Package org.rcsb.strucmotif.domain.query

Class QueryBuilder

java.lang.Object

org.rcsb.strucmotif.domain.query.QueryBuilder

@Service
public class QueryBuilder
extends Object

The entry point to create MotifSearchQuery instances.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	QueryBuilder.MandatoryBuilder	Parameters are considered mandatory arguments (in the sense that some value has to be given - nonetheless, default values will be used).
class	QueryBuilder.OptionalStepBuilder	Optional parameters of the algorithm.

Constructor Summary

Constructors

Constructor	Description
QueryBuilder(StructureDataProvider structureDataProvider, KruskalMotifPruner kruskalMotifPruner, NoOperationMotifPruner noOperationMotifPruner, MotifSearchRuntime motifSearchRuntime, MotifSearchConfig motifSearchConfig)	Construct a new query builder.

Method Summary

Modifier and Type	Method	Description
QueryBuilder.MandatoryBuilder	defineByFile(InputStream inputStream)	Routine if stream of structure data contains extracted motif.
QueryBuilder.MandatoryBuilder	defineByFileAndSelection(InputStream inputStream, List<LabelSelection> selection)	Define a motif based on a stream of structure data and a selection of components.
QueryBuilder.MandatoryBuilder	defineByPdbIdAndSelection(String structureIdentifier, List<LabelSelection> selection)	Define a motif based on the id of the reference structure and a selection of components.
QueryBuilder.MandatoryBuilder	defineByStructureAndSelection(Structure structure, List<LabelSelection> labelSelections)	Routine if structure files contains extracted motif.

Methods inherited from class java.lang.Object

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

Constructor Details

QueryBuilder

@Autowired
public QueryBuilder(StructureDataProvider structureDataProvider,
 KruskalMotifPruner kruskalMotifPruner,
 NoOperationMotifPruner noOperationMotifPruner,
 MotifSearchRuntime motifSearchRuntime,
 MotifSearchConfig motifSearchConfig)

Construct a new query builder.

Parameters:

structureDataProvider - injectable structure provider

kruskalMotifPruner - injectable motif pruner

noOperationMotifPruner - injectable nop motif pruner

motifSearchRuntime - injectable runtime

motifSearchConfig - injectable config

Method Details

defineByPdbIdAndSelection

public QueryBuilder.MandatoryBuilder defineByPdbIdAndSelection(String structureIdentifier,
 List<LabelSelection> selection)

Define a motif based on the id of the reference structure and a selection of components.

Parameters:

structureIdentifier - the id to acquire

selection - which components to select to define the motif

Returns:

mandatory parameter step

Throws:

IllegalQueryDefinitionException - if chains/residues aren't found or if distance constraints are violated

defineByFileAndSelection

public QueryBuilder.MandatoryBuilder defineByFileAndSelection(InputStream inputStream,
 List<LabelSelection> selection)

Define a motif based on a stream of structure data and a selection of components.

Parameters:

inputStream - the data to read

selection - which components to select to define the motif

Returns:

mandatory parameter step

Throws:

IllegalQueryDefinitionException - if chains/residues aren't found or if distance constraints are violated

defineByStructureAndSelection

public QueryBuilder.MandatoryBuilder defineByStructureAndSelection(Structure structure,
 List<LabelSelection> labelSelections)

Routine if structure files contains extracted motif. Checks that the structure contains a reasonable number of components to rule out erroneous arguments.

Parameters:

structure - the file to ready - all components are considered the motif

labelSelections - the residues of interest

Returns:

mandatory parameter step

Throws:

IllegalQueryDefinitionException - if chains/residues aren't found or if distance constraints are violated

defineByFile

public QueryBuilder.MandatoryBuilder defineByFile(InputStream inputStream)

Routine if stream of structure data contains extracted motif.

Parameters:

inputStream - the data to ready - all components are considered the motif

Returns:

mandatory parameter step