org.jmol.shapebio
Class BioShapeCollection

java.lang.Object
  extended by org.jmol.shape.Shape
      extended by 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, java.util.BitSet bsNot)
           
(package private)  BioShape getBioShape(int i)
           
(package private)  int getMpsShapeCount()
           
 java.lang.String getShapeState()
           
 int getSize(Group group)
           
(package private)  void initialize()
           
 void initModelSet()
           
 void setModelClickability()
           
 void setProperty(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bsSelected)
          may come from any source -- executed AFTER a shape's own setProperty method
 void setShapeSize(int size, RadiusData rd, java.util.BitSet bsSelected)
           
 void setVisibilityFlags(java.util.BitSet bs)
           
 
Methods inherited from class org.jmol.shape.Shape
appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, getColix, getColorCommand, getColorCommand, getFontCommand, getIndexFromName, getProperty, getProperty, getShapeCommands, getShapeCommands, getShapeDetail, getSize, 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,
                         java.util.BitSet bsSelected)
Overrides:
setShapeSize in class Shape

setProperty

public void setProperty(java.lang.String propertyName,
                        java.lang.Object value,
                        java.util.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 java.lang.String getShapeState()
Overrides:
getShapeState in class Shape

initialize

void initialize()

findNearestAtomIndex

public void findNearestAtomIndex(int xMouse,
                                 int yMouse,
                                 Atom[] closest,
                                 java.util.BitSet bsNot)
Overrides:
findNearestAtomIndex in class Shape

setVisibilityFlags

public void setVisibilityFlags(java.util.BitSet bs)
Overrides:
setVisibilityFlags in class Shape

setModelClickability

public void setModelClickability()
Overrides:
setModelClickability in class Shape

getMpsShapeCount

int getMpsShapeCount()

getBioShape

BioShape getBioShape(int i)