Package org.openscience.jmol.app.surfacetool

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()