org.cellmicrocosmos.cm2.misc

Class Cm2_Toolkit

java.lang.Object

org.cellmicrocosmos.cm2.misc.Cm2_Toolkit

public class Cm2_Toolkit
extends java.lang.Object

A Toolkit that offers various useful Methods

Author:

Tim Dingersen dackelnose@gmx.net, Sebastian Rubert, Bjoern Sommer bjoern@CELLmicrocosmos.org

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Cm2_Toolkit.Membrane_Image2D_Generator
static class	Cm2_Toolkit.ToolkitMembranePackingAlgorithm This class is only used for direct access to the different methods of the MembranePackingAlgorithm interface.

Field Summary

Fields

Modifier and Type	Field and Description
static char[]	CHARS Creates a copy of the passed matrix.
static java.lang.String[]	MONTHS

Constructor Summary

Constructors

Constructor and Description
Cm2_Toolkit()

Method Summary

Modifier and Type	Method and Description
static boolean	amIRunningOnWebstart() This is a dirty approach, i know
static int[]	calcPercentages(int reference, int[] olds) Calculates the passed array of numbers
static float	calculateLengthBetween(javax.vecmath.Point3f a, javax.vecmath.Point3f b)
static java.util.Vector<java.lang.Object>	combineVectors(java.util.Vector<java.lang.Object> v1, java.util.Vector<java.lang.Object> v2) Puts the contents of first v1 and then v2 into a new Vector.
static void	complain(java.lang.String text, java.lang.String title)
static void	complainInternet()
static void	complainXML(java.lang.String fileName)
static void	compressToJar(java.io.File javafile, java.io.File dest)
static java.lang.String	convertAtomNameToElementName(java.lang.String key)
static java.lang.String	convertFileSizeToString(long d) Makes the passed Filesize to a string
static void	copyFile(java.io.File sourceFile, java.io.File destinationFile) This method makes a copy of the given sourceFile to the defined destinationFile.
static javax.vecmath.Matrix3f	copyMatrix(javax.vecmath.Matrix3f m)
static javax.vecmath.Matrix3f	createAUnitMatrix()
static java.lang.String	createCurrentDate()
static java.awt.Color	createRandomCholesterolColor()
static void	deleteDir(java.io.File dir, boolean instantly)
static java.lang.String	extendLeft(java.lang.String sample, int cols)
static java.lang.String	extendRight(java.lang.String sample, int cols)
static void	extractFromJar(java.lang.String source, java.lang.String dest)
static java.util.Vector<java.lang.Object>	fromArrayToVector(java.lang.Object[] obj) Copies the array into a new Vector
static int	getCharacterPosOf(char c)
static java.awt.Color	getRandomLipidColor() Get a randomly created Color for Lipids
static java.awt.Color	getRandomProteinColor() Get a randomly created Color for Proteins
static java.lang.String	getSimpleName(java.io.File file) Returns the simple name without the file extension
static javax.vecmath.Point3f	normalVectorInPlane(javax.vecmath.Point3f pointX, javax.vecmath.Point3f pointX0) Returns the normal vector of two given points which are lying in one plane.
static void	openWebPageOnSystemBrowser(java.lang.String url) Tries to display the passed url in the Default OS Webbrowser
static void	popUpLayoutDescription(net.infonode.docking.RootWindow root) This is for development purposes only.
static void	rotate_X_Axis_Matrix(javax.vecmath.Matrix3f current, float angle)
static void	rotate_X_Axis_Of_CoordinateSystem(javax.vecmath.Matrix3f current, float angle)
static void	rotate_Y_Axis_Matrix(javax.vecmath.Matrix3f current, float angle)
static void	rotate_Y_Axis_Of_CoordinateSystem(javax.vecmath.Matrix3f current, float angle)
static void	rotate_Z_Axis_Matrix(javax.vecmath.Matrix3f current, float angle)
static void	rotate_Z_Axis_Of_CoordinateSystem(javax.vecmath.Matrix3f current, float angle)
static java.awt.image.BufferedImage	rotateImage90(java.awt.image.BufferedImage img)
static void	setAllCapabilitysForBranchGroup(javax.media.j3d.BranchGroup branch) sets up capabilitys for BranchGroup
static void	setAllCapabilitysForShape3D(javax.media.j3d.Shape3D shape) Sets up the required capabilities for a molecule
static void	setAllCapabilitysForTransformGroup(javax.media.j3d.TransformGroup trans) sets up capabilitys for TransformGroup
static void	setRenderingAttributes(javax.media.j3d.Appearance appear) The given Appearance is assigned to the RenderingAttributes.
static java.lang.String	showInputDialog(java.awt.Component component, java.lang.String message, java.lang.String title, java.lang.String[] choices, java.lang.String[] exclusions, java.lang.String initial)
static javax.vecmath.Point3f	transformToNewPoint(javax.vecmath.Matrix3f matrix, javax.vecmath.Point3f point3f) Rotates a point according to the passed matrix.

Methods inherited from class java.lang.Object

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

Field Detail

CHARS

public static final char[] CHARS

Creates a copy of the passed matrix. Used as a workaround for the clone() method

MONTHS

public static final java.lang.String[] MONTHS

Constructor Detail

Cm2_Toolkit

public Cm2_Toolkit()

Method Detail

copyMatrix

public static javax.vecmath.Matrix3f copyMatrix(javax.vecmath.Matrix3f m)

getSimpleName

public static java.lang.String getSimpleName(java.io.File file)

Returns the simple name without the file extension

Returns:

popUpLayoutDescription

public static void popUpLayoutDescription(net.infonode.docking.RootWindow root)

This is for development purposes only. Shows the layout in a seperate Frame

calcPercentages

public static int[] calcPercentages(int reference,
                                    int[] olds)

Calculates the passed array of numbers

Parameters:

newval -

integers -

Returns:

convertFileSizeToString

public static java.lang.String convertFileSizeToString(long d)

Makes the passed Filesize to a string

Parameters:

d -

Returns:

getRandomProteinColor

public static java.awt.Color getRandomProteinColor()

Get a randomly created Color for Proteins

Returns:

getRandomLipidColor

public static java.awt.Color getRandomLipidColor()

Get a randomly created Color for Lipids

Returns:

createRandomCholesterolColor

public static java.awt.Color createRandomCholesterolColor()

transformToNewPoint

public static javax.vecmath.Point3f transformToNewPoint(javax.vecmath.Matrix3f matrix,
                                                        javax.vecmath.Point3f point3f)

Rotates a point according to the passed matrix. The passed point, which represents the starting location wont be changed; a new point will be returned instead. So its up to the caller to replace the old point with the returned value or to use it for something else. Besides, this method proves to work better than the transform of Matrix3f

Parameters:

matrix -

point3f -

Returns:

createAUnitMatrix

public static javax.vecmath.Matrix3f createAUnitMatrix()

rotate_X_Axis_Of_CoordinateSystem

public static void rotate_X_Axis_Of_CoordinateSystem(javax.vecmath.Matrix3f current,
                                                     float angle)

rotate_Y_Axis_Of_CoordinateSystem

public static void rotate_Y_Axis_Of_CoordinateSystem(javax.vecmath.Matrix3f current,
                                                     float angle)

rotate_Z_Axis_Of_CoordinateSystem

public static void rotate_Z_Axis_Of_CoordinateSystem(javax.vecmath.Matrix3f current,
                                                     float angle)

rotate_X_Axis_Matrix

public static void rotate_X_Axis_Matrix(javax.vecmath.Matrix3f current,
                                        float angle)

rotate_Y_Axis_Matrix

public static void rotate_Y_Axis_Matrix(javax.vecmath.Matrix3f current,
                                        float angle)

rotate_Z_Axis_Matrix

public static void rotate_Z_Axis_Matrix(javax.vecmath.Matrix3f current,
                                        float angle)

getCharacterPosOf

public static int getCharacterPosOf(char c)

createCurrentDate

public static java.lang.String createCurrentDate()

extendLeft

public static java.lang.String extendLeft(java.lang.String sample,
                                          int cols)

extendRight

public static java.lang.String extendRight(java.lang.String sample,
                                           int cols)

openWebPageOnSystemBrowser

public static void openWebPageOnSystemBrowser(java.lang.String url)

Tries to display the passed url in the Default OS Webbrowser

complainInternet

public static void complainInternet()

complainXML

public static void complainXML(java.lang.String fileName)

complain

public static void complain(java.lang.String text,
                            java.lang.String title)

extractFromJar

public static void extractFromJar(java.lang.String source,
                                  java.lang.String dest)
                           throws java.lang.Exception

Throws:

java.lang.Exception

compressToJar

public static void compressToJar(java.io.File javafile,
                                 java.io.File dest)
                          throws java.lang.Exception

Throws:

java.lang.Exception

deleteDir

public static void deleteDir(java.io.File dir,
                             boolean instantly)

amIRunningOnWebstart

public static boolean amIRunningOnWebstart()

This is a dirty approach, i know

Returns:

rotateImage90

public static java.awt.image.BufferedImage rotateImage90(java.awt.image.BufferedImage img)

setAllCapabilitysForBranchGroup

public static void setAllCapabilitysForBranchGroup(javax.media.j3d.BranchGroup branch)

sets up capabilitys for BranchGroup

Parameters:

branch -

setAllCapabilitysForTransformGroup

public static void setAllCapabilitysForTransformGroup(javax.media.j3d.TransformGroup trans)

sets up capabilitys for TransformGroup

Parameters:

trans -

setAllCapabilitysForShape3D

public static void setAllCapabilitysForShape3D(javax.media.j3d.Shape3D shape)

Sets up the required capabilities for a molecule

Parameters:

m -

setRenderingAttributes

public static void setRenderingAttributes(javax.media.j3d.Appearance appear)

The given Appearance is assigned to the RenderingAttributes. This method is important for the Stereo3D Rendering. Otherwise one eye is rendered using the wrong Z-Order. Note: This method is not used at the moment if there is no compatible Stereo3D device found

Parameters:

appear - the Appearance which should get the RenderingAttributes

combineVectors

public static java.util.Vector<java.lang.Object> combineVectors(java.util.Vector<java.lang.Object> v1,
                                                                java.util.Vector<java.lang.Object> v2)

Puts the contents of first v1 and then v2 into a new Vector.

Parameters:

v1 -

v2 -

Returns:

fromArrayToVector

public static java.util.Vector<java.lang.Object> fromArrayToVector(java.lang.Object[] obj)

Copies the array into a new Vector

Parameters:

obj -

Returns:

normalVectorInPlane

public static javax.vecmath.Point3f normalVectorInPlane(javax.vecmath.Point3f pointX,
                                                        javax.vecmath.Point3f pointX0)

Returns the normal vector of two given points which are lying in one plane. So it is the normal vector to a plane. Uses the cross product.

calculateLengthBetween

public static float calculateLengthBetween(javax.vecmath.Point3f a,
                                           javax.vecmath.Point3f b)

showInputDialog

public static java.lang.String showInputDialog(java.awt.Component component,
                                               java.lang.String message,
                                               java.lang.String title,
                                               java.lang.String[] choices,
                                               java.lang.String[] exclusions,
                                               java.lang.String initial)

convertAtomNameToElementName

public static java.lang.String convertAtomNameToElementName(java.lang.String key)

copyFile

public static void copyFile(java.io.File sourceFile,
                            java.io.File destinationFile)
                     throws java.io.IOException

This method makes a copy of the given sourceFile to the defined destinationFile. Note: This method should not be used for large files.

Parameters:

sourceFile -

destinationFile -

Throws:

java.io.IOException