InteractionArcModel.java

package org.seqcode.projects.seqview.model;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.seqcode.data.readdb.Client;
import org.seqcode.data.readdb.ClientException;
import org.seqcode.data.readdb.PairedHit;
import org.seqcode.data.readdb.PairedHitLeftComparator;
import org.seqcode.data.seqdata.SeqAlignment;
import org.seqcode.genome.location.Region;


public class InteractionArcModel extends SeqViewModel implements RegionModel, Runnable {

	private Client client;
	private Set<SeqAlignment> alignments;
	private Set<String> ids;
	private Region region;
	private boolean newinput;
	private List<PairedHit> results, otherchrom;
	private Comparator<PairedHit> comparator;
	private InteractionArcModelProperties props;

	public InteractionArcModel(Collection<SeqAlignment> alignments) throws IOException, ClientException {
		client = new Client();
		comparator = new PairedHitLeftComparator();
		this.alignments = new HashSet<SeqAlignment>();
		this.alignments.addAll(alignments);
		ids = new HashSet<String>();
		for (SeqAlignment a : alignments) {
			ids.add(Integer.toString(a.getDBID()));
			if(!client.exists(Integer.toString(a.getDBID()))){
            	System.err.println("SeqHistogramModel: Error: "+a.getExpt().getName()+";"+a.getExpt().getReplicate()+";"+a.getName()+"\tRDBID:"+a.getDBID()+" does not exist in ReadDB.");
            	dataError=true;
            }
		}
		results = null;
		otherchrom = null;
		props = new InteractionArcModelProperties();
	}

	public InteractionArcModelProperties getProperties() {return props;}

	public void clearValues() {
		results = null;
		otherchrom = null;
	}
	
	public boolean isReady() {return !newinput;}

	public synchronized void run() {
		while(keepRunning()) {
			try {
				if (!newinput) {
					wait();
				}
			} catch (InterruptedException ex) { }
			if (newinput) {
				try {
					HashMap<PairedHit, Float> deduper = new HashMap<PairedHit, Float>();  
					results = new ArrayList<PairedHit>();
					otherchrom = new ArrayList<PairedHit>();
					for (String alignid : ids) {
						List<PairedHit> r = client.getPairedHits(alignid,
								region.getGenome().getChromID(region.getChrom()),
								true,
								region.getStart(),
								region.getEnd(),
								null,
								null);
						for (PairedHit h : r) {
							if(!deduper.containsKey(h)){ deduper.put(h, h.weight);
							}else{float currw = deduper.get(h); deduper.put(h, currw+h.weight);} 
								
							if(props.ArcDeDuplicate>0 && deduper.get(h)<=props.ArcDeDuplicate){
								if (h.leftChrom == h.rightChrom) { 
									if (h.rightPos >= region.getStart() &&
											h.rightPos <= region.getEnd()) {
										results.add(h);
									}
								} else {
									otherchrom.add(h);
								}
							}
						}
					}
					for (PairedHit h : results) {
						if (h.leftPos > h.rightPos) {
							h.flipSides();
						}
					}
					Collections.sort(results, comparator);
					Collections.sort(otherchrom, comparator);
				} catch (Exception ex) {
					ex.printStackTrace();
					// assign empty output.  This is useful because Client
					// throws an exception for non-existant chromosomes, such
					// as those for which there were no alignment results
					results = new ArrayList<PairedHit>();
				}
				newinput = false;
				notifyListeners();
			}
		}
		client.close();
	}

	public void setRegion(Region r) {
		if (newinput == false) {
			if (!r.equals(region)) {
				region = r;
				newinput = true;
			} else {
				notifyListeners();
			}
		}
	}
	public void resetRegion(Region r) {
		if (newinput == false) {
			region = r;
			newinput = true;
		}
	}

	public Region getRegion() {return region;}

	public List<PairedHit> getResults () {return results;}
	public List<PairedHit> getOtherChromResults() {return otherchrom;}

}