/////////////////////////////////////////////////////////////////////////
// cylinder
/////////////////////////////////////////////////////////////////////////

cylinderGeometry = new THREE.CylinderGeometry( 0.30, 0.30, 0.80, 20, 4 );
cylinder = new THREE.Mesh( cylinderGeometry, diffuseMaterial);
scene.add( cylinder );            
// cylinder.matrix transforms the cylinder relative to its parent
// By default, the parent is the world coordinate system

///////// Below are 3 different ways to position the cylinder wrt its parent
///////// Of course, you should only want to use one of these, i.e., comment out the other two.

////////    (1) directly setting M_model

cylinder.matrixAutoUpdate = false;
cylinder.matrix.set(
 0.7,-0.7,0,2,
 0.7,0.7,0,0,
 0,0,1,0,
 0,0,0,1);

////////    (2) using a typical graphics API setup, i.e., right multiplying, therefore local coordinates

cylinder.matrixAutoUpdate = false;
cylinder.matrix.identity();
var tempMatrix = new THREE.Matrix4;

tempMatrix.makeTranslation(3,1,0);       // build translation matrix
cylinder.matrix.multiply(tempMatrix);    // right multiply

tempMatrix.makeRotationZ(Math.PI/4);     // build rotation matrix
cylinder.matrix.multiply(tempMatrix);    // right multiply

////////    (3) default threejs setup
//   upon rendering, the transformation is defined by the following sequence  (right multiplied, i.e., local coords)
//      Translate(  cylinder.position );
//      RotateX  (  cylinder.rotate.x );
//      RotateY  (  cylinder.rotate.y );
//      RotateZ  (  cylinder.rotate.z );

 cylinder.matrixAutoUpdate = true;
 cylinder.position.set(2, 0, 0);
 cylinder.rotation.set(0,0,Math.PI/4);     // Euler angle sequence of rotations: X,Y,Z