srcjar/fr/orsay/lri/varna/applications/templateEditor/TemplatePanel.java

   1 /**
   2  *
   3  */
   4 package fr.orsay.lri.varna.applications.templateEditor;
   5
   6 import java.awt.BasicStroke;
   7 import java.awt.Color;
   8 import java.awt.Dimension;
   9 import java.awt.Graphics;
  10 import java.awt.Graphics2D;
  11 import java.awt.Point;
  12 import java.awt.Polygon;
  13 import java.awt.Rectangle;
  14 import java.awt.RenderingHints;
  15 import java.awt.Stroke;
  16 import java.awt.geom.Point2D;
  17 import java.io.File;
  18 import java.util.ArrayList;
  19 import java.util.HashMap;
  20 import java.util.Hashtable;
  21 import java.util.Iterator;
  22 import java.util.List;
  23 import java.util.Map;
  24 import java.util.Stack;
  25
  26 import javax.swing.JOptionPane;
  27 import javax.swing.JPanel;
  28 import javax.swing.undo.UndoManager;
  29
  30 import fr.orsay.lri.varna.applications.templateEditor.GraphicalTemplateElement.RelativePosition;
  31 import fr.orsay.lri.varna.controlers.ControleurMolette;
  32 import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate;
  33 import fr.orsay.lri.varna.exceptions.ExceptionXmlLoading;
  34 import fr.orsay.lri.varna.models.templates.RNATemplate;
  35 import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement;
  36 import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateHelix;
  37 import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateUnpairedSequence;
  38 import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement.EdgeEndPoint;
  39
  40
  41
  42
  43 /**
  44  * @author ponty
  45  *
  46  */
  47 public class TemplatePanel extends JPanel {
  48   /**
  49          *
  50          */
  51         private static final long serialVersionUID = 3162771335587335679L;
  52
  53
  54         private ArrayList<GraphicalTemplateElement> _RNAComponents;
  55         private ArrayList<Connection> _RNAConnections;
  56         private Hashtable<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Connection> _helixToConnection;
  57         private TemplateEditorPanelUI _ui;
  58
  59         private RNATemplate _template;
  60
  61
  62         private static Color[] BackgroundColors = {Color.blue,Color.red,Color.cyan,Color.green,Color.lightGray,Color.magenta,Color.PINK};
  63
  64         private int _nextBackgroundColor = 0;
  65
  66         private static double scaleFactorDefault = 0.7;
  67         private double scaleFactor = scaleFactorDefault;
  68
  69
  70         private TemplateEditor _editor;
  71
  72
  73         public double getScaleFactor() {
  74                 return scaleFactor;
  75         }
  76
  77         public void setScaleFactor(double scaleFactor) {
  78                 this.scaleFactor = scaleFactor;
  79         }
  80
  81         public Color nextBackgroundColor()
  82         {
  83                 Color c = BackgroundColors[_nextBackgroundColor++];
  84                 _nextBackgroundColor = _nextBackgroundColor % BackgroundColors.length;
  85                 return new Color(c.getRed(),c.getBlue(),c.getGreen(),50);
  86         }
  87
  88         public TemplatePanel(TemplateEditor parent)
  89         {
  90                 _editor = parent;
  91                 init();
  92         }
  93
  94         public RNATemplate getTemplate()
  95         {
  96                 return _template;
  97         }
  98
  99         List<GraphicalTemplateElement> getRNAComponents() {
 100                 return _RNAComponents;
 101         }
 102
 103         private void init()
 104         {
 105                 _ui = new TemplateEditorPanelUI(this);
 106
 107                 _RNAComponents = new ArrayList<GraphicalTemplateElement>();
 108                 _RNAConnections = new ArrayList<Connection>();
 109                 _helixToConnection = new Hashtable<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Connection>();
 110
 111                 _template = new RNATemplate();
 112
 113                 setBackground(Color.WHITE);
 114                 MouseControler mc = new MouseControler(this,_ui);
 115                 addMouseListener(mc);
 116                 addMouseMotionListener(mc);
 117                 addMouseWheelListener(mc);
 118                 _solidStroke = new BasicStroke(1.5f, BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND, 3.0f);
 119                 float[] dash = { 5.0f, 5.0f };
 120                 _dashedStroke = new BasicStroke(1.5f, BasicStroke.CAP_ROUND,BasicStroke.JOIN_ROUND, 3.0f, dash, 0);
 121         }
 122
 123         public void addUndoableEditListener(UndoManager manager)
 124         {
 125                 _ui.addUndoableEditListener(manager);
 126         }
 127
 128         public TemplateEditorPanelUI getTemplateUI()
 129         {
 130                 return _ui;
 131         }
 132
 133
 134         public void flip(Helix h)
 135         {
 136                 h.toggleFlipped();
 137         }
 138
 139         public void addElement(GraphicalTemplateElement h)
 140         {
 141                 _RNAComponents.add(h);
 142         }
 143
 144         public void removeElement(GraphicalTemplateElement h)
 145         {
 146                 _RNAComponents.remove(h);
 147                 try {
 148                         _template.removeElement(h.getTemplateElement());
 149                 } catch (ExceptionInvalidRNATemplate e) {
 150                         //e.printStackTrace();
 151                 }
 152         }
 153
 154         private GraphicalTemplateElement _selected = null;
 155
 156         public GraphicalTemplateElement getSelected()
 157         {
 158                 return _selected;
 159         }
 160
 161         public void setSelected(GraphicalTemplateElement sel)
 162         {
 163                 _selected = sel;
 164                 if (_selected instanceof Helix) {
 165                         _editor.flipButtonEnable();
 166                 } else {
 167                         _editor.flipButtonDisable();
 168                 }
 169         }
 170
 171         Helix.RelativePosition _relpos = Helix.RelativePosition.RP_OUTER;
 172
 173         public void setSelectedEdge(Helix.RelativePosition rel)
 174         {
 175                 _relpos = rel;
 176         }
 177
 178         public void unselectEdge(Helix.RelativePosition rel)
 179         {
 180                 _relpos = rel;
 181         }
 182
 183         Point2D.Double _mousePos = new Point2D.Double();
 184
 185         public void setPointerPos(Point2D.Double p)
 186         {
 187                 _mousePos = p;
 188         }
 189
 190         public void Unselect()
 191         {
 192                 _editor.flipButtonDisable();
 193                 _selected = null;
 194         }
 195
 196         public GraphicalTemplateElement getElement(RNATemplateElement t)
 197         {
 198                 for(GraphicalTemplateElement t2: _RNAComponents)
 199                         if (t==t2.getTemplateElement())
 200                                 return t2;
 201                 return null;
 202         }
 203
 204
 205         public GraphicalTemplateElement getElementAt(double x, double y)
 206         {
 207                 return getElementAt(x, y, null);
 208         }
 209         public GraphicalTemplateElement getElementAt(double x, double y, GraphicalTemplateElement excluded)
 210         {
 211                 GraphicalTemplateElement h = null;
 212                 for (int i=0; i<_RNAComponents.size();i++)
 213                 {
 214                         GraphicalTemplateElement h2 = _RNAComponents.get(i);
 215                         if ((
 216                                            (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_END3)
 217                                         || (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_END5)
 218                                         || (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_START3)
 219                                         || (h2.getRelativePosition(x, y)== Helix.RelativePosition.RP_CONNECT_START5))
 220                                 && (excluded!=h2))
 221                         {
 222                                 h = h2;
 223                         }
 224                 }
 225                 if (h==null)
 226                 { h = getElementCloseTo(x, y, excluded);};
 227                 return h;
 228         }
 229
 230         public GraphicalTemplateElement getElementCloseTo(double x, double y)
 231         {
 232                 return getElementCloseTo(x, y, null);
 233         }
 234         public GraphicalTemplateElement getElementCloseTo(double x, double y, GraphicalTemplateElement excluded)
 235         {
 236                 GraphicalTemplateElement h = null;
 237                 for (int i=0; i<_RNAComponents.size();i++)
 238                 {
 239                         GraphicalTemplateElement h2 = _RNAComponents.get(i);
 240                         if ((h2.getRelativePosition(x, y) != Helix.RelativePosition.RP_OUTER)
 241                                 && (excluded!=h2))
 242                         {
 243                                 h = h2;
 244                         }
 245                 }
 246                 return h;
 247         }
 248
 249         public void addConnection(Connection c)
 250         {
 251                 _RNAConnections.add(c);
 252                 _helixToConnection.put(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h1,c._edge1), c);
 253                 _helixToConnection.put(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h2,c._edge2), c);
 254                         try {
 255                                 c._h1.attach(c._h2, c._edge1, c._edge2);
 256                                 c._h2.attach(c._h1, c._edge2, c._edge1);
 257                         } catch (ExceptionInvalidRNATemplate e) {
 258                                 System.out.println(e.toString());// TODO Auto-generated catch block
 259                 }
 260
 261         }
 262
 263         public Connection addConnection(GraphicalTemplateElement h1, GraphicalTemplateElement.RelativePosition edge1,GraphicalTemplateElement h2, GraphicalTemplateElement.RelativePosition edge2)
 264         {
 265                 if ((h1!=h2)&&(getPartner(h1,edge1)==null)&&(getPartner(h2,edge2)==null))
 266                 {
 267                         Connection c = new Connection(h1,edge1,h2,edge2);
 268                         addConnection(c);
 269                         return c;
 270                 }
 271                 return null;
 272         }
 273
 274         /**
 275          * When there is already a connection in the underlying RNATemplate
 276          * and we want to create one at the graphical level.
 277          */
 278         public void addGraphicalConnection(GraphicalTemplateElement h1, GraphicalTemplateElement.RelativePosition edge1,GraphicalTemplateElement h2, GraphicalTemplateElement.RelativePosition edge2) {
 279                 //System.out.println("Connecting " + h1 + " " + edge1 + " to " + h2 + " " + edge2);
 280                 Connection c = new Connection(h1,edge1,h2,edge2);
 281                 _RNAConnections.add(c);
 282                 _helixToConnection.put(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h1,c._edge1), c);
 283                 _helixToConnection.put(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h2,c._edge2), c);
 284                 c._h1.graphicalAttach(c._h2, c._edge1, c._edge2);
 285                 c._h2.graphicalAttach(c._h1, c._edge2, c._edge1);
 286         }
 287
 288
 289         public void removeConnection(Connection c)
 290         {
 291                 _RNAConnections.remove(c);
 292                 _helixToConnection.remove(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h1,c._edge1));
 293                 _helixToConnection.remove(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h2,c._edge2));
 294                 System.out.println("[A]"+c);
 295                 c._h1.detach(c._edge1);
 296         }
 297
 298         public boolean isInCycle(GraphicalTemplateElement el, GraphicalTemplateElement.RelativePosition edge)
 299         {
 300                 Stack<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> > p = new Stack<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>>();
 301                 Hashtable<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer> alreadySeen = new Hashtable<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer>();
 302                 p.add(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(el,edge));
 303                 while(!p.empty())
 304                 {
 305                         Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> c2 = p.pop();
 306                         if (alreadySeen.containsKey(c2))
 307                         {
 308                                 return true;
 309                         }
 310                         else
 311                         {
 312                                 alreadySeen.put(c2, new Integer(1));
 313                         }
 314                         GraphicalTemplateElement.RelativePosition next = c2.first.getConnectedEdge(c2.second);
 315                         Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> otherEnd = new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c2.first,next);
 316                         if (!alreadySeen.containsKey(otherEnd))
 317                         {
 318                                 p.push(otherEnd);
 319                         }
 320                         else
 321                         {
 322                                 Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> child =  getPartner(c2.first,c2.second);
 323                                 if (child!=null)
 324                                 {
 325                                         p.push(child);
 326                                 }
 327                         }
 328
 329                 }
 330
 331                 return false;
 332         }
 333
 334         private static Color[] _colors = {Color.gray,Color.pink,Color.cyan,Color.RED,Color.green,Color.orange};
 335
 336         public static Color getIndexedColor(int n)
 337         {
 338                 return _colors[n%_colors.length];
 339         }
 340
 341         public HashMap<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer> buildConnectedComponents()
 342         {
 343                 HashMap<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer> alreadySeen = new HashMap<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>,Integer>();
 344                 int numConnectedComponents = 0;
 345                 for (GraphicalTemplateElement el : this._RNAComponents)
 346                 {
 347                         for (GraphicalTemplateElement.RelativePosition edge : el.getConnectedEdges())
 348                         {
 349                                 Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> c = new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(el,edge);
 350                                 if (!alreadySeen.containsKey(c))
 351                                 {
 352                                         Stack<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> > p = new Stack<Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>>();
 353                                         p.add(c);
 354                                         p.add(new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(el,el.getConnectedEdge(edge)));
 355                                         while(!p.empty())
 356                                         {
 357                                                 Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> c2 = p.pop();
 358                                                 if (!alreadySeen.containsKey(c2))
 359                                                 {
 360                                                         //System.out.println("  "+numConnectedComponents+"  "+c2);
 361                                                         c2.first.setMainColor(c2.second, getIndexedColor(numConnectedComponents));
 362                                                         alreadySeen.put(c2, new Integer(numConnectedComponents));
 363                                                         GraphicalTemplateElement.RelativePosition next = c2.first.getConnectedEdge(c2.second);
 364                                                         Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> otherEnd = new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c2.first,next);
 365                                                         p.push(otherEnd);
 366                                                         Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> child =  getPartner(c2.first,c2.second);
 367                                                         if (child!=null)
 368                                                         { p.push(child); }
 369                                                 }
 370                                         }
 371                                         numConnectedComponents += 1;
 372                                 }
 373                         }
 374                 }
 375                 return alreadySeen;
 376         }
 377
 378         public boolean isInCycle(Connection c)
 379         {
 380                 return isInCycle(c._h1,c._edge1);
 381         }
 382
 383         public Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> getPartner(GraphicalTemplateElement h, GraphicalTemplateElement.RelativePosition edge)
 384         {
 385                 Connection c = getConnection(h, edge);
 386                 if (c != null)
 387                 {
 388                           if ((c._h1==h)&&(c._edge1==edge))
 389                           {  return new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h2,c._edge2);  }
 390                           else
 391                           {  return new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(c._h1,c._edge1); }
 392                 }
 393                 else
 394                 {
 395                         return null;
 396                 }
 397         }
 398
 399         public Connection getConnection(GraphicalTemplateElement h, Helix.RelativePosition edge)
 400         {
 401                 Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> target = new Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition>(h,edge);
 402                 if (_helixToConnection.containsKey(target))
 403                 {
 404                         return _helixToConnection.get(target);
 405                 }
 406                 else
 407                 { return null; }
 408         }
 409
 410         private boolean isConnected(Helix h, GraphicalTemplateElement.RelativePosition edge)
 411         {
 412                 Couple<GraphicalTemplateElement,GraphicalTemplateElement.RelativePosition> partner = getPartner(h,edge);
 413                 return partner!=null;
 414         }
 415
 416
 417         // Aspects graphiques
 418
 419         private static final Color  CYCLE_COLOR = Color.red;
 420         private static final Color  NON_EXISTANT_COLOR = Color.gray.brighter();
 421         private static final Color  CONTROL_COLOR = Color.gray.darker();
 422         private static final Color  BACKGROUND_COLOR = Color.white;
 423
 424         private Stroke  _solidStroke;
 425         private Stroke  _dashedStroke;
 426
 427
 428
 429
 430         private void drawConnections(Graphics2D g2d, Connection c)
 431         {
 432                 GraphicalTemplateElement h1 = c._h1;
 433                 GraphicalTemplateElement.RelativePosition edge1 = c._edge1;
 434                 Point2D.Double p1 = h1.getEdgePosition(edge1);
 435                 GraphicalTemplateElement h2 = c._h2;
 436                 GraphicalTemplateElement.RelativePosition edge2 = c._edge2;
 437                 Point2D.Double p2 = h2.getEdgePosition(edge2);
 438                 if (isInCycle(c))
 439                 {
 440                         g2d.setColor(CYCLE_COLOR);
 441                 }
 442                 else
 443                 {
 444                         g2d.setColor(GraphicalTemplateElement.BACKBONE_COLOR);
 445                 }
 446                 g2d.drawLine((int)p1.x,(int)p1.y,(int)p2.x,(int)p2.y);
 447         }
 448
 449
 450         public void paintComponent(Graphics g)
 451         {
 452                 //rescale();
 453
 454                 // Debug code to show drawing area
 455 //              g.setColor(Color.red);
 456 //              g.fillRect(0,0,getWidth(),getHeight());
 457 //              g.setColor(Color.white);
 458 //              g.fillRect(10,10,getWidth()-20,getHeight()-20);
 459
 460                 g.setColor(Color.white);
 461                 g.fillRect(0,0,getWidth(),getHeight());
 462
 463                 Graphics2D g2d = (Graphics2D) g;
 464                 g2d.scale(scaleFactor, scaleFactor);
 465                 g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
 466                                 RenderingHints.VALUE_ANTIALIAS_ON);
 467                 removeAll();
 468                 //super.paintComponent(g2d);
 469
 470                 buildConnectedComponents();
 471
 472                 if (_selected!=null)
 473                 {
 474                         if (_relpos != GraphicalTemplateElement.RelativePosition.RP_OUTER)
 475                         {
 476                         Point2D.Double p = _selected.getEdgePosition(_relpos);
 477                         g2d.setStroke(_solidStroke);
 478                         g2d.drawLine((int)_mousePos.x, (int)_mousePos.y, (int)p.x, (int)p.y);
 479                         }
 480                 }
 481                 for (int i=0;i<_RNAConnections.size();i++)
 482                 {
 483                         Connection c = _RNAConnections.get(i);
 484                         drawConnections(g2d,c);
 485                 }
 486                 for (int i=0;i<_RNAComponents.size();i++)
 487                 {
 488                         GraphicalTemplateElement elem = _RNAComponents.get(i);
 489                         //g2d.setColor(elem.getDominantColor());
 490                         //g2d.fill(elem.getArea());
 491                         if (_selected == elem)
 492                         {
 493                                 elem.draw(g2d,true);
 494                         }
 495                         else
 496                         {  elem.draw(g2d,false);  }
 497                 }
 498         }
 499
 500         /**
 501          * Get the bounding rectangle of the RNA components, always including the origin (0,0).
 502          */
 503         public Rectangle getBoundingRectange() {
 504                 int minX = 0;
 505                 int maxX = 0;
 506                 int minY = 0;
 507                 int maxY = 0;
 508                 for(int i=0;i<this._RNAComponents.size();i++)
 509                 {
 510                         GraphicalTemplateElement h = _RNAComponents.get(i);
 511                         Polygon p = h.getBoundingPolygon();
 512                         Rectangle r = p.getBounds();
 513                         minX = Math.min(minX,r.x);
 514                         maxX = Math.max(maxX,r.x+r.width);
 515                         minY = Math.min(minY,r.y);
 516                         maxY = Math.max(maxY,r.y+r.height);
 517                 }
 518                 Rectangle res = new Rectangle();
 519                 res.x = minX;
 520                 res.y = minY;
 521                 res.width = maxX - minX;
 522                 res.height = maxY - minY;
 523                 return res;
 524         }
 525
 526         public void rescale()
 527         {
 528                 Rectangle rect = getBoundingRectange();
 529
 530                 if (rect.x < 0 || rect.y < 0) {
 531             for(int i=0;i<this._RNAComponents.size();i++)
 532             {
 533                     GraphicalTemplateElement h = _RNAComponents.get(i);
 534                     h.translate(rect.x<0 ? -rect.x : 0, rect.y<0 ? -rect.y : 0);
 535             }
 536             rect = getBoundingRectange();
 537                 }
 538
 539                 // areaW and H are width and height, in pixels, of the drawing area
 540                 // including the "outside" parts available with scrolling
 541                 int areaW = (int) ((rect.width + 100) * scaleFactor);
 542                 int areaH = (int) ((rect.height + 100) * scaleFactor);
 543                 // make it cover at least the space visible in the window
 544                 //areaW = Math.max(areaW, (int) (_editor.getJp().getViewport().getViewSize().width));
 545                 //areaH = Math.max(areaH, (int) (_editor.getJp().getViewport().getViewSize().height));
 546                 //System.out.println(areaW + " x " + areaH);
 547                 setPreferredSize(new Dimension(areaW, areaH));
 548                 revalidate();
 549         }
 550
 551         public void clearTemplate() {
 552                 loadTemplate(new RNATemplate());
 553         }
 554
 555         /**
 556          * Load an existing RNATemplate object in this panel.
 557          */
 558         public void loadTemplate(RNATemplate template) {
 559                 _template = template;
 560                 _RNAComponents.clear();
 561                 _RNAConnections.clear();
 562                 _helixToConnection.clear();
 563
 564                 // We need a template element -> graphical template element mapping
 565                 Map<RNATemplateElement, GraphicalTemplateElement> map = new HashMap<RNATemplateElement, GraphicalTemplateElement>();
 566
 567                 // First, we load elements
 568                 {
 569                         Iterator<RNATemplateElement> iter = template.classicIterator();
 570                         while (iter.hasNext()) {
 571                                 RNATemplateElement templateElement = iter.next();
 572                                 if (templateElement instanceof RNATemplateHelix) {
 573                                         RNATemplateHelix templateHelix = (RNATemplateHelix) templateElement;
 574                                         Helix graphicalHelix = new Helix(templateHelix);
 575                                         graphicalHelix.setDominantColor(nextBackgroundColor());
 576                                         _RNAComponents.add(graphicalHelix);
 577                                         map.put(templateHelix, graphicalHelix);
 578                                 } else if (templateElement instanceof RNATemplateUnpairedSequence) {
 579                                         RNATemplateUnpairedSequence templateSequence = (RNATemplateUnpairedSequence) templateElement;
 580                                         UnpairedRegion graphicalSequence = new UnpairedRegion(templateSequence);
 581                                         graphicalSequence.setDominantColor(nextBackgroundColor());
 582                                         _RNAComponents.add(graphicalSequence);
 583                                         map.put(templateSequence, graphicalSequence);
 584                                 }
 585                         }
 586                 }
 587
 588                 // Now, we load edges
 589                 {
 590                         Iterator<EdgeEndPoint> iter = template.makeEdgeList().iterator();
 591                         while (iter.hasNext()) {
 592                                 EdgeEndPoint v1 = iter.next();
 593                                 EdgeEndPoint v2 = v1.getOtherEndPoint();
 594                                 GraphicalTemplateElement gte1 = map.get(v1.getElement());
 595                                 GraphicalTemplateElement gte2 = map.get(v2.getElement());
 596                                 RelativePosition rp1 = gte1.relativePositionFromEdgeEndPointPosition(v1.getPosition());
 597                                 RelativePosition rp2 = gte2.relativePositionFromEdgeEndPointPosition(v2.getPosition());
 598                                 addGraphicalConnection(gte1, rp1, gte2, rp2);
 599                         }
 600                 }
 601
 602                 zoomFit();
 603                 //repaint();
 604         }
 605
 606         /**
 607          * Load a template from an XML file.
 608          */
 609         public void loadFromXmlFile(File filename) {
 610                 try {
 611                         RNATemplate newTemplate = RNATemplate.fromXMLFile(filename);
 612                         loadTemplate(newTemplate);
 613                 } catch (ExceptionXmlLoading e) {
 614                         e.printStackTrace();
 615                         JOptionPane.showMessageDialog(this, e.getMessage(), "Template loading error", JOptionPane.ERROR_MESSAGE);
 616                 }
 617         }
 618
 619         private void zoomFinish() {
 620                 rescale();
 621                 repaint();
 622         }
 623
 624         public void zoomIn() {
 625                 scaleFactor *= 1.2;
 626                 zoomFinish();
 627         }
 628
 629         public void zoomOut() {
 630                 scaleFactor /= 1.2;
 631                 zoomFinish();
 632         }
 633
 634         public void zoomReset() {
 635                 scaleFactor = scaleFactorDefault;
 636                 zoomFinish();
 637         }
 638
 639         public void zoomFit() {
 640                 if (_RNAComponents.isEmpty()) {
 641                         zoomReset();
 642                 } else {
 643                         Rectangle rect = getBoundingRectange();
 644                         double areaW = (rect.width + 100);
 645                         double areaH = (rect.height + 100);
 646                         // make it cover at least the space visible in the window
 647                         scaleFactor = 1;
 648                         scaleFactor = Math.min(scaleFactor, _editor.getJp().getViewport().getSize().width / areaW);
 649                         scaleFactor = Math.min(scaleFactor, _editor.getJp().getViewport().getSize().height / areaH);
 650                         zoomFinish();
 651                 }
 652         }
 653
 654         public void translateView(Point trans) {
 655                 int newX = _editor.getJp().getHorizontalScrollBar().getValue() - trans.x;
 656                 int newY = _editor.getJp().getVerticalScrollBar().getValue() - trans.y;
 657                 newX = Math.max(0, Math.min(newX, _editor.getJp().getHorizontalScrollBar().getMaximum()));
 658                 newY = Math.max(0, Math.min(newY, _editor.getJp().getVerticalScrollBar().getMaximum()));
 659                 _editor.getJp().getHorizontalScrollBar().setValue(newX);
 660                 _editor.getJp().getVerticalScrollBar().setValue(newY);
 661         }
 662 }