X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FtemplateEditor%2FTemplatePanel.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FtemplateEditor%2FTemplatePanel.java;h=ce477169495faaaf5f61129e4828d0810bc6f2c3;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=0000000000000000000000000000000000000000;hpb=056dad85a910551cc95e44d451a61f6b8c4dd35d;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/applications/templateEditor/TemplatePanel.java b/srcjar/fr/orsay/lri/varna/applications/templateEditor/TemplatePanel.java
new file mode 100644
index 0000000..ce47716
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/applications/templateEditor/TemplatePanel.java
@@ -0,0 +1,662 @@
+/**
+ * 
+ */
+package fr.orsay.lri.varna.applications.templateEditor;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.Polygon;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Stack;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.undo.UndoManager;
+
+import fr.orsay.lri.varna.applications.templateEditor.GraphicalTemplateElement.RelativePosition;
+import fr.orsay.lri.varna.controlers.ControleurMolette;
+import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate;
+import fr.orsay.lri.varna.exceptions.ExceptionXmlLoading;
+import fr.orsay.lri.varna.models.templates.RNATemplate;
+import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement;
+import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix;
+import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence;
+import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint;
+
+
+
+
+/**
+ * @author ponty
+ *
+ */
+public class TemplatePanel extends JPanel {
+  /**
+	 * 
+	 */
+	private static final long serialVersionUID = 3162771335587335679L;
+	
+	
+	private ArrayList<GraphicalTemplateElement> _RNAComponents;
+	private ArrayList<Connection> _RNAConnections;
+	private Hashtable<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Connection> _helixToConnection;
+	private TemplateEditorPanelUI _ui;
+	
+	private RNATemplate _template;
+
+	
+	private static Color[] BackgroundColors = {Color.blue,Color.red,Color.cyan,Color.green,Color.lightGray,Color.magenta,Color.PINK};
+
+	private int _nextBackgroundColor = 0;
+	
+	private static double scaleFactorDefault = 0.7;
+	private double scaleFactor = scaleFactorDefault;
+	
+	
+	private TemplateEditor _editor;
+	
+	
+	public double getScaleFactor() {
+		return scaleFactor;
+	}
+
+	public void setScaleFactor(double scaleFactor) {
+		this.scaleFactor = scaleFactor;
+	}
+
+	public Color nextBackgroundColor()
+	{
+		Color c = BackgroundColors[_nextBackgroundColor++];
+		_nextBackgroundColor = _nextBackgroundColor % BackgroundColors.length;
+		return new Color(c.getRed(),c.getBlue(),c.getGreen(),50);
+	}
+	
+	public TemplatePanel(TemplateEditor parent)
+	{
+		_editor = parent;
+		init();
+	}
+
+	public RNATemplate getTemplate()
+	{
+		return _template;
+	}
+	
+	List<GraphicalTemplateElement> getRNAComponents() {
+		return _RNAComponents;
+	}
+	
+	private void init()
+	{
+		_ui = new TemplateEditorPanelUI(this); 
+		
+		_RNAComponents = new ArrayList<GraphicalTemplateElement>();
+		_RNAConnections = new ArrayList<Connection>();
+		_helixToConnection = new Hashtable<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Connection>();
+		
+		_template = new RNATemplate();
+		
+		setBackground(Color.WHITE);
+		MouseControler mc = new MouseControler(this,_ui); 
+		addMouseListener(mc);
+		addMouseMotionListener(mc);
+		addMouseWheelListener(mc);
+		_solidStroke = new BasicStroke(1.5f, BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND, 3.0f);
+		float[] dash = { 5.0f, 5.0f };
+		_dashedStroke = new BasicStroke(1.5f, BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND, 3.0f, dash, 0);
+	}
+	
+	public void addUndoableEditListener(UndoManager manager)
+	{
+		_ui.addUndoableEditListener(manager);
+	}
+	
+	public TemplateEditorPanelUI getTemplateUI()
+	{
+		return _ui;
+	}
+
+	
+	public void flip(Helix h)
+	{ 
+		h.toggleFlipped(); 
+	}
+	
+	public void addElement(GraphicalTemplateElement h)
+	{ 
+		_RNAComponents.add(h); 
+	}
+
+	public void removeElement(GraphicalTemplateElement h)
+	{ 
+		_RNAComponents.remove(h);
+		try {
+			_template.removeElement(h.getTemplateElement());
+		} catch (ExceptionInvalidRNATemplate e) {
+			//e.printStackTrace();
+		}
+	}
+
+	private GraphicalTemplateElement _selected = null;
+	
+	public GraphicalTemplateElement getSelected()
+	{
+		return _selected;
+	}
+
+	public void setSelected(GraphicalTemplateElement sel)
+	{
+		_selected = sel;
+		if (_selected instanceof Helix) {
+			_editor.flipButtonEnable();
+		} else {
+			_editor.flipButtonDisable();
+		}
+	}
+
+	Helix.RelativePosition _relpos = Helix.RelativePosition.RP_OUTER;
+	
+	public void setSelectedEdge(Helix.RelativePosition rel)
+	{
+		_relpos = rel;
+	}
+
+	public void unselectEdge(Helix.RelativePosition rel)
+	{
+		_relpos = rel;
+	}
+	
+	Point2D.Double _mousePos = new Point2D.Double();
+
+	public void setPointerPos(Point2D.Double p)
+	{
+		_mousePos = p;
+	}	
+	
+	public void Unselect()
+	{
+		_editor.flipButtonDisable();
+		_selected = null;
+	}
+
+	public GraphicalTemplateElement getElement(RNATemplateElement t)
+	{
+		for(GraphicalTemplateElement t2: _RNAComponents)
+			if (t==t2.getTemplateElement())
+				return t2;
+		return null;
+	}
+
+	
+	public GraphicalTemplateElement getElementAt(double x, double y)
+	{
+		return getElementAt(x, y, null);
+	}
+	public GraphicalTemplateElement getElementAt(double x, double y, GraphicalTemplateElement excluded)
+	{
+		GraphicalTemplateElement h = null;
+		for (int i=0; i<_RNAComponents.size();i++)
+		{
+			GraphicalTemplateElement h2 = _RNAComponents.get(i);
+			if ((
+					   (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_END3)
+					|| (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_END5)
+					|| (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_START3)
+					|| (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_START5))
+				&& (excluded!=h2))
+			{
+				h = h2;
+			}
+		}
+		if (h==null)
+		{ h = getElementCloseTo(x, y, excluded);};
+		return h;
+	}
+
+	public GraphicalTemplateElement getElementCloseTo(double x, double y)
+	{
+		return getElementCloseTo(x, y, null);
+	}
+	public GraphicalTemplateElement getElementCloseTo(double x, double y, GraphicalTemplateElement excluded)
+	{
+		GraphicalTemplateElement h = null;
+		for (int i=0; i<_RNAComponents.size();i++)
+		{
+			GraphicalTemplateElement h2 = _RNAComponents.get(i);
+			if ((h2.getRelativePosition(x, y) != Helix.RelativePosition.RP_OUTER)
+				&& (excluded!=h2))
+			{
+				h = h2;
+			}
+		}
+		return h;
+	}
+	
+	public void addConnection(Connection c)
+	{
+		_RNAConnections.add(c);
+		_helixToConnection.put(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h1,c._edge1), c);
+		_helixToConnection.put(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h2,c._edge2), c);
+			try {
+				c._h1.attach(c._h2, c._edge1, c._edge2);
+				c._h2.attach(c._h1, c._edge2, c._edge1);
+			} catch (ExceptionInvalidRNATemplate e) {
+				System.out.println(e.toString());// TODO Auto-generated catch block
+		}
+
+	}
+
+	public Connection addConnection(GraphicalTemplateElement h1, GraphicalTemplateElement.RelativePosition edge1,GraphicalTemplateElement h2, GraphicalTemplateElement.RelativePosition edge2)
+	{
+		if ((h1!=h2)&&(getPartner(h1,edge1)==null)&&(getPartner(h2,edge2)==null))
+		{
+			Connection c = new Connection(h1,edge1,h2,edge2);
+			addConnection(c);
+			return c;
+		}
+		return null;
+	}
+	
+	/**
+	 * When there is already a connection in the underlying RNATemplate
+	 * and we want to create one at the graphical level.
+	 */
+	public void addGraphicalConnection(GraphicalTemplateElement h1, GraphicalTemplateElement.RelativePosition edge1,GraphicalTemplateElement h2, GraphicalTemplateElement.RelativePosition edge2) {
+		//System.out.println("Connecting " + h1 + " " + edge1 + " to " + h2 + " " + edge2);
+		Connection c = new Connection(h1,edge1,h2,edge2);
+		_RNAConnections.add(c);
+		_helixToConnection.put(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h1,c._edge1), c);
+		_helixToConnection.put(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h2,c._edge2), c);
+		c._h1.graphicalAttach(c._h2, c._edge1, c._edge2);
+		c._h2.graphicalAttach(c._h1, c._edge2, c._edge1);
+	}
+	
+
+	public void removeConnection(Connection c)
+	{
+		_RNAConnections.remove(c);
+		_helixToConnection.remove(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h1,c._edge1));
+		_helixToConnection.remove(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h2,c._edge2));
+		System.out.println("[A]"+c);
+		c._h1.detach(c._edge1);
+	}
+	
+	public boolean isInCycle(GraphicalTemplateElement el, GraphicalTemplateElement.RelativePosition edge)
+	{
+		Stack<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> > p = new Stack<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>>();
+		Hashtable<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer> alreadySeen = new Hashtable<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer>(); 
+		p.add(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(el,edge));
+		while(!p.empty())
+		{
+			Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> c2 = p.pop();
+			if (alreadySeen.containsKey(c2))
+			{
+				return true;
+			}
+			else
+			{
+				alreadySeen.put(c2, new Integer(1));
+			}
+			GraphicalTemplateElement.RelativePosition next = c2.first.getConnectedEdge(c2.second);
+			Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> otherEnd = new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c2.first,next);
+			if (!alreadySeen.containsKey(otherEnd))
+			{
+				p.push(otherEnd);
+			}
+			else
+			{
+				Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> child =  getPartner(c2.first,c2.second);
+				if (child!=null)
+				{
+					p.push(child);
+				}
+			}
+			
+		}
+		
+		return false;	
+	}
+	
+	private static Color[] _colors = {Color.gray,Color.pink,Color.cyan,Color.RED,Color.green,Color.orange};
+	
+	public static Color getIndexedColor(int n)
+	{
+		return _colors[n%_colors.length];
+	}
+	
+	public HashMap<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer> buildConnectedComponents()
+	{
+		HashMap<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer> alreadySeen = new HashMap<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer>();
+		int numConnectedComponents = 0;
+		for (GraphicalTemplateElement el : this._RNAComponents)
+		{
+			for (GraphicalTemplateElement.RelativePosition edge : el.getConnectedEdges())
+			{
+				Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> c = new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(el,edge);
+				if (!alreadySeen.containsKey(c))
+				{
+					Stack<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> > p = new Stack<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>>();
+					p.add(c);
+					p.add(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(el,el.getConnectedEdge(edge)));
+					while(!p.empty())
+					{
+						Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> c2 = p.pop();
+						if (!alreadySeen.containsKey(c2))
+						{
+							//System.out.println("  "+numConnectedComponents+"  "+c2);
+							c2.first.setMainColor(c2.second, getIndexedColor(numConnectedComponents));
+							alreadySeen.put(c2, new Integer(numConnectedComponents));
+							GraphicalTemplateElement.RelativePosition next = c2.first.getConnectedEdge(c2.second);
+							Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> otherEnd = new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c2.first,next);
+							p.push(otherEnd);
+							Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> child =  getPartner(c2.first,c2.second);
+							if (child!=null)
+							{ p.push(child); }
+						}	
+					}
+					numConnectedComponents += 1;
+				}
+			}
+		}
+		return alreadySeen;
+	}
+	
+	public boolean isInCycle(Connection c)
+	{
+		return isInCycle(c._h1,c._edge1); 
+	}
+	
+	public Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> getPartner(GraphicalTemplateElement h, GraphicalTemplateElement.RelativePosition edge)
+	{
+		Connection c = getConnection(h, edge);
+		if (c != null)
+		{
+			  if ((c._h1==h)&&(c._edge1==edge))
+			  {  return new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h2,c._edge2);  }
+			  else 
+			  {  return new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h1,c._edge1); }
+		}
+		else
+		{
+			return null;
+		}
+	}
+
+	public Connection getConnection(GraphicalTemplateElement h, Helix.RelativePosition edge)
+	{
+		Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> target = new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(h,edge);
+		if (_helixToConnection.containsKey(target))
+		{
+			return _helixToConnection.get(target);
+		}
+		else
+		{ return null; }
+	}
+	
+	private boolean isConnected(Helix h, GraphicalTemplateElement.RelativePosition edge)
+	{
+		Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> partner = getPartner(h,edge);
+		return partner!=null;
+	}
+	
+
+	// Aspects graphiques
+	
+	private static final Color  CYCLE_COLOR = Color.red;
+	private static final Color  NON_EXISTANT_COLOR = Color.gray.brighter();
+	private static final Color  CONTROL_COLOR = Color.gray.darker();
+	private static final Color  BACKGROUND_COLOR = Color.white;
+	
+	private Stroke  _solidStroke;
+	private Stroke  _dashedStroke;
+	
+
+	
+	
+	private void drawConnections(Graphics2D g2d, Connection c)
+	{
+		GraphicalTemplateElement h1 = c._h1;
+		GraphicalTemplateElement.RelativePosition edge1 = c._edge1;
+		Point2D.Double p1 = h1.getEdgePosition(edge1);
+		GraphicalTemplateElement h2 = c._h2;
+		GraphicalTemplateElement.RelativePosition edge2 = c._edge2;
+		Point2D.Double p2 = h2.getEdgePosition(edge2);
+		if (isInCycle(c))
+		{
+			g2d.setColor(CYCLE_COLOR);
+		}
+		else
+		{
+			g2d.setColor(GraphicalTemplateElement.BACKBONE_COLOR);
+		}
+		g2d.drawLine((int)p1.x,(int)p1.y,(int)p2.x,(int)p2.y);
+	}
+	
+
+	public void paintComponent(Graphics g)
+	{
+		//rescale();
+		
+		// Debug code to show drawing area
+//		g.setColor(Color.red);
+//		g.fillRect(0,0,getWidth(),getHeight());
+//		g.setColor(Color.white);
+//		g.fillRect(10,10,getWidth()-20,getHeight()-20);
+		
+		g.setColor(Color.white);
+		g.fillRect(0,0,getWidth(),getHeight());
+		
+		Graphics2D g2d = (Graphics2D) g;
+		g2d.scale(scaleFactor, scaleFactor);
+		g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+				RenderingHints.VALUE_ANTIALIAS_ON);
+		removeAll();
+		//super.paintComponent(g2d);
+
+		buildConnectedComponents();
+		
+		if (_selected!=null)
+		{
+			if (_relpos != GraphicalTemplateElement.RelativePosition.RP_OUTER)
+			{	
+			Point2D.Double p = _selected.getEdgePosition(_relpos);
+			g2d.setStroke(_solidStroke);
+			g2d.drawLine((int)_mousePos.x, (int)_mousePos.y, (int)p.x, (int)p.y);
+			}
+		}
+		for (int i=0;i<_RNAConnections.size();i++)
+		{
+			Connection c = _RNAConnections.get(i);
+			drawConnections(g2d,c);
+		}
+		for (int i=0;i<_RNAComponents.size();i++)
+		{
+			GraphicalTemplateElement elem = _RNAComponents.get(i);
+			//g2d.setColor(elem.getDominantColor());
+			//g2d.fill(elem.getArea());
+			if (_selected == elem)
+			{  
+				elem.draw(g2d,true); 
+			}
+			else
+			{  elem.draw(g2d,false);  }
+		}
+	}
+	
+	/**
+	 * Get the bounding rectangle of the RNA components, always including the origin (0,0).
+	 */
+	public Rectangle getBoundingRectange() {
+		int minX = 0;
+		int maxX = 0;
+		int minY = 0;
+		int maxY = 0;
+		for(int i=0;i<this._RNAComponents.size();i++)
+		{
+			GraphicalTemplateElement h = _RNAComponents.get(i);
+			Polygon p = h.getBoundingPolygon();
+			Rectangle r = p.getBounds();
+			minX = Math.min(minX,r.x);
+			maxX = Math.max(maxX,r.x+r.width);
+			minY = Math.min(minY,r.y);
+			maxY = Math.max(maxY,r.y+r.height);
+		}
+		Rectangle res = new Rectangle();
+		res.x = minX;
+		res.y = minY;
+		res.width = maxX - minX;
+		res.height = maxY - minY;
+		return res;
+	}
+
+	public void rescale()
+	{
+		Rectangle rect = getBoundingRectange();
+		
+		if (rect.x < 0 || rect.y < 0) {
+            for(int i=0;i<this._RNAComponents.size();i++)
+            {
+                    GraphicalTemplateElement h = _RNAComponents.get(i);
+                    h.translate(rect.x<0 ? -rect.x : 0, rect.y<0 ? -rect.y : 0);
+            }
+            rect = getBoundingRectange();
+		}
+		
+		// areaW and H are width and height, in pixels, of the drawing area
+		// including the "outside" parts available with scrolling
+		int areaW = (int) ((rect.width + 100) * scaleFactor);
+		int areaH = (int) ((rect.height + 100) * scaleFactor);
+		// make it cover at least the space visible in the window
+		//areaW = Math.max(areaW, (int) (_editor.getJp().getViewport().getViewSize().width));
+		//areaH = Math.max(areaH, (int) (_editor.getJp().getViewport().getViewSize().height));
+		//System.out.println(areaW + " x " + areaH);
+		setPreferredSize(new Dimension(areaW, areaH));
+		revalidate();
+	}
+
+	public void clearTemplate() {
+		loadTemplate(new RNATemplate());
+	}
+
+	/**
+	 * Load an existing RNATemplate object in this panel.
+	 */
+	public void loadTemplate(RNATemplate template) {
+		_template = template;
+		_RNAComponents.clear();
+		_RNAConnections.clear();
+		_helixToConnection.clear();
+		
+		// We need a template element -> graphical template element mapping
+		Map<RNATemplateElement, GraphicalTemplateElement> map = new HashMap<RNATemplateElement, GraphicalTemplateElement>();
+		
+		// First, we load elements
+		{
+			Iterator<RNATemplateElement> iter = template.classicIterator();
+			while (iter.hasNext()) {
+				RNATemplateElement templateElement = iter.next();
+				if (templateElement instanceof RNATemplateHelix) {
+					RNATemplateHelix templateHelix = (RNATemplateHelix) templateElement;
+					Helix graphicalHelix = new Helix(templateHelix);
+					graphicalHelix.setDominantColor(nextBackgroundColor());
+					_RNAComponents.add(graphicalHelix);
+					map.put(templateHelix, graphicalHelix);
+				} else if (templateElement instanceof RNATemplateUnpairedSequence) {
+					RNATemplateUnpairedSequence templateSequence = (RNATemplateUnpairedSequence) templateElement;
+					UnpairedRegion graphicalSequence = new UnpairedRegion(templateSequence);
+					graphicalSequence.setDominantColor(nextBackgroundColor());
+					_RNAComponents.add(graphicalSequence);
+					map.put(templateSequence, graphicalSequence);
+				}
+			}
+		}
+		
+		// Now, we load edges
+		{
+			Iterator<EdgeEndPoint> iter = template.makeEdgeList().iterator();
+			while (iter.hasNext()) {
+				EdgeEndPoint v1 = iter.next();
+				EdgeEndPoint v2 = v1.getOtherEndPoint();
+				GraphicalTemplateElement gte1 = map.get(v1.getElement());
+				GraphicalTemplateElement gte2 = map.get(v2.getElement());
+				RelativePosition rp1 = gte1.relativePositionFromEdgeEndPointPosition(v1.getPosition());
+				RelativePosition rp2 = gte2.relativePositionFromEdgeEndPointPosition(v2.getPosition());
+				addGraphicalConnection(gte1, rp1, gte2, rp2);
+			}
+		}
+		
+		zoomFit();
+		//repaint();
+	}
+
+	/**
+	 * Load a template from an XML file.
+	 */
+	public void loadFromXmlFile(File filename) {
+		try {
+			RNATemplate newTemplate = RNATemplate.fromXMLFile(filename);
+			loadTemplate(newTemplate);
+		} catch (ExceptionXmlLoading e) {
+			e.printStackTrace();
+			JOptionPane.showMessageDialog(this, e.getMessage(), "Template loading error", JOptionPane.ERROR_MESSAGE);
+		}
+	}
+	
+	private void zoomFinish() {
+		rescale();
+		repaint();
+	}
+	
+	public void zoomIn() {
+		scaleFactor *= 1.2;
+		zoomFinish();
+	}
+	
+	public void zoomOut() {
+		scaleFactor /= 1.2;
+		zoomFinish();
+	}
+	
+	public void zoomReset() {
+		scaleFactor = scaleFactorDefault;
+		zoomFinish();
+	}
+	
+	public void zoomFit() {
+		if (_RNAComponents.isEmpty()) {
+			zoomReset();
+		} else {
+			Rectangle rect = getBoundingRectange();
+			double areaW = (rect.width + 100);
+			double areaH = (rect.height + 100);
+			// make it cover at least the space visible in the window
+			scaleFactor = 1;
+			scaleFactor = Math.min(scaleFactor, _editor.getJp().getViewport().getSize().width / areaW);
+			scaleFactor = Math.min(scaleFactor, _editor.getJp().getViewport().getSize().height / areaH);
+			zoomFinish();
+		}
+	}
+	
+	public void translateView(Point trans) {
+		int newX = _editor.getJp().getHorizontalScrollBar().getValue() - trans.x;
+		int newY = _editor.getJp().getVerticalScrollBar().getValue() - trans.y;
+		newX = Math.max(0, Math.min(newX, _editor.getJp().getHorizontalScrollBar().getMaximum()));
+		newY = Math.max(0, Math.min(newY, _editor.getJp().getVerticalScrollBar().getMaximum()));
+		_editor.getJp().getHorizontalScrollBar().setValue(newX);
+		_editor.getJp().getVerticalScrollBar().setValue(newY);
+	}
+}