Uses of Class
org.proteinshader.structure.enums.VisibilityEnum

Packages that use VisibilityEnum

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.enums	Holds the enums needed by org.proteinshader.structure and its subpackages.
org.proteinshader.structure.io	Holds the classes needed for reading Protein Data Bank structure files.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.
org.proteinshader.structure.visitor.modifiers	Holds helper classes for the ModifierVisitor class, which is used to modify Drawable objects (Atoms, Bonds, and Segments).

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

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

void	VisibilityPanel.applyVisibility(VisibilityEnum visibility, float alpha) Applies the requested visiblity status and alpha value to whatever item or items are currently selected in the RadioPanel.
abstract void	VisibilityPanel.modifyGlobal(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up whatever DrawableModifiers are needed and then calls on the modifyGlobal() method of the radio panel.
void	CartoonVisibilityPanel.modifyGlobal(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up the the SegmentModifier and then calls on modifyGlobal() method of the radio panel.
void	AtomVisibilityPanel.modifyGlobal(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up the the AtomModifier and then calls on modifyGlobal() method of the radio panel.
abstract void	VisibilityPanel.modifyHelices(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up whatever DrawableModifiers are needed and then calls on the modifyHelices() method of the radio panel.
void	CartoonVisibilityPanel.modifyHelices(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up a SegmentModifier and then calls on modifyHelices() method of the radio panel.
void	AtomVisibilityPanel.modifyHelices(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up an AtomModifier and a BondModifier, and then calls on modifyHelices() method of the radio panel.
abstract void	VisibilityPanel.modifyLoops(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up whatever DrawableModifiers are needed and then calls on the modifyLoops() method of the radio panel.
void	CartoonVisibilityPanel.modifyLoops(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up a SegmentModifier and then calls on the modifyLoops() method of the radio panel.
void	AtomVisibilityPanel.modifyLoops(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up an AtomModifier and then calls on modifyLoops() method of the radio panel.
abstract void	VisibilityPanel.modifySelected(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up whatever DrawableModifiers are needed and then calls on the modifySelected() method of the radio panel.
void	CartoonVisibilityPanel.modifySelected(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up the SegmentModifier and then calls on the modifySelected() method of the radio panel.
void	AtomVisibilityPanel.modifySelected(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up the AtomModifier and the BondModifier and then calls on the modifySelected() method of the radio panel.
abstract void	VisibilityPanel.modifyStrands(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up whatever DrawableModifiers are needed and then calls on the modifyStrands() method of the radio panel.
void	CartoonVisibilityPanel.modifyStrands(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up a SegmentModifier and then calls on the modifyStrands() method of the radio panel.
void	AtomVisibilityPanel.modifyStrands(VisibilityEnum visibility, float alpha) This helper method for applyVisibility() sets up an AtomModifier and then calls on modifyStrands() method of the radio panel.

Uses of VisibilityEnum in org.proteinshader.structure

Methods in org.proteinshader.structure that return VisibilityEnum

VisibilityEnum

Drawable.getVisibility() Returns the visibility status of the Drawable object.

Methods in org.proteinshader.structure with parameters of type VisibilityEnum

Atom	AminoAcid.addNewAtom(int serialNo, AtomEnum type, String atomID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new Atom with the type and Atom ID given as arguments, adds the Atom to the Residue's collection of Atoms, and returns a reference to the new Atom.
Atom	Residue.addNewAtom(int serialNo, AtomEnum type, String atomID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new Atom with the type and Atom ID given as arguments, adds the Atom to the Residue's collection of Atoms, and returns a reference to the new Atom.
Atom	Structure.addNewAtom(int atomSerialNo, AtomEnum atomType, String atomID, String aminoAcidType, String residueID, String chainID, String modelID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new atom with the atomID given as an argument, adds the new Atom to the requested Model-Chain-AminoAcid, and then returns a reference to the new Atom.
void	Atom.addNewBond(Atom dstAtom, BondEnum type, VisibilityEnum visibility) Adds a new Bond with this Atom as the source Atom and the Atom given as an argument as the destination Atom.
Atom	Structure.addNewHetAtom(int atomSerialNo, AtomEnum atomType, String atomID, String hetName, String residueID, String chainID, String modelID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility) Creates a new atom with the atomID given as an argument, adds the new Atom to the requested Model-Chain-(Heterogen or Water), and then returns a reference to the new Atom.
void	Drawable.setVisibility(VisibilityEnum visibility) Sets the visibility status of the Drawable object.

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

Atom(int serialNo, AtomEnum type, String atomID, String residueID, String chainID, String modelID, String structureID, double temperature, int charge, double occupancy, String altLocation, double x, double y, double z, VisibilityEnum visibility)
This constructor uses the type argument (an AtomEnum) to set the default radius and CPK color for the Atom.

Bond(Atom srcAtom, Atom dstAtom, BondEnum type, VisibilityEnum visibility)
Constructs a Bond for the source and destination Atoms given as arguments.

Drawable(double x, double y, double z, VisibilityEnum visibility, DrawableEnum drawableType)
Constructor for use by subclasses.

Drawable(double x, double y, double z, VisibilityEnum visibility, DrawableEnum drawableType, float red, float green, float blue, float alpha)
Constructor for use by subclasses.

Uses of VisibilityEnum in org.proteinshader.structure.enums

Methods in org.proteinshader.structure.enums that return VisibilityEnum

static VisibilityEnum	VisibilityEnum.valueOf(String name) Returns the enum constant of this type with the specified name.
static VisibilityEnum[]	VisibilityEnum.values() Returns an array containing the constants of this enum type, in the order they're declared.

Uses of VisibilityEnum in org.proteinshader.structure.io

Fields in org.proteinshader.structure.io declared as VisibilityEnum

static VisibilityEnum	PDBLineParser.ATOM_VISIBILITY The default visibilty for Atoms.
static VisibilityEnum	PDBLineParser.BOND_VISIBILITY The default visibilty for Bonds.

Uses of VisibilityEnum in org.proteinshader.structure.visitor

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

void	BondGeneratorVisitor.setAABondVisibility(VisibilityEnum visibility) Determines what visibility status the Bond generator will use when generating Bonds for AminoAcids.
void	BondGeneratorVisitor.setWaterBondVisibility(VisibilityEnum visibility) Determines what visibility status the Bond generator use when generating Bonds for Waters.

Uses of VisibilityEnum in org.proteinshader.structure.visitor.modifiers

Methods in org.proteinshader.structure.visitor.modifiers with parameters of type VisibilityEnum

void	DrawableModifier.setVisibility(VisibilityEnum visibility) Stores a memory that the visibility status needs to be set to the value given as an argument.