Field Detail

• 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 java.util.List<SurfaceStatus> surfaces

• DEGREES

  static final int DEGREES

  See Also:

  Constant Field Values

• RADIANS

  static final int RADIANS

  See Also:

  Constant Field Values

• GRADIANS

  static final int GRADIANS

  See Also:

  Constant Field Values

• CIRCLE_FRACTION

  static final int CIRCLE_FRACTION

  See Also:

  Constant Field Values

• UNITS_PI

  static final int UNITS_PI

  See Also:

  Constant Field Values

• angleUnits

  private int angleUnits

• angleUnitsList

  private java.lang.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 Detail

• SurfaceTool

  public SurfaceTool​(JmolViewer vwr,
                     HistoryFile hfile,
                     java.lang.String winName,
                     boolean useGUI)

Method Detail

• 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​(java.lang.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

  java.lang.String[] getAngleUnitsList()

• getCapOn

  boolean getCapOn()

• setCapOn

  void setCapOn​(boolean b)

• getSurfaces

  public java.util.List<SurfaceStatus> getSurfaces()