org.biojava.nbio.structure

Class PassthroughIdentifier

java.lang.Object

org.biojava.nbio.structure.PassthroughIdentifier

All Implemented Interfaces:

Serializable, StructureIdentifier

public class PassthroughIdentifier
extends Object
implements StructureIdentifier

A stub StructureIdentifier, representing the full structure in all cases.

Author:

Spencer Bliven

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PassthroughIdentifier(String identifier)

Method Summary

Modifier and Type	Method and Description
String	getIdentifier() Get the String form of this identifier.
Structure	loadStructure(AtomCache cache) Passthrough identifiers don't know how to load a structure
Structure	reduce(Structure input) Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
SubstructureIdentifier	toCanonical() Convert to a canonical SubstructureIdentifier.

Methods inherited from class java.lang.Object

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

Constructor Detail

PassthroughIdentifier

public PassthroughIdentifier(String identifier)

Method Detail

getIdentifier

public String getIdentifier()

Description copied from interface: StructureIdentifier

Get the String form of this identifier. It is recommended that the #toString() method also return the identifier, for consistency during serialization.

Specified by:

getIdentifier in interface StructureIdentifier

Returns:

The String form of this identifier

toCanonical

public SubstructureIdentifier toCanonical()

Description copied from interface: StructureIdentifier

Convert to a canonical SubstructureIdentifier.

This allows all domains to be converted to a standard format String.

Specified by:

toCanonical in interface StructureIdentifier

Returns:

A SubstructureIdentifier without ranges (e.g. including all residues)

reduce

public Structure reduce(Structure input)
                 throws StructureException

Description copied from interface: StructureIdentifier

Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.

Specified by:

reduce in interface StructureIdentifier

Parameters:

input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.

Returns:

Throws:

StructureException

See Also:

StructureTools.getReducedStructure(Structure, String)

loadStructure

public Structure loadStructure(AtomCache cache)
                        throws StructureException,
                               IOException

Passthrough identifiers don't know how to load a structure

Specified by:

loadStructure in interface StructureIdentifier

Returns:

null

Throws:

StructureException - For errors loading and parsing the structure

IOException - Errors reading the structure from disk