org.proteinshader.graphics
Class FrenetFrames

java.lang.Object
  org.proteinshader.graphics.Shape
      org.proteinshader.graphics.ExtrudedShape
          org.proteinshader.graphics.FrenetFrames

public class FrenetFrames
extends ExtrudedShape

Provides a visual representation of the LocalFrame objects of a Segment by drawing an x-axis, a y-axis, and z-axis.

Field Summary

static double	AXIS_RADIUS The radius for an axis is 0.05 angtroms.
static float[]	BASE The small sphere at the base of the xyz-axes is gray.
static int	FRAMES_PER_SEGMENT The default number of frames per segment in a FRENET_FRAME display is 21.
static double	MAJOR_AXIS_SCALE The scale factor for major axes is 1.5.
static double	MAJOR_SPHERE_RADIUS The radius for spheres at major points is 0.3.
static int	MAJOR_SPHERE_TILING The number of slices and stacks for a major sphere is 30.
static double	MINOR_AXIS_SCALE The scale factor for minor axes is 0.5.
static double	MINOR_SPHERE_RADIUS The radius for spheres at minor points is 0.0375.
static int	MINOR_SPHERE_TILING The number of slices and stacks for a minor sphere is 10.
static int	SLICES The number of slices for a cylinder is 10.
static float	SPECULAR_EXP The value for the specular exponent is 20.0.
static int	STACKS The number of stacks for a cylinder is 1.
static double	TIP_FRACTION The length of an arrow tip as a fraction of the axis length is 0.1.
static double	TIP_RADIUS The radius of the large end of an arrow tip is 0.08 angstroms.
static float[]	X The x-axis is green.
static float[]	Y The y-axis is yellow.
static float[]	Z The z-axis is red.

Fields inherited from class org.proteinshader.graphics.ExtrudedShape

END_CAP_COLOR, START_CAP_COLOR

Fields inherited from class org.proteinshader.graphics.Shape

HALF_PI, PI, SPECULAR_COLOR, TWO_PI

Constructor Summary

FrenetFrames()
Constructs a FrenetFrames object.

Method Summary

void	draw(GL gl, LocalFrame[] frames) Uses an array of LocalFrame objects to draw xyz-axes.
void	draw(GL gl, LocalFrame frame, double scale, double sphereRadius, int sphereTiling, float sphereRed, float sphereGreen, float sphereBlue, float sphereAlpha) Draws an xyz-axis based on the rotation and translation in the LocalFrame given as an argument.
void	drawEndCap(GL gl, LocalFrame frame) Draws the local frame using red for the sphere at the base.
void	drawStartCap(GL gl, LocalFrame frame) Draws the local frame using light blue for the sphere at the base.
void	setShaders(ShaderManager shaders) The ShaderManager is only needed because of an apparent bug on some Mac OS X machines where material color can only be set once after a custom shader is set, so to draw Frenet frames with more than one color, the shaders must be reset each time.

Methods inherited from class org.proteinshader.graphics.ExtrudedShape

applyEndCapColor, applyStartCapColor, createDisplayList, createDisplayLists, createEndCapDisplayList, createStartCapDisplayList

Methods inherited from class org.proteinshader.graphics.Shape

deleteDisplayList, executeDisplayList, executeDisplayList, setMaterial

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FRAMES_PER_SEGMENT

public static final int FRAMES_PER_SEGMENT

The default number of frames per segment in a FRENET_FRAME display is 21.

See Also:

Constant Field Values

AXIS_RADIUS

public static final double AXIS_RADIUS

The radius for an axis is 0.05 angtroms.

See Also:

Constant Field Values

TIP_RADIUS

public static final double TIP_RADIUS

The radius of the large end of an arrow tip is 0.08 angstroms.

See Also:

Constant Field Values

TIP_FRACTION

public static final double TIP_FRACTION

The length of an arrow tip as a fraction of the axis length is 0.1.

See Also:

Constant Field Values

MINOR_AXIS_SCALE

public static final double MINOR_AXIS_SCALE

The scale factor for minor axes is 0.5.

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Constant Field Values

MAJOR_AXIS_SCALE

public static final double MAJOR_AXIS_SCALE

The scale factor for major axes is 1.5.

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Constant Field Values

MAJOR_SPHERE_RADIUS

public static final double MAJOR_SPHERE_RADIUS

The radius for spheres at major points is 0.3.

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Constant Field Values

MINOR_SPHERE_RADIUS

public static final double MINOR_SPHERE_RADIUS

The radius for spheres at minor points is 0.0375.

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Constant Field Values

SLICES

public static final int SLICES

The number of slices for a cylinder is 10.

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Constant Field Values

STACKS

public static final int STACKS

The number of stacks for a cylinder is 1.

See Also:

Constant Field Values

MAJOR_SPHERE_TILING

public static final int MAJOR_SPHERE_TILING

The number of slices and stacks for a major sphere is 30.

See Also:

Constant Field Values

MINOR_SPHERE_TILING

public static final int MINOR_SPHERE_TILING

The number of slices and stacks for a minor sphere is 10.

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Constant Field Values

SPECULAR_EXP

public static final float SPECULAR_EXP

The value for the specular exponent is 20.0.

See Also:

Constant Field Values

X

public static final float[] X

The x-axis is green.

Y

public static final float[] Y

The y-axis is yellow.

Z

public static final float[] Z

The z-axis is red.

BASE

public static final float[] BASE

The small sphere at the base of the xyz-axes is gray.

Constructor Detail

FrenetFrames

public FrenetFrames()

Constructs a FrenetFrames object.

Method Detail

setShaders

public void setShaders(ShaderManager shaders)

The ShaderManager is only needed because of an apparent bug on some Mac OS X machines where material color can only be set once after a custom shader is set, so to draw Frenet frames with more than one color, the shaders must be reset each time.

Parameters:

shaders - the shader manager object.

draw

public void draw(GL gl,
                 LocalFrame[] frames)

Uses an array of LocalFrame objects to draw xyz-axes.

If the number of frames is odd, then the frame in the very middle will be drawn at full scale while all other frames will be drawn smaller by using the MINOR_AXES_SCALE, which should be between 0.0 and 1.0. If the number of frames is even, then the frame right after the exact middle will be drawn at full scale with all others reduced. It makes the most sense to always use an odd number of frames because then the largest set of axes will coorespond to the alpha-carbon.

The capStart and capEnd arguments are not currently used, but might be used in the future to draw a special mark or perhaps a waist polygon to indicate that one or the other end of a Segment is capped.

Specified by:

draw in class ExtrudedShape

Parameters:

gl - the current GL object.

frames - array of LocalFrames for positioning a waist polygon.

drawStartCap

public void drawStartCap(GL gl,
                         LocalFrame frame)

Draws the local frame using light blue for the sphere at the base. The sphere will be one-half the size of the alpha-carbon sphere.

Specified by:

drawStartCap in class ExtrudedShape

Parameters:

gl - the current GL object.

frame - the frame for positioning the waist polygon.

drawEndCap

public void drawEndCap(GL gl,
                       LocalFrame frame)

Draws the local frame using red for the sphere at the base. The sphere will be one-half the size of the alpha-carbon sphere.

Specified by:

drawEndCap in class ExtrudedShape

Parameters:

gl - the current GL object.

frame - the frame for positioning the waist polygon.

draw

public void draw(GL gl,
                 LocalFrame frame,
                 double scale,
                 double sphereRadius,
                 int sphereTiling,
                 float sphereRed,
                 float sphereGreen,
                 float sphereBlue,
                 float sphereAlpha)

Draws an xyz-axis based on the rotation and translation in the LocalFrame given as an argument.

Parameters:

gl - the current GL object.

frame - a LocalFrame with a rotation and a translation.

scale - a scale factor for the axes to draw.

sphereRadius - the radius of the sphere at the base of the xyz-axes.

sphereTiling - the number of slices and stacks for the sphere.

sphereRed - the red channel for sphere at base of xyz-axes.

sphereGreen - the green channel for sphere at base of xyz-axes.

sphereBlue - the blue channel for sphere at base of xyz-axes.

sphereAlpha - the alpha channel for sphere at base of xyz-axes.