Package org.jmol.shape

Class Shape

  • Direct Known Subclasses:
    AtomShape, BioShapeCollection, Dipoles, FontLineShape, Frank, MeshCollection, Sticks, TextShape
    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 Detail

      • myType

        public java.lang.String myType

      • shapeID

        public int shapeID

      • vf

        public int vf
        shape visibility flag

      • translucentLevel

        protected float translucentLevel

      • translucentAllowed

        public boolean translucentAllowed

      • isBioShape

        public boolean isBioShape

      • bsSizeSet

        public BS bsSizeSet

      • bsColixSet

        public BS bsColixSet

    • Constructor Detail

      • Shape

        public Shape()

    • Method Detail

      • getShapeState

        public abstract java.lang.String getShapeState()

      • setProperty

        public abstract void setProperty​(java.lang.String propertyName,
                                 java.lang.Object value,
                                 BS bsSelected)

      • initializeShape

        public final void initializeShape​(Viewer vwr,
                                  ModelSet modelSet,
                                  int shapeID)

      • initShape

        public abstract void initShape()

      • setModelVisibilityFlags

        public void setModelVisibilityFlags​(BS bsModels)
        Parameters:
        bsModels -

      • getSize

        public int getSize​(int atomIndex)
        overridden in Dots, CGOMesh, and AtomShape
        Parameters:
        atomIndex -
        Returns:
        size

      • getSizeG

        public int getSizeG​(Group group)
        Parameters:
        group -
        Returns:
        size

      • replaceGroup

        public void replaceGroup​(Group g0,
                         Group g1)
        Parameters:
        g0 -
        g1 -

      • setModelSet

        public void setModelSet​(ModelSet modelSet)

      • initModelSet

        protected void initModelSet()

      • setShapeSizeRD

        public void setShapeSizeRD​(int size,
                           RadiusData rd,
                           BS bsSelected)

      • setSize

        protected void setSize​(int size,
                       BS bsSelected)
        Parameters:
        size -
        bsSelected -

      • setSizeRD

        protected void setSizeRD​(RadiusData rd,
                         BS bsSelected)
        Parameters:
        rd -
        bsSelected -

      • setPropS

        protected void setPropS​(java.lang.String propertyName,
                        java.lang.Object value,
                        BS bsSelected)

      • getPropertyData

        public boolean getPropertyData​(java.lang.String property,
                               java.lang.Object[] data)
        Parameters:
        property -
        data -
        Returns:
        true if serviced

      • getPropShape

        protected boolean getPropShape​(java.lang.String property,
                               java.lang.Object[] data)

      • getProperty

        public java.lang.Object getProperty​(java.lang.String property,
                                    int index)
        Parameters:
        property -
        index -
        Returns:
        true if serviced

      • getIndexFromName

        public int getIndexFromName​(java.lang.String thisID)
        Parameters:
        thisID -
        Returns:
        index

      • wasClicked

        public boolean wasClicked​(int x,
                          int y)
        Parameters:
        x -
        y -
        Returns:
        T/F

      • findNearestAtomIndex

        public void findNearestAtomIndex​(int xMouse,
                                 int yMouse,
                                 Atom[] closest,
                                 BS bsNot)
        Parameters:
        xMouse -
        yMouse -
        closest -
        bsNot -

      • checkBoundsMinMax

        public void checkBoundsMinMax​(javajs.util.P3 pointMin,
                              javajs.util.P3 pointMax)
        Parameters:
        pointMin -
        pointMax -

      • setAtomClickability

        public void setAtomClickability()

      • checkObjectClicked

        public java.util.Map<java.lang.String,​java.lang.Object> checkObjectClicked​(int x,
                                                                                 int y,
                                                                                 int modifiers,
                                                                                 BS bsVisible,
                                                                                 boolean drawPicking)
        Parameters:
        x -
        y -
        modifiers -
        bsVisible -
        drawPicking - TODO
        Returns:
        Hashtable containing information about pt clicked

      • checkObjectHovered

        public boolean checkObjectHovered​(int x,
                                  int y,
                                  BS bsVisible)
        Parameters:
        x -
        y -
        bsVisible -
        Returns:
        T/F

      • checkObjectDragged

        public boolean checkObjectDragged​(int prevX,
                                  int prevY,
                                  int x,
                                  int y,
                                  int dragAction,
                                  BS bsVisible)
        Parameters:
        prevX -
        prevY -
        x -
        y -
        dragAction -
        bsVisible -
        Returns:
        T/F

      • coordinateInRange

        protected int coordinateInRange​(int x,
                                int y,
                                javajs.util.T3 vertex,
                                int dmin2,
                                javajs.util.P3i ptXY)

      • getColixI

        public short getColixI​(short colix,
                       byte paletteID,
                       int atomIndex)

      • getColixA

        protected short getColixA​(short colix,
                          byte paletteID,
                          Atom atom)

      • getColixB

        protected short getColixB​(short colix,
                          int pid,
                          Bond bond)

      • getShapeDetail

        public java.lang.Object getShapeDetail()

      • getColix

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

      • getFontCommand

        public static java.lang.String getFontCommand​(java.lang.String type,
                                              javajs.awt.Font font)

      • getColorCommandUnk

        public static java.lang.String getColorCommandUnk​(java.lang.String type,
                                                  short colix,
                                                  boolean translucentAllowed)

      • getColorCommand

        public static java.lang.String getColorCommand​(java.lang.String type,
                                               byte pid,
                                               short colix,
                                               boolean translucentAllowed)

      • encodeColor

        public static java.lang.String encodeColor​(short colix)

      • getTranslucentLabel

        public static java.lang.String getTranslucentLabel​(short colix)

      • appendCmd

        protected static void appendCmd​(javajs.util.SB s,
                                java.lang.String cmd)