gt: 		for (int i = 0; i < numOfTrees; ++i) {
context: /*
   * #%L
   * AnalyzeSkeleton_ plugin for ImageJ.
   * %%
   * Copyright (C) 2008 - 2016 Ignacio Arganda-Carreras.
   * %%
   * This program is free software: you can redistribute it and/or modify
   * it under the terms of the GNU General Public License as
   * published by the Free Software Foundation, either version 3 of the
   * License, or (at your option) any later version.
   * 
   * This program is distributed in the hope that it will be useful,
   * but WITHOUT ANY WARRANTY; without even the implied warranty of
   * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   * GNU General Public License for more details.
   * 
   * You should have received a copy of the GNU General Public
   * License along with this program.  If not, see
   * <http://www.gnu.org/licenses/gpl-3.0.html>.
   * #L%
   */
  package motiQ3D.skeleton_analysis;
  
  import java.util.ArrayList;
  
  /**
   * Utility class to transfer the analysis results between different plugins.
   * <p>
   * The meaning of its members should become clear when looking at
   * AnalyzeSkeleton_'s source code.
   *
   * @version 1.0 2009-12-17
   * @author Daniel Hornung <daniel.hornung@ds.mpg.de>
   */
  public class SkeletonResult
  {
  	int numOfTrees;
  
  	// skeleton tree fields
  	/** number of branches for every specific tree */
  	int[] numberOfBranches = null;
  	/** number of end points voxels of every tree */
  	int[] numberOfEndPoints = null;
  	/** number of junctions voxels of every tree*/
  	int[] numberOfJunctionVoxels = null;
  	/** number of slab voxels of every specific tree */
  	int[] numberOfSlabs = null;
  	/** number of junctions of every specific tree*/
  	int[] numberOfJunctions = null;
  	/** number of triple points in every tree */
  	int[] numberOfTriplePoints = null;
  	/** number of quadruple points in every tree */
  	int[] numberOfQuadruplePoints = null;
  	/** average branch length */
  	double[] averageBranchLength = null;
  	/** maximum branch length */
  	double[] maximumBranchLength = null;
  	/** total number of voxels of every tree */
  	int[] numberOfVoxels = null;
  
  	/** list of end point coordinates in the entire image */
  	ArrayList <Point> listOfEndPoints = null;
  	/** list of junction coordinates in the entire image */
  	ArrayList <Point> listOfJunctionVoxels = null;
  	/** list of slab coordinates in the entire image */
  	ArrayList <Point> listOfSlabVoxels = null;
  	/** list of slab coordinates in the entire image */
  	ArrayList <Point> listOfStartingSlabVoxels = null;
  
  	// Shortest path variables
  	/** list of longest shortest paths from the skeletons in the image */
  	ArrayList <Double> shortestPathList;
  	/** shortest path start position array */
  	double[][] spStartPosition;
  
  	/** array of graphs (one per tree) */
  	private Graph[] graph = null;
  
  
  	public SkeletonResult(int numOfTrees)
  	{
  		this.numOfTrees = numOfTrees;
  	}
  
  	// setter methods
  	public void setNumOfTrees(int numOfTrees)
  	{
  		this.numOfTrees = numOfTrees;
  	}
  
  	public void setBranches(int[] numberOfBranches)
  	{
  		this.numberOfBranches = numberOfBranches;
  	}
  
  	public void setJunctions(int[] numberOfJunctions)
  	{
  		this.numberOfJunctions = numberOfJunctions;
  	}
  
  	public void setEndPoints(int[] numberOfEndPoints)
  	{
  		this.numberOfEndPoints = numberOfEndPoints;
  	}
  
  	public void setJunctionVoxels(int[] numberOfJunctionVoxels)
  	{
  		this.numberOfJunctionVoxels = numberOfJunctionVoxels;
  	}
  
  	public void setSlabs(int[] numberOfSlabs)
  	{
  		this.numberOfSlabs = numberOfSlabs;
  	}
  
  	public void setNumberOfVoxels(int[] numberOfVoxels)
  	{
  		this.numberOfVoxels = numberOfVoxels;
  	}
  
  	public void setTriples(int[] numberOfTriplePoints)
  	{
  		this.numberOfTriplePoints = numberOfTriplePoints;
  	}
  
  	public void setQuadruples(int[] numberOfQuadruplePoints)
  	{
  		this.numberOfQuadruplePoints = numberOfQuadruplePoints;
  	}
  
  	public void setAverageBranchLength(double[] averageBranchLength)
  	{
  		this.averageBranchLength = averageBranchLength;
  	}
  
  	public void setMaximumBranchLength(double[] maximumBranchLength)
  	{
  		this.maximumBranchLength = maximumBranchLength;
  	}
  
  
  	public void setListOfEndPoints(ArrayList <Point> listOfEndPoints)
  	{
  		this.listOfEndPoints = listOfEndPoints;
  	}
  
  	public void setListOfJunctionVoxels(ArrayList <Point> listOfJunctionVoxels)
  	{
  		this.listOfJunctionVoxels = listOfJunctionVoxels;
  	}
  
  	public void setListOfSlabVoxels(ArrayList <Point> listOfSlabVoxels)
  	{
  		this.listOfSlabVoxels = listOfSlabVoxels;
  	}
  
  	public void setListOfStartingSlabVoxels(ArrayList <Point> listOfStartingSlabVoxels)
  	{
  		this.listOfStartingSlabVoxels = listOfStartingSlabVoxels;
  	}
  	public void setShortestPathList(ArrayList <Double> shortestPathList)
  	{
  		this.shortestPathList = shortestPathList;
  	}
  	public void setSpStartPosition(double[][] spStartPosition)
  	{
  		this.spStartPosition = spStartPosition;
  	}
  
  
  	public void setGraph(Graph[] graph)
  	{
  		this.graph = graph;
  	}
  
  
  
  	// getter methods
  	public int getNumOfTrees()
  	{
  		return numOfTrees;
  	}
  
  	public int[] getBranches()
  	{
  		return numberOfBranches;
  	}
  
  	public int[] getJunctions()
  	{
  		return numberOfJunctions;
  	}
  
  	public int[] getEndPoints()
  	{
  		return numberOfEndPoints;
  	}
  
  	public int[] getJunctionVoxels()
  	{
  		return numberOfJunctionVoxels;
  	}
  
  	public int[] getSlabs()
  	{
  		return numberOfSlabs;
  	}
  
  	public int[] getTriples()
  	{
  		return numberOfTriplePoints;
  	}
  
  	public int[] getQuadruples()
  	{
  		return numberOfQuadruplePoints;
  	}
  
  	public double[] getAverageBranchLength()
  	{
  		return averageBranchLength;
  	}
  
  	public double[] getMaximumBranchLength()
  	{
  		return maximumBranchLength;
  	}
  
  	public int[] getNumberOfVoxels()
  	{
  		return numberOfVoxels;
  	}
  
  
  	public ArrayList <Point> getListOfEndPoints()
  	{
  		return listOfEndPoints;
  	}
  
  	public ArrayList <Point> getListOfJunctionVoxels()
  	{
  		return listOfJunctionVoxels;
  	}
  
  	public ArrayList <Point> getListOfSlabVoxels()
  	{
  		return listOfSlabVoxels;
  	}
  
  	public ArrayList <Point> getListOfStartingSlabVoxels()
  	{
  		return listOfStartingSlabVoxels;
  	}
  
  	public ArrayList <Double> getShortestPathList()
  	{
  		return shortestPathList;
  	}
  
  	public double[][] getSpStartPosition()
  	{
  		return spStartPosition;
  	}
  
  
  	public Graph[] getGraph()
  	{
  		return graph;
  	}
  
  	// utility methods
  
  	/**
  	 * Calculates and saves the sum of voxels for every tree as the sum of end
  	 * points, junction voxels and "normal" voxels.
  	 * <p>
  	 *
  	 * numberOfEndPoints, numberOfJunctionVoxels and numberOfSlabs must exit
  	 * and have at least numOfTrees fields each.
  	 *
  	 * @return An array with the number of voxels in every tree
  	 */
  	public int[] calculateNumberOfVoxels()
  	{
  		numberOfVoxels = new int[numOfTrees];
  