org.rcsb.cif.schema.mm.StructRef Maven / Gradle / Ivy
package org.rcsb.cif.schema.mm;
import org.rcsb.cif.model.*;
import org.rcsb.cif.schema.*;
import javax.annotation.Generated;
/**
* Data items in the STRUCT_REF category allow the author of a
* data block to relate the entities or biological units
* described in the data block to information archived in external
* databases.
*
* For references to the sequence of a polymer, the value of
* the data item _struct_ref.seq_align is used to indicate
* whether the correspondence between the sequence of the entity
* or biological unit in the data block and the sequence in the
* referenced database entry is 'complete' or 'partial'. If
* this value is 'partial', the region (or regions) of the
* alignment may be delimited using data items in the
* STRUCT_REF_SEQ category.
*
* Similarly, the value of _struct_ref.seq_dif is used to indicate
* whether the two sequences contain point differences. If the
* value is 'yes', the differences may be identified and annotated
* using data items in the STRUCT_REF_SEQ_DIF category.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class StructRef extends DelegatingCategory {
public StructRef(Category delegate) {
super(delegate);
}
@Override
protected Column createDelegate(String columnName, Column column) {
switch (columnName) {
case "biol_id":
return getBiolId();
case "db_code":
return getDbCode();
case "db_name":
return getDbName();
case "details":
return getDetails();
case "entity_id":
return getEntityId();
case "id":
return getId();
case "seq_align":
return getSeqAlign();
case "seq_dif":
return getSeqDif();
case "pdbx_db_accession":
return getPdbxDbAccession();
case "pdbx_db_isoform":
return getPdbxDbIsoform();
case "pdbx_seq_one_letter_code":
return getPdbxSeqOneLetterCode();
case "pdbx_align_begin":
return getPdbxAlignBegin();
case "pdbx_align_end":
return getPdbxAlignEnd();
default:
return new DelegatingColumn(column);
}
}
/**
* This data item is a pointer to _struct_biol.id in the
* STRUCT_BIOL category.
* @return StrColumn
*/
public StrColumn getBiolId() {
return delegate.getColumn("biol_id", DelegatingStrColumn::new);
}
/**
* The code for this entity or biological unit or for a closely
* related entity or biological unit in the named database.
* @return StrColumn
*/
public StrColumn getDbCode() {
return delegate.getColumn("db_code", DelegatingStrColumn::new);
}
/**
* The name of the database containing reference information about
* this entity or biological unit.
* @return StrColumn
*/
public StrColumn getDbName() {
return delegate.getColumn("db_name", DelegatingStrColumn::new);
}
/**
* A description of special aspects of the relationship between
* the entity or biological unit described in the data block and
* that in the referenced database entry.
* @return StrColumn
*/
public StrColumn getDetails() {
return delegate.getColumn("details", DelegatingStrColumn::new);
}
/**
* This data item is a pointer to _entity.id in the ENTITY category.
* @return StrColumn
*/
public StrColumn getEntityId() {
return delegate.getColumn("entity_id", DelegatingStrColumn::new);
}
/**
* The value of _struct_ref.id must uniquely identify a record
* in the STRUCT_REF list.
*
* Note that this item need not be a number; it can be any unique
* identifier.
* @return StrColumn
*/
public StrColumn getId() {
return delegate.getColumn("id", DelegatingStrColumn::new);
}
/**
* A flag to indicate the scope of the alignment between the
* sequence of the entity or biological unit described in the data
* block and that in the referenced database entry. 'entire'
* indicates that alignment spans the entire length of both
* sequences (although point differences may occur and can be
* annotated using the data items in the STRUCT_REF_SEQ_DIF
* category). 'partial' indicates a partial alignment. The region
* (or regions) of the alignment may be delimited using data items
* in the STRUCT_REF_SEQ category. This data item may also take
* the value '.', indicating that the reference is not to a
* sequence.
* @return StrColumn
*/
public StrColumn getSeqAlign() {
return delegate.getColumn("seq_align", DelegatingStrColumn::new);
}
/**
* A flag to indicate the presence ('yes') or absence ('no') of
* point differences between the sequence of the entity or
* biological unit described in the data block and that in
* the referenced database entry. This data item may also
* take the value '.', indicating that the reference is not to a
* sequence.
* @return StrColumn
*/
public StrColumn getSeqDif() {
return delegate.getColumn("seq_dif", DelegatingStrColumn::new);
}
/**
* Accession code assigned by the reference database.
* @return StrColumn
*/
public StrColumn getPdbxDbAccession() {
return delegate.getColumn("pdbx_db_accession", DelegatingStrColumn::new);
}
/**
* Database code assigned by the reference database for a sequence isoform. An isoform sequence is an
* alternative protein sequence that can be generated from the same gene by a single or by a combination of
* biological events such as: alternative promoter usage, alternative splicing, alternative initiation
* and ribosomal frameshifting.
* @return StrColumn
*/
public StrColumn getPdbxDbIsoform() {
return delegate.getColumn("pdbx_db_isoform", DelegatingStrColumn::new);
}
/**
* Database chemical sequence expressed as string of one-letter
* amino acid codes.
* @return StrColumn
*/
public StrColumn getPdbxSeqOneLetterCode() {
return delegate.getColumn("pdbx_seq_one_letter_code", DelegatingStrColumn::new);
}
/**
* Beginning index in the chemical sequence from the
* reference database.
* @return StrColumn
*/
public StrColumn getPdbxAlignBegin() {
return delegate.getColumn("pdbx_align_begin", DelegatingStrColumn::new);
}
/**
* Ending index in the chemical sequence from the
* reference database.
* @return StrColumn
*/
public StrColumn getPdbxAlignEnd() {
return delegate.getColumn("pdbx_align_end", DelegatingStrColumn::new);
}
}