org.jmol.shape
Class Shape

java.lang.Object
  extended by org.jmol.shape.Shape
Direct Known Subclasses:
AtomShape, BioShapeCollection, Dipoles, FontLineShape, Measures, MeshCollection, Object2dShape, Sticks

public abstract class Shape
extends java.lang.Object

Shape now encompasses: AtomShape (abstract) | Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors | GeoSurface BioShapeCollection (abstract) | Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace Dipoles FontLineShape (abstract) | Axes, Bbcage, Frank, Uccage Measures MeshCollection (abstract) | | Draw Isosurface | LcaoCartoon, MolecularOrbital, Pmesh Sticks | Hsticks, Sssticks TextShape (abstract) | Echo, Hover


Field Summary
 Graphics3D g3d
           
 boolean isBioShape
           
 ModelSet modelSet
           
 int myVisibilityFlag
           
 int shapeID
           
protected  boolean translucentAllowed
           
protected  float translucentLevel
           
 Viewer viewer
           
 
Constructor Summary
Shape()
           
 
Method Summary
static void appendCmd(java.lang.StringBuffer s, java.lang.String cmd)
           
 void checkBoundsMinMax(javax.vecmath.Point3f pointMin, javax.vecmath.Point3f pointMax)
           
 Point3fi checkObjectClicked(int x, int y, int modifiers, java.util.BitSet bsVisible)
           
 boolean checkObjectDragged(int prevX, int prevY, int x, int y, int modifiers, java.util.BitSet bsVisible)
           
 boolean checkObjectHovered(int x, int y, java.util.BitSet bsVisible)
           
protected  int coordinateInRange(int x, int y, javax.vecmath.Point3f vertex, int dmin2, javax.vecmath.Point3i ptXY)
           
(package private)  java.lang.String encodeColor(short colix)
           
private  java.lang.String encodeTransColor(byte pid, short colix, boolean translucentAllowed)
           
 void findNearestAtomIndex(int xMouse, int yMouse, Atom[] closest)
           
static short getColix(short[] colixes, int i, Atom atom)
           
 java.lang.String getColorCommand(java.lang.String type, byte pid, short colix)
           
 java.lang.String getColorCommand(java.lang.String type, short colix)
           
static java.lang.String getFontCommand(java.lang.String type, Font3D font)
           
 int getIndexFromName(java.lang.String thisID)
           
 java.lang.Object getProperty(java.lang.String property, int index)
           
 boolean getProperty(java.lang.String property, java.lang.Object[] data)
           
static java.lang.String getShapeCommands(java.util.Hashtable htDefine, java.util.Hashtable htMore, int atomCount)
           
static java.lang.String getShapeCommands(java.util.Hashtable htDefine, java.util.Hashtable htMore, int count, java.lang.String selectCmd)
           
 java.util.Vector getShapeDetail()
           
 java.lang.String getShapeState()
           
private static java.lang.String getTranslucentLabel(short colix)
           
 Viewer getViewer()
           
 void initializeShape(Viewer viewer, Graphics3D g3d, ModelSet modelSet, int shapeID)
           
protected  void initModelSet()
           
 void initShape()
           
protected  void remapColors()
           
protected  short setColix(short colix, byte paletteID, Atom atom)
           
protected  short setColix(short colix, byte paletteID, Bond bond)
           
 short setColix(short colix, byte paletteID, int atomIndex)
           
 void setModelClickability()
           
 void setModelSet(ModelSet modelSet)
           
 void setProperty(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bsSelected)
           
 void setSize(int size, java.util.BitSet bsSelected)
           
 void setSize(int flags, float size, java.util.BitSet bsSelected)
           
static void setStateInfo(java.util.Hashtable ht, int i1, int i2, java.lang.String key)
           
static void setStateInfo(java.util.Hashtable ht, int i, java.lang.String key)
           
 void setVisibilityFlags(java.util.BitSet bs)
           
 boolean wasClicked(int x, int y)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

viewer

public Viewer viewer

modelSet

public ModelSet modelSet

g3d

public Graphics3D g3d

shapeID

public int shapeID

myVisibilityFlag

public int myVisibilityFlag

translucentLevel

protected float translucentLevel

translucentAllowed

protected boolean translucentAllowed

isBioShape

public boolean isBioShape
Constructor Detail

Shape

public Shape()
Method Detail

getViewer

public Viewer getViewer()

initializeShape

public final void initializeShape(Viewer viewer,
                                  Graphics3D g3d,
                                  ModelSet modelSet,
                                  int shapeID)

setModelSet

public void setModelSet(ModelSet modelSet)

initModelSet

protected void initModelSet()

initShape

public void initShape()

setSize

public void setSize(int size,
                    java.util.BitSet bsSelected)

setSize

public void setSize(int flags,
                    float size,
                    java.util.BitSet bsSelected)

setProperty

public void setProperty(java.lang.String propertyName,
                        java.lang.Object value,
                        java.util.BitSet bsSelected)

getProperty

public boolean getProperty(java.lang.String property,
                           java.lang.Object[] data)

getProperty

public java.lang.Object getProperty(java.lang.String property,
                                    int index)

getIndexFromName

public int getIndexFromName(java.lang.String thisID)

wasClicked

public boolean wasClicked(int x,
                          int y)

findNearestAtomIndex

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

checkBoundsMinMax

public void checkBoundsMinMax(javax.vecmath.Point3f pointMin,
                              javax.vecmath.Point3f pointMax)

setModelClickability

public void setModelClickability()

checkObjectClicked

public Point3fi checkObjectClicked(int x,
                                   int y,
                                   int modifiers,
                                   java.util.BitSet bsVisible)

checkObjectHovered

public boolean checkObjectHovered(int x,
                                  int y,
                                  java.util.BitSet bsVisible)

checkObjectDragged

public boolean checkObjectDragged(int prevX,
                                  int prevY,
                                  int x,
                                  int y,
                                  int modifiers,
                                  java.util.BitSet bsVisible)

coordinateInRange

protected int coordinateInRange(int x,
                                int y,
                                javax.vecmath.Point3f vertex,
                                int dmin2,
                                javax.vecmath.Point3i ptXY)

setColix

public short setColix(short colix,
                      byte paletteID,
                      int atomIndex)

setColix

protected short setColix(short colix,
                         byte paletteID,
                         Atom atom)

setColix

protected short setColix(short colix,
                         byte paletteID,
                         Bond bond)

remapColors

protected void remapColors()

getShapeDetail

public java.util.Vector getShapeDetail()

getShapeState

public java.lang.String getShapeState()

setVisibilityFlags

public void setVisibilityFlags(java.util.BitSet bs)

setStateInfo

public static void setStateInfo(java.util.Hashtable ht,
                                int i,
                                java.lang.String key)

setStateInfo

public static void setStateInfo(java.util.Hashtable ht,
                                int i1,
                                int i2,
                                java.lang.String key)

getShapeCommands

public static java.lang.String getShapeCommands(java.util.Hashtable htDefine,
                                                java.util.Hashtable htMore,
                                                int atomCount)

getShapeCommands

public static java.lang.String getShapeCommands(java.util.Hashtable htDefine,
                                                java.util.Hashtable htMore,
                                                int count,
                                                java.lang.String selectCmd)

appendCmd

public static void appendCmd(java.lang.StringBuffer s,
                             java.lang.String cmd)

getFontCommand

public static java.lang.String getFontCommand(java.lang.String type,
                                              Font3D font)

getColorCommand

public java.lang.String getColorCommand(java.lang.String type,
                                        short colix)

getColorCommand

public java.lang.String getColorCommand(java.lang.String type,
                                        byte pid,
                                        short colix)

encodeTransColor

private java.lang.String encodeTransColor(byte pid,
                                          short colix,
                                          boolean translucentAllowed)

encodeColor

java.lang.String encodeColor(short colix)

getTranslucentLabel

private static java.lang.String getTranslucentLabel(short colix)

getColix

public static short getColix(short[] colixes,
                             int i,
                             Atom atom)