de.bioforscher.singa.structure.model.oak

Class OakModel

java.lang.Object

de.bioforscher.singa.structure.model.oak.OakModel

All Implemented Interfaces:

AtomContainer, ChainContainer, LeafSubstructureContainer, Model

public class OakModel
extends Object
implements Model

Author:

cl

Constructor Summary

Constructors

Constructor and Description
OakModel(int identifier) Creates a new BranchSubstructure.
OakModel(OakModel model)

Method Summary

Modifier and Type	Method and Description
void	addChain(OakChain chain)
boolean	equals(Object o)
Set<String>	getAllChainIdentifiers() Returns A set of all chin identifiers referenced in th model.
List<Chain>	getAllChains() Returns all Chains.
List<LeafSubstructure<?>>	getAllLeafSubstructures() Returns all LeafSubstructures.
Optional<Atom>	getAtom(Integer atomIdentifier) Returns an Optional of the Atom with the given identifier.
Optional<Chain>	getChain(String chainIdentifier) Returns an Optional of the Chain with the given identifier.
OakModel	getCopy() Returns a copy of this model.
Chain	getFirstChain() Returns the first Chain.
LeafSubstructure<?>	getFirstLeafSubstructure()
Optional<LeafSubstructure<?>>	getLeafSubstructure(LeafIdentifier leafIdentifier) Returns an Optional of the LeafSubstructure with the given identifier.
Integer	getModelIdentifier() Returns the model identifier, an integer greater or equal to 1.
int	hashCode()
void	removeAtom(Integer atomIdentifier) Removes an atom from this container.
void	removeChain(String chainIdentifier) Removes a Chain with the given identifier from the structure.
boolean	removeLeafSubstructure(LeafIdentifier leafIdentifier) Removes a LeafSubstructure from this container.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface de.bioforscher.singa.structure.model.interfaces.Model

flatToString

Methods inherited from interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer

getAllAminoAcids, getAllAtoms, getAllLigands, getAllNucleotides, getAminoAcid, getAtom, getLigand, getNucleotide, getNumberOfLeafSubstructures, removeLeafSubstructure, removeLeafSubstructuresNotRelevantFor

Constructor Detail

OakModel

public OakModel(int identifier)

Creates a new BranchSubstructure. The identifier is considered in the superordinate BranchSubstructure.

Parameters:

identifier - The identifier of this BranchSubstructure.

OakModel

public OakModel(OakModel model)

Method Detail

getModelIdentifier

public Integer getModelIdentifier()

Description copied from interface: Model

Returns the model identifier, an integer greater or equal to 1.

Specified by:

getModelIdentifier in interface Model

Returns:

The model identifier.

getFirstChain

public Chain getFirstChain()

Description copied from interface: ChainContainer

Returns the first Chain.

Specified by:

getFirstChain in interface ChainContainer

Returns:

The first Chain.

getAllChains

public List<Chain> getAllChains()

Description copied from interface: ChainContainer

Returns all Chains.

Specified by:

getAllChains in interface ChainContainer

Returns:

All Chains.

getAllChainIdentifiers

public Set<String> getAllChainIdentifiers()

Description copied from interface: Model

Returns A set of all chin identifiers referenced in th model.

Specified by:

getAllChainIdentifiers in interface Model

Returns:

A set of all chin identifiers referenced in th model.

getChain

public Optional<Chain> getChain(String chainIdentifier)

Description copied from interface: Model

Returns an Optional of the Chain with the given identifier. If no chain with the identifier could be found, an empty optional is returned.

Specified by:

getChain in interface Model

Parameters:

chainIdentifier - The identifier of the chain.

Returns:

An Optional encapsulating the Chain.

addChain

public void addChain(OakChain chain)

removeChain

public void removeChain(String chainIdentifier)

Description copied from interface: Model

Removes a Chain with the given identifier from the structure.

Specified by:

removeChain in interface Model

Parameters:

chainIdentifier - The identifier of the chain.

getAllLeafSubstructures

public List<LeafSubstructure<?>> getAllLeafSubstructures()

Description copied from interface: LeafSubstructureContainer

Returns all LeafSubstructures.

Specified by:

getAllLeafSubstructures in interface LeafSubstructureContainer

Returns:

All LeafSubstructures.

getLeafSubstructure

public Optional<LeafSubstructure<?>> getLeafSubstructure(LeafIdentifier leafIdentifier)

Description copied from interface: LeafSubstructureContainer

Returns an Optional of the LeafSubstructure with the given identifier. If no LeafSubstructure with the identifier could be found, an empty optional is returned.

Specified by:

getLeafSubstructure in interface LeafSubstructureContainer

Parameters:

leafIdentifier - The identifier of the leaf.

Returns:

An Optional encapsulating the LeafSubstructure.

getFirstLeafSubstructure

public LeafSubstructure<?> getFirstLeafSubstructure()

Specified by:

getFirstLeafSubstructure in interface LeafSubstructureContainer

removeLeafSubstructure

public boolean removeLeafSubstructure(LeafIdentifier leafIdentifier)

Description copied from interface: LeafSubstructureContainer

Removes a LeafSubstructure from this container.

Specified by:

removeLeafSubstructure in interface LeafSubstructureContainer

Parameters:

leafIdentifier - The identifier of the leaf.

Returns:

True if the LeafSubstructure was removed.

getAtom

public Optional<Atom> getAtom(Integer atomIdentifier)

Description copied from interface: AtomContainer

Returns an Optional of the Atom with the given identifier. If no Atom with the identifier could be found, an empty optional is returned.

Specified by:

getAtom in interface AtomContainer

Parameters:

atomIdentifier - The identifier of the atom.

Returns:

An Optional encapsulating the Atom.

removeAtom

public void removeAtom(Integer atomIdentifier)

Description copied from interface: AtomContainer

Removes an atom from this container.

Specified by:

removeAtom in interface AtomContainer

Parameters:

atomIdentifier - The identifier of the atom to be removed.

getCopy

public OakModel getCopy()

Description copied from interface: Model

Returns a copy of this model.

Specified by:

getCopy in interface LeafSubstructureContainer

Specified by:

getCopy in interface Model

Returns:

A copy of this model.

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object