Package edu.sdsc.mbt.viewables

This package provides classes which enable molecular biology data to be represented as visible/renderable viewable objects, plus, this package defines a top-level StructureDocument object to encapsulate the complete state of these objects and properties.

See:
Description

Interface Summary

AtomColor	This interface defines how all AtomColor implementation classes should generate a color for a given atomIndex+Atom.
AtomLabel	This interface defines how all AtomLabel implementation classes should generate a String label for a given Atom.
AtomRadius	This interface defines how all AtomRadius implementation classes should generate a radius for a given atomIndex+Atom.
BondColor	This interface defines how all BondColor implementation classes should fill in a color for a given atomIndex+Atom.
BondForm	This interface defines how all BondForm implementation classes should fill in a form for a given bondIndex.
BondLabel	This interface defines how all BondLabel implementation classes should generate a String label for a given Bond.
BondRadius	This interface defines how all BondRadius implementation classes should provide a radius for a given Bond.
ChainColor	This interface defines how all ChainColor implementation classes should generate a color for a given Chain.
ColorMap	This interface defines how all ColorMap implementation classes should generate a color for a given normalized float (0.0-1.0).
FragmentColor	This interface defines how all FragmentColor implementation classes should generate a color for a given Fragment.
FragmentForm	This interface defines how all FragmentForm implementation classes should generate a style for a given Fragment.
ResidueColor	This interface defines how all ResidueColor implementation classes should generate a color for a given Residue.
RibbonColor	This interface defines how all ResidueColor implementation classes should generate a color for a given Residue.
StructureStylesEventListener	Properties, data, or the organizational structure of data changed.

Class Summary

AtomColorByCharge
AtomColorByElement	This class implements the AtomColor interface by applying a color to the given atomIndex+Atom by using the ElementColor class.
AtomColorFactory
AtomColorRegistry	A class used to register AtomColor implementation objects.
AtomColorUniform
AtomLabelByAtomCompound	This class implements the AtomLabel interface by producing a string label from the Atom record's compound.
AtomLabelByAtomElement	This class implements the AtomLabel interface by producing a string label from the Atom record's element.
AtomLabelByAtomName	This class implements the AtomLabel interface by producing a string label from the Atom record's name.
AtomLabelByChainId	This class implements the AtomLabel interface by producing a string label from the Atom record's chain_id.
AtomLabelNone	This class implements the AtomLabel interface by producing a null string label.
AtomLabelRegistry	A class used to register AtomLabel implementation objects.
AtomRadiusByConstant	This class implements the AtomRadius interface by applying a radius to the given an Atom by using the radius of the bond.
AtomRadiusByCpk	This class implements the AtomRadius interface by applying a radius to the given an Atom by using the ElementRadius class.
AtomRadiusByScaledCpk	This class implements the AtomRadius interface by applying a radius to the given an Atom by using the ElementRadius class.
AtomRadiusRegistry	A class used to register AtomRadius implementation objects.
BondColorByAtomColor	This class implements the BondColor interface by applying a color to the given Bond by using the Atom colors.
BondColorByElement	This class implements the BondColor interface by applying a color to the given bondIndex+Bond by using the ElementColor class.
BondColorRegistry	A class used to register BondColor implementation objects.
BondFormOrder	Implements the BondForm interface as a "Order" bond type.
BondFormRegistry	A class used to register BondForm implementation objects.
BondFormSimple	Implements the BondForm interface as a "Simple" bond type.
BondFormSplit	Implements the BondForm interface as a "Split" bond type.
BondLabelByDistance	This class implements the BondLabel interface by producing a string label based upon the Bond atom's distance..
BondLabelNone	This class implements the BondLabel interface by producing a null string label.
BondLabelRegistry	A class used to register BondLabel implementation objects.
BondRadiusAsStick	This class implements the BondRadius interface by applying a fixed radius representing the width IN PIXELS of the wireframe bond.
BondRadiusAsWire	This class implements the BondRadius interface by applying a fixed radius representing the width IN PIXELS of the wireframe bond.
BondRadiusByAtomRadius	This class implements the BondRadius interface by applying a radius to the given Bond by using the AtomRadius class.
BondRadiusByScaledAtomRadius	This class implements the BondRadius interface by applying a radius to the given Bond by using the AtomRadius class.
BondRadiusRegistry	A class used to register BondRadius implementation objects.
ChainColorById	This class implements the ChainColor interface by applying a color to the given Chain by using its chainId.
ChainColorRegistry	A class used to register ChainColor implementation objects.
ConservationColorMap	This class implements the ColorMap interface by generating a linear interpolated color from a list of user-defined color knots.
ElementPreferences	This class encapsulates element color settings and is used to provide persistence to user settings by saving current colors to filesystem storage and reading them when loading the application and opening the element editing dialog.
FragmentColorByType	This class implements the FragmentColor interface by applying a color to the given Fragment by using its Conformation type.
FragmentColorRegistry	A class used to register FragmentColor implementation objects.
FragmentFormCartoon	This class implements the FragmentForm interface by applying a secondary structure cartoon style.
FragmentFormCylinder	This class implements the FragmentForm interface by applying a cylinder style.
FragmentFormLadder	This class implements the FragmentForm interface by applying a secondary structure ladder style.
FragmentFormRegistry	A class used to register FragmentForm implementation objects.
FragmentFormRibbon	This class implements the FragmentForm interface by applying a ribbon style.
FragmentFormTube	This class implements the FragmentForm interface by applying a tube style.
FragmentFormWireframe	This class implements the FragmentForm interface by applying a wireframe style.
InterpolatedColorMap	This class implements the ColorMap interface by generating a linear interpolated color from a list of user-defined color knots.
ResidueAnnotation
ResidueColorByCharge	This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.
ResidueColorByElement	This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.
ResidueColorByHydrophobicity	This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.
ResidueColorByType	This class implements the ResidueColor interface by applying a color to the given Residue by its nature (a color scheme similar to that used by BioEdit).
ResidueColorDefault	This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.
ResidueColorFactory	This class implements a dispatcher keeping track of the currently available ResidueColors.
ResidueColorRegistry	A class used to register ResidueColor implementation objects.
ResidueColorScaled	This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.
ResidueColorUniform	This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.
RibbonColorDefault	This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.
RibbonColorFactory	This class implements a dispatcher keeping track of the currently available ResidueColors.
RibbonColorUniform	This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.
StructureDocument	This class implements the top-level container document for one or more Structure objects.
StructureDocumentEvent	An event generated when structural changes are made to a StructureDocument.
StructureStyles	Stores and retrieves styles associated with viewable objects of a Structure (typically one StructureStyle object is assocated with each Structure by a StructureDocument class).
StructureStylesEvent	An event generated when changes are made to a StructureStyles object.
StylesPreferences	This class is a storage and manipulation utility to handle viewing options set through PreferencesDialog.

Package edu.sdsc.mbt.viewables Description

This package provides classes which enable molecular biology data to be represented as visible/renderable viewable objects, plus, this package defines a top-level StructureDocument object to encapsulate the complete state of these objects and properties.

Each Viewable object represents a visible/renderable encapsulation of some subset of StructureComponent objects from a Structure, plus its viewer-independant visual attributes (eg: color, size, etc).