Class SurfaceTool

java.lang.Object
org.openscience.jmol.app.surfacetool.SurfaceTool

public class SurfaceTool extends Object
  • Field Details

    • gui

      private SurfaceToolGUI gui
    • useGUI

      boolean useGUI
    • vwr

      protected JmolViewer vwr
    • negCorner

      private final javajs.util.P3 negCorner
    • posCorner

      private final javajs.util.P3 posCorner
    • center

      private final javajs.util.P3 center
    • boxVec

      private final javajs.util.V3 boxVec
    • surfaces

      private final List<SurfaceStatus> surfaces
    • DEGREES

      static final int DEGREES
      See Also:
    • RADIANS

      static final int RADIANS
      See Also:
    • GRADIANS

      static final int GRADIANS
      See Also:
    • CIRCLE_FRACTION

      static final int CIRCLE_FRACTION
      See Also:
    • UNITS_PI

      static final int UNITS_PI
      See Also:
    • angleUnits

      private int angleUnits
    • angleUnitsList

      private String[] angleUnitsList
    • angleXY

      private float angleXY
    • anglefromZ

      private float anglefromZ
    • positionMin

      private float positionMin
    • position

      private float position
    • thickness

      private float thickness
    • thicknessMax

      private float thicknessMax
    • slice

      private Slice slice
    • leftOn

      private boolean leftOn
    • rightOn

      private boolean rightOn
    • ghostOn

      private boolean ghostOn
    • capOn

      private boolean capOn
    • useMolecular

      private boolean useMolecular
    • usePercent

      private boolean usePercent
  • Constructor Details

  • Method Details

    • toFront

      public void toFront()
    • toFrontOrGotFocus

      void toFrontOrGotFocus()
    • chooseBestBoundBox

      private void chooseBestBoundBox()
    • checkMeshBB

      BoxInfo checkMeshBB(Shape[] shapes, int kind, BoxInfo box)
    • setSurfaceToolParam

      void setSurfaceToolParam()
    • updateSurfaceInfo

      private void updateSurfaceInfo()
    • setSyncStarting

      private void setSyncStarting()
    • syncDone

      private void syncDone()
    • updateMeshInfo

      private void updateMeshInfo(Shape[] shapes, int kind)
    • checkMesh

      private boolean checkMesh(Mesh m)
    • setAngleUnits

      void setAngleUnits(int units)
    • getNegCorner

      javajs.util.P3 getNegCorner()
    • getPosCorner

      javajs.util.P3 getPosCorner()
    • initSlice

      private void initSlice()
    • showSliceBoundaryPlanes

      void showSliceBoundaryPlanes(boolean onOrOff)
    • setSlice

      void setSlice(float angleXY, float anglefromZ, float position, float thickness)
      Defines a slice within which isosurfaces (and in future? atoms) are displayed.
      Parameters:
      angleXY - (float)angle in radians from X-axis to projection in XY plane
      anglefromZ - (float)angle in radians from z-axis to vector
      position - (float) position along direction vector in absolute units
      thickness - (float) thickness of slice in absolute units
    • setSliceAngleXY

      void setSliceAngleXY(float angle)
      Parameters:
      angle - (float) angle from X-axis of projection on XY plane in radians.
    • getSliceAngleXY

      float getSliceAngleXY()
    • setSliceAnglefromZ

      void setSliceAnglefromZ(float angle)
      Parameters:
      angle - (float) angle of vector from Z axis in radians.
    • getAnglefromZ

      float getAnglefromZ()
    • setSlicePosition

      void setSlicePosition(float where)
      Parameters:
      where - (float) position of slice center along direction vector.
    • getSlicePosition

      float getSlicePosition()
    • setSliceThickness

      void setSliceThickness(float width)
      Parameters:
      width - (float) thickness of slice.
    • getSliceThickness

      float getSliceThickness()
    • updateSlices

      void updateSlices()
    • sliceObject

      void sliceObject(String objectName, int kind)
    • drawSlicePlane

      private void drawSlicePlane(javajs.util.SB cmd, int side, boolean on)
    • getAngleUnits

      int getAngleUnits()
      Returns:
      (int) possible values: SurfaceTool.RADIANS, SurfaceTool.DEGREES, SurfaceTool.GRADIANS, SurfaceTool.CIRCLE_FRACTION, SurfaceTool.UNITS_PI.
    • getGhostOn

      boolean getGhostOn()
      Returns:
      (boolean) true = ghost showing; false = ghost hiding.
    • setGhostOn

      void setGhostOn(boolean b)
      Parameters:
      b - (boolean) true for ghost on.
    • getUseMolecular

      boolean getUseMolecular()
      Returns:
      (boolean) true = using molecular coordinates; false = using boundbox coordinates.
    • setUseMolecular

      void setUseMolecular(boolean on)
    • getPositionMin

      float getPositionMin()
    • getThicknessMax

      float getThicknessMax()
    • getCenter

      javajs.util.P3 getCenter()
    • getBoxVec

      javajs.util.V3 getBoxVec()
    • getSliceMiddle

      javajs.util.P4 getSliceMiddle()
    • getAngleUnitsList

      String[] getAngleUnitsList()
    • getCapOn

      boolean getCapOn()
    • setCapOn

      void setCapOn(boolean b)
    • getSurfaces

      public List<SurfaceStatus> getSurfaces()