AbstractDataCollection.java

package phylonet.coalescent;

import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import phylonet.tree.model.Tree;
import phylonet.tree.model.sti.STITreeCluster;
import phylonet.tree.model.sti.STITreeCluster.Vertex;
import phylonet.util.BitSet;

/**
 * This class is used in the inference class, and does two things:
 *  -- Keeps an instance of the top level IClusterCollection
 *  -- Has methods for building the set X
 * @author smirarab
 *
 * @param <T>
 */
public abstract class AbstractDataCollection <T> {

	protected IClusterCollection clusters;

	protected boolean addToClusters(STITreeCluster c, int size) {
	
		if (size == 0) return false;
		Vertex nv = c.new Vertex();
		return clusters.addCluster(nv, size);
	}
	
	protected boolean removeCluster(STITreeCluster c, int size) {
		if (size == GlobalMaps.taxonIdentifier.taxonCount()
		|| size == 0) {
			return false;
		}	
		Vertex nv = c.new Vertex();
		return clusters.removeCluster(nv, size);
	}

	// TODO: Figure out what to do with this in case of a mapper
	// Should only add species-consistent bipartitions?
	void addAllPossibleSubClusters(STITreeCluster cluster) {
	    int size = GlobalMaps.taxonIdentifier.taxonCount();
		BitSet bs = (BitSet) cluster.getBitSet().clone();
		bs.clear(0, size);
		while (true) {
			int tsb = bs.nextClearBit(0);
			if (tsb >= size) {
				break;
			}
			bs.set(tsb);
			bs.clear(0, tsb);
			STITreeCluster c = new STITreeCluster(GlobalMaps.taxonIdentifier);
			c.setCluster((BitSet) bs.clone());
			addToClusters(c, c.getClusterSize());
		}
		System.err
				.println("Number of Clusters After Adding All possible clusters: "
						+ clusters.getClusterCount());
	}

	public abstract void addExtraBipartitionsByInput(
			List<Tree> trees, boolean extraTreeRooted);
	
	public abstract void removeExtraBipartitionsByInput(List<Tree> extraTrees,
			boolean extraTreeRooted);
	
	//public abstract void computeTreePartitions(AbstractInference<T> inference);

    //public abstract void addExtraBipartitionByExtension(AbstractInference<T> inference);
	
	public abstract void formSetX(AbstractInference<T> inference);
	
	@Override
	protected Object clone() throws CloneNotSupportedException {
		AbstractDataCollection clone = (AbstractDataCollection) super.clone();
		return clone;
	}

}