ContinuousTreeToProcessing.java

package templates;

import java.io.FileReader;
import java.io.IOException;
import java.util.List;

import jebl.evolution.graphs.Node;
import jebl.evolution.io.ImportException;
import jebl.evolution.io.NexusImporter;
import jebl.evolution.io.TreeImporter;
import jebl.evolution.trees.RootedTree;
import processing.core.PApplet;
import structure.Coordinates;
import utils.Utils;

@SuppressWarnings("serial")
public class ContinuousTreeToProcessing extends PApplet {

	private TreeImporter importer;
	private RootedTree tree;
	private String longitudeName;
	private String latitudeName;
	private double treeHeightMax;
	private String HPDString;
	private MapBackground mapBackground;

	private double minPolygonRedMapping;
	private double minPolygonGreenMapping;
	private double minPolygonBlueMapping;
	private double minPolygonOpacityMapping;

	private double maxPolygonRedMapping;
	private double maxPolygonGreenMapping;
	private double maxPolygonBlueMapping;
	private double maxPolygonOpacityMapping;

	private double minBranchRedMapping;
	private double minBranchGreenMapping;
	private double minBranchBlueMapping;
	private double minBranchOpacityMapping;

	private double maxBranchRedMapping;
	private double maxBranchGreenMapping;
	private double maxBranchBlueMapping;
	private double maxBranchOpacityMapping;

	private double branchWidth;

	// min/max longitude
	private float minX, maxX;
	// min/max latitude
	private float minY, maxY;

	public ContinuousTreeToProcessing() {
	}// END:ContinuousTreeToProcessing

	public void setHPDString(String HPDString) {
		this.HPDString = HPDString;
	}

	public void setLongitudeName(String name) {
		longitudeName = name;
	}
	
	public void setLatitudeName(String name) {
		latitudeName = name;
	}

	public void setTreePath(String path) throws IOException, ImportException {

		importer = new NexusImporter(new FileReader(path));
		tree = (RootedTree) importer.importNextTree();
		// this is for mappings
		treeHeightMax = Utils.getTreeHeightMax(tree);
	}

	public void setMinPolygonRedMapping(double min) {
		minPolygonRedMapping = min;
	}

	public void setMinPolygonGreenMapping(double min) {
		minPolygonGreenMapping = min;
	}

	public void setMinPolygonBlueMapping(double min) {
		minPolygonBlueMapping = min;
	}

	public void setMinPolygonOpacityMapping(double min) {
		minPolygonOpacityMapping = min;
	}

	public void setMaxPolygonRedMapping(double max) {
		maxPolygonRedMapping = max;
	}

	public void setMaxPolygonGreenMapping(double max) {
		maxPolygonGreenMapping = max;
	}

	public void setMaxPolygonBlueMapping(double max) {
		maxPolygonBlueMapping = max;
	}

	public void setMaxPolygonOpacityMapping(double max) {
		maxPolygonOpacityMapping = max;
	}

	public void setMinBranchRedMapping(double min) {
		minBranchRedMapping = min;
	}

	public void setMinBranchGreenMapping(double min) {
		minBranchGreenMapping = min;
	}

	public void setMinBranchBlueMapping(double min) {
		minBranchBlueMapping = min;
	}

	public void setMinBranchOpacityMapping(double min) {
		minBranchOpacityMapping = min;
	}

	public void setMaxBranchRedMapping(double max) {
		maxBranchRedMapping = max;
	}

	public void setMaxBranchGreenMapping(double max) {
		maxBranchGreenMapping = max;
	}

	public void setMaxBranchBlueMapping(double max) {
		maxBranchBlueMapping = max;
	}

	public void setMaxBranchOpacityMapping(double max) {
		maxBranchOpacityMapping = max;
	}

	public void setBranchWidth(double width) {
		branchWidth = width;
	}

	public void setup() {

		minX = -180;
		maxX = 180;

		minY = -90;
		maxY = 90;

		mapBackground = new MapBackground(this);

	}// END:setup

	public void draw() {

		smooth();
		mapBackground.drawMapBackground();
		drawPolygons();
		drawBranches();

	}// END:draw

	// ////////////////
	// ---BRANCHES---//
	// ////////////////
	
	private void drawBranches() {

		strokeWeight((float) branchWidth);

		for (Node node : tree.getNodes()) {
			if (!tree.isRoot(node)) {

				Double longitude = (Double) node.getAttribute(longitudeName);

				Double latitude = (Double) node.getAttribute(latitudeName);

				Double nodeHeight = Utils.getNodeHeight(tree, node);

				Node parentNode = tree.getParent(node);

				Double parentLongitude = (Double) parentNode
						.getAttribute(longitudeName);

				Double parentLatitude = (Double) parentNode
						.getAttribute(latitudeName);

				if (longitude != null && latitude != null
						&& parentLongitude != null && parentLatitude != null) {

					// Equirectangular projection:
					double x0 = Utils
							.map(parentLongitude, minX, maxX, 0, width);
					double y0 = Utils
							.map(parentLatitude, maxY, minY, 0, height);

					double x1 = Utils.map(longitude, minX, maxX, 0, width);
					double y1 = Utils.map(latitude, maxY, minY, 0, height);

					/**
					 * Color mapping
					 * */
					int red = (int) Utils.map(nodeHeight, 0, treeHeightMax,
							minBranchRedMapping, maxBranchRedMapping);

					int green = (int) Utils.map(nodeHeight, 0, treeHeightMax,
							minBranchGreenMapping, maxBranchGreenMapping);

					int blue = (int) Utils.map(nodeHeight, 0, treeHeightMax,
							minBranchBlueMapping, maxBranchBlueMapping);

					int alpha = (int) Utils.map(nodeHeight, 0, treeHeightMax,
							maxBranchOpacityMapping, minBranchOpacityMapping);

					stroke(red, green, blue, alpha);

					line((float) x0, (float) y0, (float) x1, (float) y1);

				}// END: null check
			}// END: root check
		}// END: nodes loop
	}// END: DrawBranches

	// ////////////////
	// ---POLYGONS---//
	// ////////////////
	private void drawPolygons() {

		String modalityAttributeName = Utils.getModalityAttributeName(longitudeName, HPDString);
		
		for (Node node : tree.getNodes()) {
			if (!tree.isRoot(node)) {
				if (!tree.isExternal(node)) {

					Integer modality = (Integer) node
							.getAttribute(modalityAttributeName);

					if (modality != null) {

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

							Object[] longitudeHPD = Utils
									.getObjectArrayNodeAttribute(node,
											longitudeName + "_" + HPDString
													+ "_" + i);
							
							Object[] latitudeHPD = Utils
									.getObjectArrayNodeAttribute(node,
											latitudeName + "_" + HPDString
													+ "_" + i);
							
							/**
							 * Color mapping
							 * */
							double nodeHeight = Utils.getNodeHeight(tree, node);

							int red = (int) Utils.map(nodeHeight, 0,
									treeHeightMax, minPolygonRedMapping,
									maxPolygonRedMapping);

							int green = (int) Utils.map(nodeHeight, 0,
									treeHeightMax, minPolygonGreenMapping,
									maxPolygonGreenMapping);

							int blue = (int) Utils.map(nodeHeight, 0,
									treeHeightMax, minPolygonBlueMapping,
									maxPolygonBlueMapping);

							int alpha = (int) Utils.map(nodeHeight, 0,
									treeHeightMax, maxPolygonOpacityMapping,
									minPolygonOpacityMapping);

							stroke(red, green, blue, alpha);
							fill(red, green, blue, alpha);

							List<Coordinates> coordinates = Utils
									.parsePolygons(longitudeHPD, latitudeHPD);

							beginShape();

							for (int row = 0; row < coordinates.size() - 1; row++) {

								double X = Utils.map(coordinates.get(row)
										.getLongitude(), minX, maxX, 0, width);
								double Y = Utils.map(coordinates.get(row)
										.getLatitude(), maxY, minY, 0, height);

								double XEND = Utils.map(coordinates
										.get(row + 1).getLongitude(), minX,
										maxX, 0, width);
								double YEND = Utils.map((coordinates
										.get(row + 1).getLatitude()), maxY,
										minY, 0, height);

								vertex((float) X, (float) Y);
								vertex((float) XEND, (float) YEND);

							}// END: coordinates loop

							endShape(CLOSE);

						}// END: modality loop
					}// END: null check
				}// END: external node check
			}// END: root check
		}// END: node loop
	}// END: drawPolygons

}// END: PlotOnMap class