Uses of Class
org.proteinshader.structure.Chain

Packages that use Chain

org.proteinshader.gui	Holds all of the Swing GUI components and their associated listeners, including class Renderer, which is registered as a listener for the GLCanvas object that is used a drawing surface.
org.proteinshader.gui.components.controlpanel	Holds the JPanels used in the right-side retractable control panel of the GUI.
org.proteinshader.structure	Holds the classes that store information from a Protein Data Bank file: Structure, Model, Chain, AminoAcid, Heterogen, Water, Atom, Bond, Helix, BetaStrand, Loop, etc.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.

Uses of Chain in org.proteinshader.gui

Methods in org.proteinshader.gui that return Chain

Chain	MediatorImpl.getCurrentChain() Returns the current Chain.
Chain	Mediator.getCurrentChain() Returns the current Chain.

Methods in org.proteinshader.gui with parameters of type Chain

void	MediatorImpl.setCurrentChain(Chain chain) Sets the current Chain.
void	Mediator.setCurrentChain(Chain chain) Sets the current Chain.

Uses of Chain in org.proteinshader.gui.components.controlpanel

Methods in org.proteinshader.gui.components.controlpanel that return Chain

Chain

SelectorPanel.getSelectedChain() Returns the currently selected Chain from the Chain menu.

Methods in org.proteinshader.gui.components.controlpanel with parameters of type Chain

void	SelectorPanel.setResidueList(Chain chain) Checks the currently selected Residue type (AminoAcids, Heterogens, or Waters) and copies them from the Chain to the Residue list.

Uses of Chain in org.proteinshader.structure

Methods in org.proteinshader.structure that return Chain

Chain	Model.addNewChain(String chainID) Creates a new Chain with the chainID given as an argument, adds the Chain to the Model's collection of Chains, and returns a reference to the new Chain.
Chain	Model.getChain(String chainID) Returns the Chain with the chainID given as an argument.
Chain	Structure.getChain(String chainID, String modelID) Returns the Chain with the IDs given as arguments.

Methods in org.proteinshader.structure that return types with arguments of type Chain

Iterator<Chain>

Model.iteratorChains() Returns an Iterator for the Chains held by this Model.

Constructors in org.proteinshader.structure with parameters of type Chain

BetaStrand(String betaStrandID, String betaStrandNumber, String sheetID, String startResidueID, String endResidueID, Chain chain, int sense, int strandsInSheet)
Constructs a BetaStrand.

Helix(String helixID, String serialNo, String startResidueID, String endResidueID, Chain chain, HelixEnum type, HelixShapeEnum shape)
Constructs a Helix.

Loop(String loopID, String startResidueID, String endResidueID, Chain chain)
Constructs a Loop.

Region(String startResidueID, String endResidueID, Chain chain)
Constructor for use by subclasses.

Uses of Chain in org.proteinshader.structure.visitor

Methods in org.proteinshader.structure.visitor with parameters of type Chain

void	Visitor.visit(Chain chain) Uses the current ResidueMode to determine if it should traverse the AminoAcids, Heterogens, and/or Waters owned by the Chain.
void	SFWriterVisitor.visit(Chain chain) Writes all information held by a Chain.
void	FrenetFrameGeneratorVisitor.visit(Chain chain) All AminoAcids of the Chain will be visited.
void	LoopGeneratorVisitor.visit(Chain chain) Generates Loop objects from AminoAcids that do not already belong to any Region.
void	BondGeneratorVisitor.visit(Chain chain) Generates all standard Bonds (AminoAcids and Waters) for the Chain.