org.jmol.shapebio
Class BioShapeCollection

java.lang.Object
  org.jmol.shape.Shape
      org.jmol.shapebio.BioShapeCollection

Direct Known Subclasses:

Backbone, Ribbons, Rockets, Strands, Trace

public abstract class BioShapeCollection
extends Shape

Mps stands for Model-Polymer-Shape When a Cartoon is instantiated with a call to setSize(), it creates an MpsShape for each BioPolymer in the model set. It is these shapes that are the real "shapes". Unlike other shapes, which are indexed by atom and throughout the entire model set, these shapes are indexed by residue and are restricted to a given BioPolymer within a given Model. Model

Field Summary

(package private) Atom[]	atoms
(package private) BioShape[]	bioShapes
(package private) boolean	isActive
(package private) short	madDnaRna
(package private) short	madHelixSheet
(package private) short	madOn
(package private) short	madTurnRandom

Fields inherited from class org.jmol.shape.Shape

g3d, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer, xmlProperties

Constructor Summary

BioShapeCollection()

Method Summary

void	findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest, BitSet bsNot)
(package private) BioShape	getBioShape(int i)
(package private) int	getMpsShapeCount()
String	getShapeState()
int	getSize(Group group)
(package private) void	initialize()
void	initModelSet()
void	setModelClickability()
void	setProperty(String propertyName, Object value, BitSet bsSelected) may come from any source -- executed AFTER a shape's own setProperty method
void	setShapeSize(int size, RadiusData rd, BitSet bsSelected)
void	setVisibilityFlags(BitSet bs)

Methods inherited from class org.jmol.shape.Shape

appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, getColix, getColorCommand, getColorCommand, getFontCommand, getIndexFromName, getProperty, getProperty, getShapeCommands, getShapeCommands, getShapeDetail, getSize, getTranslucentLabel, getViewer, initializeShape, initShape, merge, setColix, setColix, setColix, setModelSet, setShapeProperty, setSize, setSize, setStateInfo, setStateInfo, wasClicked

Methods inherited from class java.lang.Object

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

Field Detail

atoms

Atom[] atoms

madOn

short madOn

madHelixSheet

short madHelixSheet

madTurnRandom

short madTurnRandom

madDnaRna

short madDnaRna

isActive

boolean isActive

bioShapes

BioShape[] bioShapes

Constructor Detail

BioShapeCollection

public BioShapeCollection()

Method Detail

initModelSet

public final void initModelSet()

Overrides:

initModelSet in class Shape

getSize

public int getSize(Group group)

Overrides:

getSize in class Shape

Returns:

size

setShapeSize

public void setShapeSize(int size,
                         RadiusData rd,
                         BitSet bsSelected)

Overrides:

setShapeSize in class Shape

setProperty

public void setProperty(String propertyName,
                        Object value,
                        BitSet bsSelected)

Description copied from class: Shape

may come from any source -- executed AFTER a shape's own setProperty method

Overrides:

setProperty in class Shape

getShapeState

public String getShapeState()

Overrides:

getShapeState in class Shape

initialize

void initialize()

findNearestAtomIndex

public void findNearestAtomIndex(int xMouse,
                                 int yMouse,
                                 Atom[] closest,
                                 BitSet bsNot)

Overrides:

findNearestAtomIndex in class Shape

setVisibilityFlags

public void setVisibilityFlags(BitSet bs)

Overrides:

setVisibilityFlags in class Shape

setModelClickability

public void setModelClickability()

Overrides:

setModelClickability in class Shape

getMpsShapeCount

int getMpsShapeCount()

getBioShape

BioShape getBioShape(int i)