VRML rotations : how to draw a cylinder between 2 spheres

package testvrmlrotations;
 
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import java.text.DecimalFormat;
 
public class Main {
 
    public static void main(String[] args) throws IOException {
        
        FileWriter fos = new FileWriter("B:/x.wrl");
        BufferedWriter out = new BufferedWriter(fos);
        
        out.write( "#VRML V2.0 utf8");
        out.write( "\r  Background { skyColor [ 0.0 0.0 0.0 ] }");       
        
        // works when in XY plane
        out.write(doit( -2.0, 1.0 , 0.0,   2.0, -3.0, 0.0  ));
        
        // doesn't work when out of XY plane : something wrong with R2
        out.write(doit( -2.0, 1.0 , 0.0,   5.0, -1.0, -5.0  ));
        
        out.close();
        
    }
 
    /**
     * returns VMRL declarations for
     * - 2 spheres at (x1,y1,z1) and (x2,y2,z2)
     * - a cylinder connecting the spheres
     */
    public static String doit(double x1, double y1, double z1 , 
                              double x2, double y2, double z2) {
        
        String s=""; // the output
        DecimalFormat df = new DecimalFormat(" 0.000");
        
        // add spheres
        s += getSpheres(x1,y1,z1);
        s += getSpheres(x2,y2,z2);
        
        // **** draw cylinder ****
        
        // get barycenter: this is (0,0,0) for the cylinder
        double x=(x1+x2)/2;
        double y=(y1+y2)/2;
        double z=(z1+z2)/2;
 
        // get height
        double h=Math.sqrt( Math.pow(x1-x2, 2) + Math.pow(y1-y2, 2) + Math.pow((z1-z2), 2) ) ;
 
        // vector: barycenter->point2
        double vx = (x2-x)/2;
        double vy = (y2-y)/2;
        double vz = (z2-z)/2;
 
        // Z angle for XY plane : this angle seems OK
        double r1 = - Math.atan2(vx, vy);
 
        // vector from XY plane to point2 : something wrong here!!!!
        double wx = vy * Math.sin(r1) + vx * Math.cos(r1);
        double wy = vx * Math.sin(r1) + vy * Math.cos(r1);
        double wz = vz;
        
        // Y angle for new XZ plane
        double r2 = - Math.atan2(wx, wz);
        
        // output VRML declarations - nested rotations
        s += "\r      Transform {";
        s += "\r         translation " + df.format(x) + df.format(y) + df.format(z);
        s += "\r         rotation 0 0 1" + df.format(r1);
        s += "\r         children Transform {";
        s += "\r            translation 0 0 0 " ;
        s += "\r            rotation 0 1 0" + df.format(r2);        
        s += "\r            children Shape {";
        s += "\r               appearance Appearance {";
        s += "\r                  material Material { diffuseColor 1.0 0.0 1.0 }";
        s += "\r               }";        
        s += "\r               geometry Cylinder {";
        s += "\r                  radius 0.1";
        s += "\r                  height " + df.format(h);
        s += "\r               }";        
        s += "\r            }";  
        s += "\r         }";                         
        s += "\r      }";                                
        
        return s;        
    }
    
    public static String getSpheres(double x , double y, double z) {
        
        String s=""; // the output        
        DecimalFormat df = new DecimalFormat(" 0.000");
 
        s += "\r      Transform {";
        s += "\r         translation " + df.format(x) + df.format(y) + df.format(z);
        s += "\r         children Shape {";
        s += "\r            appearance Appearance {";
        s += "\r               material Material { diffuseColor 1.0 1.0 1.0 }";
        s += "\r            }";        
        s += "\r            geometry Sphere { radius 0.2 }";        
        s += "\r         }";
        s += "\r      }";
        
        return s;
    }
}

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/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
 
package Java3Dthing;
 
/*
 * CylinderTransformer.java
 * 
 * http://forums.sun.com/thread.jspa?threadID=433772&messageID=1943374
 *
 * Created on 25 July 2003, 11:04
 */
 
import javax.vecmath.*;
 
/** A class to calculate the length and transformations necessary to produce a
 * cylinder to connect two points.  Useful for Java3D and VRML where a cylinder
 * object is created aligned along the y-axis.
 * @author Alastair Hill
 */
public class CylinderTransformer {
    
    /** point A */ 
    private final Point3f pointA;
    /** point B */ 
    private final Point3f pointB;
    /** the angle through which to rotate the cylinder */    
    private float angle;
    /** the axis around which to rotate the cylinder */    
    private Vector3f axis;
    /** The translation required to translate the cylinder to the midpoint of the two
     * points
     */    
    private Vector3f translation;
    /** The length of the cylinder required to join the two points */    
    private float length;
    
    /** Creates a new instance of CylinderTransformer
     * @param a point a
     * @param b point b
     */
    public CylinderTransformer(Point3f a, Point3f b) {
        pointA = a;
        pointB = b;
        
        //carry out the calculations
        doCalculations();
    }
 
    /** Carries out the necessary calculations so that values may be returned */    
    private void doCalculations() {
        length = pointA.distance(pointB);
        
        float[] arrayA = new float[3];
        pointA.get(arrayA);
        float[] arrayB = new float[3];
        pointB.get(arrayB);
        float[] arrayMid = new float[3];
        
        for (int i=0;i<arrayA.length;i++){
            arrayMid[i] = (arrayA[i] + arrayB[i]) / 2f;
        }
        
        //the translation needed is
        translation = new Vector3f(arrayMid);
        
        //the initial orientation of the bond is in the y axis
        Vector3f init = new Vector3f(0.0f,1.0f,0.0f);
        
        //the vector needed is the same as that from a to b
        Vector3f needed = new Vector3f(pointB.x-pointA.x, pointB.y-pointA.y, pointB.z-pointA.z);
        
        //so the angle to rotate the bond by is:
        angle = needed.angle(init);
        
        //and the axis to rotate by is the cross product of the initial and
        //needed vectors - ie the vector orthogonal to them both
        axis = new Vector3f();
        axis.cross(init, needed);
    }
    
    /** Returns the angle (in radians) through which to rotate the cylinder
     * @return the angle.
     */
    public float getAngle() {
        return angle;
    }
    
    /** The axis around which the cylinder must be rotated
     * @return the axis
     */
    public javax.vecmath.Vector3f getAxis() {
        return axis;
    }
    
    /** The length required for the cylinder to join the two points
     * @return the length
     */
    public float getLength() {
        return length;
    } 
    
    /** The translation required to move the cylinder to the midpoint of the two points
     * @return the translation
     */
    public javax.vecmath.Vector3f getTranslation() {
        return translation;
    }
    
    /** Generates a (pretty) string representation of the the CylinderTransformer
     * @return the string representation
     */    
    public String toString(){
        return "tr: " + translation + ", ax: " + axis + ", an: " + angle + ", le: " + length;
    }
    
    /** Generates the required axis and angle combined into an AxisAngle4f object
     * @return the axis and angle
     */
    public javax.vecmath.AxisAngle4f getAxisAngle() {
        return new AxisAngle4f(axis.x,axis.y,axis.z,angle);
    }
}
 
 
 
-------------------------
 
 
/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
 
package Java3Dthing;
 
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import java.text.DecimalFormat;
import javax.vecmath.Point3f;
import javax.vecmath.Vector3f;
 
/**
 *
 * @author olivier
 */
public class runme {
 
    public void go() throws IOException {
        
        FileWriter fos = new FileWriter("B:/xxx.wrl");
        BufferedWriter out = new BufferedWriter(fos);
        
        out.write( "#VRML V2.0 utf8");
        out.write( "\r  Background { skyColor [ 0.0 0.0 0.0 ] }");       
        
        out.write(doit( -2.0, 1.0 , 0.0,   2.0, -3.0, 0.0  ));
        
        out.write(doit( -2.0, 1.0 , 0.0,   5.0, -1.0, -5.0  ));
        
        out.close();
        
        
        
    }
 
    
    /**
     * returns VMRL declarations for
     * - 2 spheres at (x1,y1,z1) and (x2,y2,z2)
     * - a cylinder connecting the spheres
     */
    public static String doit(double x1, double y1, double z1 , 
                              double x2, double y2, double z2) {
        
        String s=""; // the output
        DecimalFormat df = new DecimalFormat("0.000");                
        
        // add spheres
        s += getSpheres(x1,y1,z1);
        s += getSpheres(x2,y2,z2);
        
        // **** draw cylinder ****
        Point3f a = new Point3f();
        a.x = (float) x1;
        a.y = (float) y1;
        a.z = (float) z1;
 
        Point3f b = new Point3f();
        b.x = (float) x2;
        b.y = (float) y2;
        b.z = (float) z2;
        
        CylinderTransformer ct = new CylinderTransformer(a,b);
        
        Vector3f vt = ct.getTranslation();
        Vector3f va = ct.getAxis();
                
        s += "\r      Transform {";
        s += "\r         translation " + df.format(vt.x) + " " + df.format(vt.y) + " " + df.format(vt.z);
        s += "\r         rotation " + df.format(va.x) + " " + df.format(va.y) + " " + df.format(va.z) + " " + df.format(ct.getAngle());
        s += "\r         children  Shape {";
        s += "\r               appearance Appearance {";
        s += "\r                  material Material { diffuseColor 1.0 0.0 1.0 }";
        s += "\r               }";        
        s += "\r               geometry Cylinder {";
        s += "\r                  radius 0.1";
        s += "\r                  height " + df.format(ct.getLength());
        s += "\r               }";        
        s += "\r         }";                         
        s += "\r      }";                                
        
        return s;        
    }
    
    public static String getSpheres(double x , double y, double z) {
        
        String s=""; // the output        
        DecimalFormat df = new DecimalFormat("0.000");
 
        s += "\r      Transform {";
        s += "\r         translation " + df.format(x) + " " + df.format(y) + " " + df.format(z);
        s += "\r         children Shape {";
        s += "\r            appearance Appearance {";
        s += "\r               material Material { diffuseColor 1.0 1.0 1.0 }";
        s += "\r            }";        
        s += "\r            geometry Sphere { radius 0.2 }";        
        s += "\r         }";
        s += "\r      }";
        
        return s;
    }
    
    
    
    public static void main(String[] args) throws IOException {
        runme demo = new runme();
        
        demo.go();
    }
    
}

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