src/jalview/ext/archaeopteryx/JalviewBinding.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.analysis.Conservation;
   4 import jalview.api.AlignViewportI;
   5 import jalview.datamodel.ColumnSelection;
   6 import jalview.datamodel.HiddenColumns;
   7 import jalview.datamodel.SequenceGroup;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
  10 import jalview.gui.AlignViewport;
  11 import jalview.gui.AlignmentPanel;
  12 import jalview.gui.Desktop;
  13 import jalview.gui.JvOptionPane;
  14 import jalview.gui.PaintRefresher;
  15 import jalview.schemes.ColourSchemeI;
  16 import jalview.schemes.ColourSchemeProperty;
  17 import jalview.schemes.UserColourScheme;
  18 import jalview.structure.SelectionSource;
  19 import jalview.structure.StructureSelectionManager;
  20 import jalview.util.MappingUtils;
  21 import jalview.util.MessageManager;
  22 import jalview.viewmodel.AlignmentViewport;
  23
  24 import java.awt.Color;
  25 import java.awt.event.ActionEvent;
  26 import java.awt.event.InputEvent;
  27 import java.awt.event.MouseEvent;
  28 import java.util.ArrayList;
  29 import java.util.HashSet;
  30 import java.util.List;
  31 import java.util.Map;
  32 import java.util.Set;
  33
  34 import javax.swing.JTabbedPane;
  35 import javax.swing.SwingUtilities;
  36 import javax.swing.event.ChangeEvent;
  37 import javax.swing.event.ChangeListener;
  38
  39 import org.forester.archaeopteryx.MainFrame;
  40 import org.forester.phylogeny.Phylogeny;
  41 import org.forester.phylogeny.PhylogenyMethods;
  42 import org.forester.phylogeny.PhylogenyNode;
  43 import org.forester.phylogeny.data.BranchColor;
  44
  45 /**
  46  * Class for binding the Archaeopteryx tree viewer to the Jalview alignment that
  47  * it originates from, meaning that selecting sequences in the tree viewer also
  48  * selects them in the alignment view and vice versa.
  49  *
  50  * @author kjvanderheide
  51  *
  52  */
  53 public final class JalviewBinding
  54         implements ExternalTreeViewerBindingI<PhylogenyNode>
  55 {
  56   private org.forester.archaeopteryx.TreePanel treeView;
  57
  58   private AlignmentViewport parentAvport;
  59
  60   private final JTabbedPane treeTabs;
  61
  62   private final StructureSelectionManager ssm;
  63
  64   private AlignmentPanel[] associatedPanels;
  65
  66   private Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
  67
  68   private Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
  69
  70   private float rootX;
  71
  72   private float furthestNodeX;
  73
  74   private int nrTreeGroups = 0;
  75
  76   /**
  77    *
  78    * @param archaeopteryx
  79    *
  80    * @param jalviewAlignmentViewport
  81    *          alignment viewport from which the tree was calculated.
  82    *
  83    * @param alignMappedToNodes
  84    *          map with sequences used to calculate the tree and matching tree
  85    *          nodes as key, value pair respectively.
  86    *
  87    * @param nodesMappedToAlign
  88    *          map with tree nodes and matching sequences used to calculate the
  89    *          tree as key, value pair respectively.
  90    */
  91   public JalviewBinding(final MainFrame archaeopteryx,
  92           final AlignmentViewport jalviewAlignmentViewport,
  93           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
  94           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
  95   {
  96
  97     if (archaeopteryx.getMainPanel().getTabbedPane().getTabCount() > 1)
  98     {
  99       JvOptionPane.showMessageDialog(Desktop.desktop,
 100               MessageManager.getString("label.tabs_detected_archaeopteryx"),
 101               MessageManager.getString("label.problem_reading_tree_file"),
 102               JvOptionPane.WARNING_MESSAGE);
 103       ;
 104     }
 105
 106     // deal with/prohibit null values here as that will cause problems
 107     parentAvport = jalviewAlignmentViewport;
 108     sequencesBoundToNodes = alignMappedToNodes;
 109     nodesBoundToSequences = nodesMappedToAlign;
 110
 111     treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
 112     treeTabs = archaeopteryx.getMainPanel().getTabbedPane();
 113     ssm = parentAvport.getStructureSelectionManager();
 114
 115     ssm.addSelectionListener(this);
 116     treeView.addMouseListener(this);
 117     PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
 118
 119     associatedPanels = PaintRefresher
 120             .getAssociatedPanels(parentAvport.getSequenceSetId());
 121
 122
 123     treeTabs.addChangeListener(new ChangeListener()
 124     {
 125
 126       @Override
 127       public void stateChanged(ChangeEvent e)
 128       {
 129
 130         SwingUtilities.invokeLater(new Runnable()
 131         {
 132
 133           @Override
 134           /**
 135            * Resend the selection to the tree view when tabs get switched, this
 136            * has to be buried in invokeLater as Forester first resets the tree
 137            * view on switching tabs, without invokeLater this would get called
 138            * before Forester resets which would nullify the selection.
 139            */
 140           public void run()
 141           {
 142             treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
 143             parentAvport.sendSelection();
 144             // PaintRefresher.Refresh(treeView,
 145             // parentAvport.getSequenceSetId());
 146
 147           }
 148         });
 149
 150       }
 151
 152     });
 153
 154   }
 155
 156   @Override
 157   public void actionPerformed(ActionEvent e)
 158   {
 159   }
 160
 161   @Override
 162   public void mouseClicked(MouseEvent e)
 163   {
 164     SwingUtilities.invokeLater(new Runnable() {
 165
 166       @Override
 167       /**
 168        * invokeLater so that this always runs after Forester's mouseClicked
 169        */
 170       public void run()
 171       {
 172         final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
 173         if (node != null)
 174         {
 175           if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
 176           // selection if shift
 177           // IS NOT pressed
 178           {
 179             parentAvport.setSelectionGroup(null);
 180
 181           }
 182           showNodeSelectionOnAlign(node);
 183         }
 184         else
 185         {
 186
 187           partitionTree(e.getX());
 188       }
 189         PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
 190         treeView.repaint();
 191
 192
 193
 194       }
 195     });
 196
 197
 198   }
 199
 200   @Override
 201   public void mousePressed(final MouseEvent e)
 202   {
 203
 204   }
 205   @Override
 206   public void mouseReleased(MouseEvent e)
 207   {
 208   }
 209
 210   @Override
 211   public void mouseEntered(MouseEvent e)
 212   {
 213   }
 214
 215   @Override
 216   public void mouseExited(MouseEvent e)
 217   {
 218   }
 219
 220
 221   @Override
 222   public void selection(final SequenceGroup seqsel,
 223           final ColumnSelection colsel, final HiddenColumns hidden,
 224           final SelectionSource source)
 225   {
 226     if (source == parentAvport) // check if source is alignment from where the
 227     // tree originates
 228     {
 229       treeView.setFoundNodes0(
 230               new HashSet<Long>(seqsel.getSequences().size()));
 231
 232       for (SequenceI selectedSequence : seqsel.getSequences())
 233       {
 234         PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence);
 235         if (matchingNode != null)
 236         {
 237           treeView.getFoundNodes0().add(matchingNode.getId());
 238
 239
 240           if (!matchingNode.getBranchData().isHasBranchColor())
 241           {
 242             Color foundNodesColour = treeView.getTreeColorSet()
 243                     .getFoundColor0();
 244           matchingNode.getBranchData()
 245                     .setBranchColor(new BranchColor(foundNodesColour));
 246
 247           }
 248
 249         }
 250
 251       }
 252
 253       treeView.repaint();
 254     }
 255
 256
 257   }
 258
 259   /**
 260    * Partially refactored from TreeCanvas
 261    */
 262   public void partitionTree(final int x)
 263   {
 264     Phylogeny tree = treeView.getPhylogeny();
 265
 266     if (!tree.isEmpty())
 267     {
 268       // should be calculated on each partition as the tree can theoretically
 269       // change in the meantime
 270       PhylogenyNode furthestNode = PhylogenyMethods
 271               .calculateNodeWithMaxDistanceToRoot(tree);
 272       furthestNodeX = furthestNode.getXcoord();
 273       rootX = tree.getRoot().getXcoord();
 274
 275       if (furthestNodeX != rootX && !(x < rootX || x > furthestNodeX)) // don't
 276                                                                        // bother
 277                                                                        // if 0
 278                                                        // distance tree or
 279                                                        // clicked x lies outside
 280                                                        // of tree
 281       {
 282
 283         // int panelHeight = treeView.getHeight();
 284         // g.drawLine(x, 0, x, panelHeight);
 285
 286         float threshold = (x - rootX) / (furthestNodeX - rootX);
 287         List<PhylogenyNode> foundNodes = getNodesAboveThreshold(threshold,
 288                 tree.getRoot());
 289
 290       }
 291     }
 292
 293
 294   }
 295
 296   public List<PhylogenyNode> getNodesAboveThreshold(double threshold,
 297           PhylogenyNode node)
 298   {
 299
 300     List<PhylogenyNode> nodesAboveThreshold = new ArrayList<>();
 301
 302     parentAvport.setSelectionGroup(null);
 303     parentAvport.getAlignment().deleteAllGroups();
 304     parentAvport.clearSequenceColours();
 305     if (parentAvport.getCodingComplement() != null)
 306     {
 307       parentAvport.getCodingComplement().setSelectionGroup(null);
 308       parentAvport.getCodingComplement().getAlignment().deleteAllGroups();
 309       parentAvport.getCodingComplement().clearSequenceColours();
 310     }
 311
 312
 313     colourNodesAboveThreshold(nodesAboveThreshold, threshold,
 314             node);
 315     return nodesAboveThreshold;
 316
 317   }
 318
 319   /**
 320    * Partially refactored from TreeCanvas colourGroups (can be made nicer).
 321    *
 322    * @param nodeList
 323    * @param threshold
 324    * @param treeLength
 325    * @param node
 326    * @return
 327    */
 328   private List<PhylogenyNode> colourNodesAboveThreshold(
 329           List<PhylogenyNode> nodeList, double threshold,
 330           PhylogenyNode node)
 331   {
 332
 333     for (PhylogenyNode childNode : node.getDescendants())
 334     {
 335       childNode.getBranchData()
 336               .setBranchColor(new BranchColor(Color.black));
 337       float nodeCutoff = (childNode.getXcoord() - rootX)
 338               / (furthestNodeX - rootX);
 339
 340       if (nodeCutoff > threshold)
 341       {
 342         nodeList.add(childNode);
 343
 344         Color randomColour = new Color((int) (Math.random() * 255),
 345                 (int) (Math.random() * 255), (int) (Math.random() * 255));
 346         childNode.getBranchData()
 347                 .setBranchColor(new BranchColor(randomColour));
 348
 349         List<SequenceI> groupSeqs = new ArrayList<>();
 350         SequenceI seq = nodesBoundToSequences.get(childNode);
 351         if (seq != null)
 352         {
 353           groupSeqs.add(seq);
 354           parentAvport.setSequenceColour(seq, randomColour);
 355         }
 356
 357         List<PhylogenyNode> descendantNodes = PhylogenyMethods
 358                 .getAllDescendants(childNode);
 359         // .forEach instead?
 360         for (PhylogenyNode descNode : descendantNodes)
 361         {
 362           seq = nodesBoundToSequences.get(descNode);
 363           if (seq != null)
 364           {
 365             groupSeqs.add(seq);
 366             parentAvport.setSequenceColour(seq, randomColour);
 367           }
 368
 369           descNode.getBranchData()
 370                   .setBranchColor(new BranchColor(randomColour));
 371         }
 372
 373         if (groupSeqs != null)
 374         {
 375           nrTreeGroups++;
 376           groupThresholdSequences(groupSeqs, randomColour);
 377         }}
 378
 379       else
 380       {
 381         colourNodesAboveThreshold(nodeList, threshold, childNode);
 382       }
 383     }
 384
 385
 386         for (AlignmentPanel associatedPanel : associatedPanels) {
 387
 388         associatedPanel.updateAnnotation();
 389
 390         final AlignViewportI codingComplement = associatedPanel.getAlignViewport()
 391                 .getCodingComplement();
 392         if (codingComplement != null)
 393         {
 394           // GROSS
 395           ((AlignViewport) codingComplement).getAlignPanel()
 396                   .updateAnnotation();
 397         }
 398       }
 399
 400
 401     return nodeList;
 402   }
 403
 404   public void groupThresholdSequences(List<SequenceI> groupedSeqs,
 405           Color groupColour)
 406   {
 407     SequenceGroup treeGroup = new SequenceGroup(groupedSeqs, null, null,
 408             true, true, false, 0,
 409             parentAvport.getAlignment().getWidth() - 1);
 410
 411     ColourSchemeI cs = null;
 412     if (parentAvport.getGlobalColourScheme() != null)
 413     {
 414       if (parentAvport.getGlobalColourScheme() instanceof UserColourScheme)
 415       {
 416         cs = new UserColourScheme(
 417                 ((UserColourScheme) parentAvport.getGlobalColourScheme())
 418                         .getColours());
 419       }
 420       else
 421       {
 422         cs = ColourSchemeProperty.getColourScheme(treeGroup,
 423                 ColourSchemeProperty.getColourName(
 424                         parentAvport.getGlobalColourScheme()));
 425       }
 426
 427     }
 428     treeGroup.setColourScheme(cs);
 429     treeGroup.getGroupColourScheme().setThreshold(
 430             parentAvport.getResidueShading().getThreshold(),
 431             parentAvport.isIgnoreGapsConsensus());
 432
 433     treeGroup.setName("Tree Group " + nrTreeGroups);
 434     treeGroup.setIdColour(groupColour);
 435
 436     for (AlignmentPanel associatedPanel : associatedPanels)
 437     {
 438       AlignViewportI altViewport = associatedPanel
 439               .getAlignViewport();
 440
 441       if (altViewport.getGlobalColourScheme() != null
 442               && altViewport.getResidueShading()
 443                       .conservationApplied())
 444       {
 445         Conservation conserv = new Conservation(treeGroup.getName(),
 446                 treeGroup.getSequences(null), treeGroup.getStartRes(),
 447                 treeGroup.getEndRes());
 448         conserv.calculate();
 449         conserv.verdict(false, altViewport.getConsPercGaps());
 450         treeGroup.getGroupColourScheme().setConservation(conserv);
 451       }
 452
 453       altViewport.getAlignment().addGroup(treeGroup);
 454       // TODO can we push all of the below into AlignViewportI?
 455       final AlignViewportI codingComplement = altViewport
 456               .getCodingComplement();
 457       if (codingComplement != null)
 458       {
 459         SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(treeGroup,
 460                 parentAvport, codingComplement);
 461         if (mappedGroup.getSequences().size() > 0)
 462         {
 463           codingComplement.getAlignment().addGroup(mappedGroup);
 464           for (SequenceI seq : mappedGroup.getSequences())
 465           {
 466             codingComplement.setSequenceColour(seq, groupColour.brighter());
 467           }
 468         }
 469       }
 470
 471     }
 472
 473   }
 474
 475   /**
 476    * may or may not need an extra repaint on the alignment view (check what kira
 477    * does)
 478    */
 479   @Override
 480   public void showNodeSelectionOnAlign(final PhylogenyNode node)
 481   {
 482
 483       if (node.isInternal())
 484       {
 485         showMatchingChildSequences(node);
 486       }
 487
 488       else
 489       {
 490         showMatchingSequence(node);
 491       }
 492
 493
 494     }
 495
 496
 497
 498
 499
 500   @Override
 501   public void showMatchingSequence(final PhylogenyNode nodeToMatch)
 502   {
 503     SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
 504     if (matchingSequence != null)
 505     {
 506       long nodeId = nodeToMatch.getId();
 507       addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
 508       treeSelectionChanged(matchingSequence);
 509       parentAvport.sendSelection();
 510
 511     }
 512   }
 513
 514   @Override
 515   public void showMatchingChildSequences(final PhylogenyNode parentNode)
 516   {
 517     List<PhylogenyNode> childNodes = PhylogenyMethods
 518             .getAllDescendants(parentNode);
 519
 520
 521     for (PhylogenyNode childNode : childNodes)
 522     {
 523       // childNode.getBranchData().setBranchColor(new BranchColor(Color.BLUE));
 524
 525       SequenceI matchingSequence = nodesBoundToSequences.get(childNode);
 526       if (matchingSequence != null)
 527       {
 528         long nodeId = childNode.getId();
 529         addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
 530
 531         treeSelectionChanged(matchingSequence);
 532
 533       }
 534
 535     }
 536     parentAvport.sendSelection();
 537
 538
 539   }
 540
 541   /**
 542    * Refactored from TreeCanvas.
 543    *
 544    * @param sequence
 545    *          of the node selected in the tree viewer.
 546    */
 547   @Override
 548   public void treeSelectionChanged(final SequenceI sequence)
 549   {
 550     if (!parentAvport.isClosed()) // alignment view could be closed
 551     {
 552       SequenceGroup selected = parentAvport.getSelectionGroup();
 553
 554       if (selected == null)
 555       {
 556         selected = new SequenceGroup();
 557         parentAvport.setSelectionGroup(selected);
 558       }
 559
 560       selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
 561         selected.addOrRemove(sequence, true);
 562     }
 563
 564   }
 565   public void sortByTree_actionPerformed() {
 566
 567   }
 568
 569
 570
 571   /**
 572    * TO BE MOVED
 573    *
 574    * @param set
 575    * @param objectToCheck
 576    */
 577   public static <E> void addOrRemoveInSet(Set<E> set, E objectToCheck)
 578   {
 579     if (set.contains(objectToCheck))
 580     {
 581       set.remove(objectToCheck);
 582     }
 583     else
 584     {
 585       set.add(objectToCheck);
 586     }
 587
 588   }
 589
 590   public AlignmentViewport getParentAvport()
 591   {
 592     return parentAvport;
 593   }
 594
 595   public void setParentAvport(final AlignmentViewport parentAvport)
 596   {
 597     this.parentAvport = parentAvport;
 598   }
 599
 600   public AlignmentPanel[] getAssociatedPanels()
 601   {
 602     return associatedPanels;
 603   }
 604
 605   public void setAssociatedPanels(AlignmentPanel[] associatedPanels)
 606   {
 607     this.associatedPanels = associatedPanels;
 608   }
 609
 610 }
 611
 612
 613