Nloc.java

package nloc;

import java.util.List;
import java.util.ArrayList;
import java.util.ListIterator;
import java.util.Arrays;

public class Nloc {

  public static final int MIN_TIMEDIFF = 6;
  private List<Channel> chanlist;
  private List<Droplet> dropletList;

  public Nloc (List<Channel> chanlist) {
    this.chanlist = chanlist;
    this.dropletList = new ArrayList<Droplet>();
  }

  public void addChannel(Channel chan) {
    chanlist.add(chan);
  }

  public Pump getPump() {
    Pump pump = null;
    for (Channel chan : chanlist) {
      if (chan instanceof Pump) pump = (Pump)chan;
    }
    return pump;
  }

  public boolean simulate() {
    boolean works = true;
    while (!allDropletsInSink()) {
      try {
        this.moveDroplets();
      } catch (CoalescedDropletException e) {
        works = false;
        System.out.println(e.getDroplet());
        break;
      }
    }
    return works;
  }

  public List<Droplet> getDropletList() {
    return dropletList;
  }

  public void moveDroplets() throws CoalescedDropletException {
    for (Droplet dr : dropletList) {
      dr.move();
    }
    for (Droplet dr: dropletList) {
      if (dr.coalesce()) throw new CoalescedDropletException(dr);
    }
  }

  public Pump generateDropletSequence(List<String> modules) 
    throws BifurcationTooShortException {

    Pump pump = this.getPump();

    int timediff = MIN_TIMEDIFF + 1;

    List<Channel> modPath = this.getModulesByName(modules);
    List<List<Channel>> pathlist = this.getAllPaths();
    List<Channel> desiredPath = getDesiredPath(modPath, pathlist);

    int noOfDroplets = this.getNumberOfDroplets(desiredPath);
    pump.setSteps(noOfDroplets + (noOfDroplets - 1) * timediff);

    for (int i = 0; i < noOfDroplets; i++){
      if (!pump.containsDroplets()) {
        dropletList.add(new Droplet(DropletType.PAYLOAD, 
            new Position(pump,1)));
      } else {
        dropletList.add(new Droplet(DropletType.HEADER, 
            new Position(pump,i + i * timediff + 1)));
      }
    }
    return pump;
  }

  public boolean allDropletsInSink() {
    boolean allInSink = true;
    for (Droplet dr : dropletList) {
      allInSink &= dr.isInSink();
    }
    return allInSink;
  }

  public int getNumberOfDroplets(List<Channel> desiredPath) 
    throws BifurcationTooShortException {

    int numOfDroplets = 1;
    ListIterator<Channel> iter = desiredPath.listIterator();
    while(iter.hasNext()) {
      Channel current = iter.next();
      if (current.isBifurcation()) {
        Channel following = iter.next();
        int neededMinLength = numOfDroplets * Nloc.MIN_TIMEDIFF + 
          numOfDroplets - 1;
        int prio = current.getChildrenList().indexOf(following) + 1;
        iter.previous();

        for (int i = 1; i < prio; i++) {

          int bifurcChildHSteps = current.getChildrenList().get(i).getHSteps();
          if (bifurcChildHSteps < neededMinLength) {
            throw new BifurcationTooShortException(current, neededMinLength);
          }
        } 
        numOfDroplets *= (current.getChildrenList().indexOf(following) + 1);
      }
    }
    return numOfDroplets;
  }

  public List<Channel> getDesiredPath(List<Channel> modules,
      List<List<Channel>> pathlist) {
    List<Channel> found = new ArrayList<Channel>();
    for (List<Channel> path : pathlist) {
      if (path.containsAll(modules)) {
        found = path;
      }
    }
    return found;
  }

  private List<Channel> getModulesByName(List<String> names) {
    List<Channel> ret = new ArrayList<Channel>();
    for (String name : names) {
      for (Channel ch : chanlist) {
        if (ch instanceof Module && ch.getName().equals(name)) {
          ret.add(ch);
        } 
      }
    }
    return ret;
  }

  public List<List<Channel>> getAllPaths() {
    List<List<Channel>> pl = new ArrayList<List<Channel>>();
    List<Channel> path = new ArrayList<Channel>();
    getAllPathsRecursive(this.getPump(), path, pl);
    return pl;
  }

  private void getAllPathsRecursive(Channel chan, List<Channel> path, List<List<Channel>> pathlist) {
    path.add(chan);
    if (chan.getChildrenList().isEmpty()) { 
      pathlist.add(path);
    } else {
      for (Channel ch : chan.getChildrenList()) {
        getAllPathsRecursive(ch, new ArrayList<Channel>(path), pathlist);
      }
    }
  }

}