInsCode()	Ending insertion code of the sequence segment of the reference database.
StrColumn	getPdbxPDBIdCode()	The PDB code of the structure.
StrColumn	getPdbxSeqAlignBegInsCode()	Initial insertion code of the PDB sequence segment.
StrColumn	getPdbxSeqAlignEndInsCode()	Ending insertion code of the sequence segment
StrColumn	getPdbxStrandId()	The PDB strand/chain ID .
StrColumn	getRefId()	This data item is a pointer to _struct_ref.id in the STRUCT_REF category.
IntColumn	getSeqAlignBeg()	The sequence position in the entity or biological unit described in the data block at which the alignment begins.
IntColumn	getSeqAlignEnd()	The sequence position in the entity or biological unit described in the data block at which the alignment ends.

Methods inherited from class org.rcsb.cif.model.BaseCategory

getBinaryColumn, getCategoryName, getColumn, getColumnNames, getRowCount, isDefined

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.rcsb.cif.model.Category

columnNames, columns, get

Constructor Detail

StructRefSeq

public StructRefSeq(String name,
                    Map<String,Column> columns)

StructRefSeq

public StructRefSeq(String name,
                    int rowCount,
                    Object[] encodedColumns)

StructRefSeq

public StructRefSeq(String name)

Method Detail

getAlignId

public StrColumn getAlignId()

The value of _struct_ref_seq.align_id must uniquely identify a record in the STRUCT_REF_SEQ list. Note that this item need not be a number; it can be any unique identifier.

Returns:

StrColumn

getDbAlignBeg

public IntColumn getDbAlignBeg()

The sequence position in the referenced database entry at which the alignment begins.

Returns:

IntColumn

getDbAlignEnd

public IntColumn getDbAlignEnd()

The sequence position in the referenced database entry at which the alignment ends.

Returns:

IntColumn

getDetails

public StrColumn getDetails()

A description of special aspects of the sequence alignment.

Returns:

StrColumn

getRefId

public StrColumn getRefId()

This data item is a pointer to _struct_ref.id in the STRUCT_REF category.

Returns:

StrColumn

getSeqAlignBeg

public IntColumn getSeqAlignBeg()

The sequence position in the entity or biological unit described in the data block at which the alignment begins. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.

Returns:

IntColumn

getSeqAlignEnd

public IntColumn getSeqAlignEnd()

The sequence position in the entity or biological unit described in the data block at which the alignment ends. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.

Returns:

IntColumn

getPdbxStrandId

public StrColumn getPdbxStrandId()

The PDB strand/chain ID .

Returns:

StrColumn

getPdbxDbAccession

public StrColumn getPdbxDbAccession()

Accession code of the reference database.

Returns:

StrColumn

getPdbxDbAlignBegInsCode

public StrColumn getPdbxDbAlignBegInsCode()

Initial insertion code of the sequence segment of the reference database.

Returns:

StrColumn

getPdbxDbAlignEndInsCode

public StrColumn getPdbxDbAlignEndInsCode()

Ending insertion code of the sequence segment of the reference database.

Returns:

StrColumn

getPdbxPDBIdCode

public StrColumn getPdbxPDBIdCode()

The PDB code of the structure.

Returns:

StrColumn

getPdbxAuthSeqAlignBeg

public StrColumn getPdbxAuthSeqAlignBeg()

Initial position in the PDB sequence segment.

Returns:

StrColumn

getPdbxAuthSeqAlignEnd

public StrColumn getPdbxAuthSeqAlignEnd()

Ending position in the PDB sequence segment

Returns:

StrColumn

getPdbxSeqAlignBegInsCode

public StrColumn getPdbxSeqAlignBegInsCode()

Initial insertion code of the PDB sequence segment.

Returns:

StrColumn

getPdbxSeqAlignEndInsCode

public StrColumn getPdbxSeqAlignEndInsCode()

Ending insertion code of the sequence segment

Returns:

StrColumn