RegionAnnotations.java

/*
 * Created on Dec 4, 2006
 */
package org.seqcode.gsebricks.verbs.assignment;

import java.util.*;

import org.seqcode.genome.Genome;
import org.seqcode.genome.location.Gene;
import org.seqcode.genome.location.NamedRegion;
import org.seqcode.genome.location.Region;
import org.seqcode.gsebricks.verbs.*;
import org.seqcode.gsebricks.verbs.location.ChromRegionIterator;
import org.seqcode.gsebricks.verbs.location.RefGeneGenerator;


/* RegionAnnotations annotations the set of genes in a genome with ChipPet binding events orBindingScan results.
   The set of genes can either be the default from RefGeneGenerator or those from a user-provided
   Gene generator
*/

public class RegionAnnotations extends CachedAnnotations<Region,Region> {
	
    public RegionAnnotations(Genome g) { 
        super();
        
        RefGeneGenerator<NamedRegion> gen = new RefGeneGenerator<NamedRegion>(g);
        Iterator<NamedRegion> chroms = new ChromRegionIterator(g);
        Iterator<Gene> genes = new ExpanderIterator<NamedRegion,Gene>(gen, chroms);
        
        TreeSet<Region> targetList = new TreeSet<Region>();
        while(genes.hasNext()) { 
            Gene gene = genes.next();
            if(!targetList.contains(gene)) { 
                targetList.add(gene);
            }
        }
        
        addItems(targetList);
    }
    
    public RegionAnnotations(Genome g, Expander<NamedRegion,Gene> gen) { 
        super();
        
        Iterator<NamedRegion> chroms = new ChromRegionIterator(g);
        Iterator<Gene> genes = new ExpanderIterator<NamedRegion,Gene>(gen, chroms);
        
        TreeSet<Region> targetList = new TreeSet<Region>();
        while(genes.hasNext()) { 
            Gene gene = genes.next();
            if(!targetList.contains(gene)) { 
                targetList.add(gene);
            }
        }
        
        addItems(targetList);
    }
    
    public RegionAnnotations(Genome g, Expander<NamedRegion,Gene> gen, Mapper<Region,Region> zoneMapper) { 
        super();
        
        Iterator<NamedRegion> chroms = new ChromRegionIterator(g);
        Iterator<Gene> genes = new ExpanderIterator<NamedRegion,Gene>(gen, chroms);
        
        TreeSet<Region> targetList = new TreeSet<Region>();
        while(genes.hasNext()) { 
            Gene gene = genes.next();
            if(!targetList.contains(gene)) { 
                targetList.add(gene);
            }
        }
        
        addItems(targetList);
    }
    
    private class AssignmentExpander<X extends Region> implements Expander<Region,Region> {
    	
    	private AssignmentPredicate pred;
    	private Expander<Region,X> exp;
    	private Mapper<Region,Region> queryMapper;
    	
    	public AssignmentExpander(AssignmentPredicate ap, Expander<Region,X> e) { 
    		pred = ap;
    		exp = e;
    		queryMapper = pred.assignmentZoneMapper();
    	}
    	
    	public Iterator<Region> execute(Region r) { 
    		Region query = queryMapper.execute(r);
    		Iterator<X> events = exp.execute(query);
    		Filter<X,Region> filter = new AssignmentPredicate.Filter(pred, r);
    		return new FilterIterator<X,Region>(filter, events);
    	}
    }
    
}