ClusteringUtil.java

package org.chesmapper.view.cluster;

import java.util.ArrayList;
import java.util.List;

import javax.vecmath.Vector3f;

import org.mg.javalib.util.Vector3fUtil;

public class ClusteringUtil
{
	public static List<Vector3f> getClusterPositions(ClusteringImpl c)
	{
		List<Vector3f> list = new ArrayList<Vector3f>();
		for (Cluster cc : c.getClusters())
			if (cc.getNumCompounds() > 0)
				list.add(cc.getCenter(true));
		return list;
	}

	public static List<Vector3f> getCompoundPositions(ZoomableCompoundGroup c)
	{
		List<Vector3f> list = new ArrayList<Vector3f>();
		for (Compound m : c.getCompounds())
			list.add(m.getPosition());
		return list;
	}

	public static Vector3f[] getCompoundPositions(ClusteringImpl c)
	{
		return getCompoundPositions(c, true);
	}

	private static Vector3f[] getCompoundPositions(ClusteringImpl c, boolean scale)
	{
		Vector3f list[] = new Vector3f[c.getNumCompounds(true)];
		int i = 0;
		for (Compound m : c.getCompounds(true))
			list[i++] = m.getPosition(scale);
		return list;
	}

	public static int COMPOUND_SIZE_MAX = 40;
	public static int COMPOUND_SIZE = 20;
	public static float SCALE = 0;

	/**
	 * scale factor is used to scale the original 3d mapping values
	 * 
	 * @param v
	 * @return
	 */
	public static void updateScaleFactor(ClusteringImpl c)
	{
		Vector3f[] v = ClusteringUtil.getCompoundPositions(c, false);

		// the average min distance mean distance of each compound to its closest neighbor compound
		float d = Vector3fUtil.avgMinDist(v);
		if (d == 0)
			d = 1;

		// the smaller the distance, the higher the scale factor
		// the neigbhor should be on average 30units away
		float s = 1 / d * 30;
		//Settings.LOGGER.debug("min avg distance: " + d + " -> scale: " + s);

		// we want to limit the scale based on the max dist
		float maxD = Vector3fUtil.maxDist(v);
		float max_scale = 100 / maxD;
		if (max_scale < s)
		{
			//Settings.LOGGER.debug("override scale\nmax distance: " + maxD + " -> scale: " + max_scale);
			s = max_scale;
		}

		if (COMPOUND_SIZE < 0 || COMPOUND_SIZE > COMPOUND_SIZE_MAX)
			throw new Error("illegal compound size");
		// convert "int range 0 - COMPOUND_SIZE_MAX" to "float range 4.0 - 0.1"  
		float density = (float) (((1 - COMPOUND_SIZE / ((double) COMPOUND_SIZE_MAX)) * 3.9f) + 0.1f);
		//Settings.LOGGER.debug("compound size: " + ClusteringUtil.COMPOUND_SIZE + " -> scale multiplier: " + density);

		// scale is multiplied with the DENSITY, which is configurable by the user
		SCALE = s * density;
	}

}