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 import javax.swing.event.InternalFrameAdapter;
  39 import javax.swing.event.InternalFrameEvent;
  40
  41 import org.forester.archaeopteryx.MainFrame;
  42 import org.forester.phylogeny.Phylogeny;
  43 import org.forester.phylogeny.PhylogenyMethods;
  44 import org.forester.phylogeny.PhylogenyNode;
  45 import org.forester.phylogeny.data.BranchColor;
  46
  47 /**
  48  * Class for binding the Archaeopteryx tree viewer to the Jalview alignment that
  49  * it originates from, meaning that selecting sequences in the tree viewer also
  50  * selects them in the alignment view and vice versa.
  51  *
  52  * @author kjvanderheide
  53  *
  54  */
  55 public final class JalviewBinding
  56         implements ExternalTreeViewerBindingI<PhylogenyNode>
  57 {
  58   private org.forester.archaeopteryx.TreePanel treeView;
  59
  60   private AlignmentViewport parentAvport;
  61
  62   private final JTabbedPane treeTabs;
  63
  64   private final StructureSelectionManager ssm;
  65
  66   private AlignmentPanel[] associatedPanels;
  67
  68   private Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
  69
  70   private Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
  71
  72   private float rootX;
  73
  74   private float furthestNodeX;
  75
  76   private int nrTreeGroups = 0;
  77
  78   private boolean applyToAllViews = false;
  79
  80   /**
  81    *
  82    * @param archaeopteryx
  83    *
  84    * @param jalviewAlignmentViewport
  85    *          alignment viewport from which the tree was calculated.
  86    *
  87    * @param alignMappedToNodes
  88    *          map with sequences used to calculate the tree and matching tree
  89    *          nodes as key, value pair respectively.
  90    *
  91    * @param nodesMappedToAlign
  92    *          map with tree nodes and matching sequences used to calculate the
  93    *          tree as key, value pair respectively.
  94    */
  95   public JalviewBinding(final MainFrame archaeopteryx,
  96           final AlignmentViewport jalviewAlignmentViewport,
  97           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
  98           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
  99   {
 100
 101     if (archaeopteryx.getMainPanel().getTabbedPane().getTabCount() > 1)
 102     {
 103       JvOptionPane.showMessageDialog(Desktop.desktop,
 104               MessageManager.getString("label.tabs_detected_archaeopteryx"),
 105               MessageManager.getString("label.problem_reading_tree_file"),
 106               JvOptionPane.WARNING_MESSAGE);
 107       ;
 108     }
 109
 110     // deal with/prohibit null values here as that will cause problems
 111     parentAvport = jalviewAlignmentViewport;
 112     sequencesBoundToNodes = alignMappedToNodes;
 113     nodesBoundToSequences = nodesMappedToAlign;
 114
 115     treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
 116     treeTabs = archaeopteryx.getMainPanel().getTabbedPane();
 117     ssm = parentAvport.getStructureSelectionManager();
 118
 119     ssm.addSelectionListener(this);
 120     treeView.addMouseListener(this);
 121     PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
 122     associatedPanels = PaintRefresher
 123             .getAssociatedPanels(parentAvport.getSequenceSetId());
 124
 125     archaeopteryx.addInternalFrameListener(new InternalFrameAdapter()
 126     {
 127
 128       @Override
 129       public void internalFrameClosed(InternalFrameEvent e)
 130       {
 131         AptxInit.getAllAptxFrames().remove(archaeopteryx);
 132       }
 133
 134     });
 135
 136     treeTabs.addChangeListener(new ChangeListener()
 137     {
 138
 139       @Override
 140       public void stateChanged(ChangeEvent e)
 141       {
 142
 143         SwingUtilities.invokeLater(new Runnable()
 144         {
 145
 146           @Override
 147           /**
 148            * Resend the selection to the tree view when tabs get switched, this
 149            * has to be buried in invokeLater as Forester first resets the tree
 150            * view on switching tabs, without invokeLater this would get called
 151            * before Forester resets which would nullify the selection.
 152            */
 153           public void run()
 154           {
 155             treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
 156             parentAvport.sendSelection();
 157             // PaintRefresher.Refresh(treeView,
 158             // parentAvport.getSequenceSetId());
 159
 160           }
 161         });
 162
 163       }
 164
 165     });
 166
 167   }
 168
 169   @Override
 170   public void actionPerformed(ActionEvent e)
 171   {
 172   }
 173
 174   @Override
 175   public void mouseClicked(MouseEvent e)
 176   {
 177     SwingUtilities.invokeLater(new Runnable() {
 178
 179       @Override
 180       /**
 181        * invokeLater so that this always runs after Forester's mouseClicked
 182        */
 183       public void run()
 184       {
 185         final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
 186         if (node != null)
 187         {
 188           if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
 189           // selection if shift
 190           // IS NOT pressed
 191           {
 192             parentAvport.setSelectionGroup(null);
 193
 194           }
 195           showNodeSelectionOnAlign(node);
 196         }
 197         else
 198         {
 199
 200           partitionTree(e.getX());
 201       }
 202         PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
 203         treeView.repaint();
 204
 205
 206
 207       }
 208     });
 209
 210
 211   }
 212
 213   @Override
 214   public void mousePressed(final MouseEvent e)
 215   {
 216
 217   }
 218   @Override
 219   public void mouseReleased(MouseEvent e)
 220   {
 221   }
 222
 223   @Override
 224   public void mouseEntered(MouseEvent e)
 225   {
 226   }
 227
 228   @Override
 229   public void mouseExited(MouseEvent e)
 230   {
 231   }
 232
 233
 234   @Override
 235   public void selection(final SequenceGroup seqsel,
 236           final ColumnSelection colsel, final HiddenColumns hidden,
 237           final SelectionSource source)
 238   {
 239     if (source == parentAvport) // check if source is alignment from where the
 240     // tree originates
 241     {
 242       treeView.setFoundNodes0(
 243               new HashSet<Long>(seqsel.getSequences().size()));
 244
 245       for (SequenceI selectedSequence : seqsel.getSequences())
 246       {
 247         PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence);
 248         if (matchingNode != null)
 249         {
 250           treeView.getFoundNodes0().add(matchingNode.getId());
 251
 252
 253           if (!matchingNode.getBranchData().isHasBranchColor())
 254           {
 255             Color foundNodesColour = treeView.getTreeColorSet()
 256                     .getFoundColor0();
 257           matchingNode.getBranchData()
 258                     .setBranchColor(new BranchColor(foundNodesColour));
 259
 260           }
 261
 262         }
 263
 264       }
 265
 266       treeView.repaint();
 267     }
 268
 269
 270   }
 271
 272   /**
 273    * Partially refactored from TreeCanvas
 274    */
 275   public void partitionTree(final int x)
 276   {
 277     Phylogeny tree = treeView.getPhylogeny();
 278
 279     if (!tree.isEmpty())
 280     {
 281       // should be calculated on each partition as the tree can theoretically
 282       // change in the meantime
 283       PhylogenyNode furthestNode = PhylogenyMethods
 284               .calculateNodeWithMaxDistanceToRoot(tree);
 285       furthestNodeX = furthestNode.getXcoord();
 286       rootX = tree.getRoot().getXcoord();
 287
 288       if (furthestNodeX != rootX && !(x < rootX || x > furthestNodeX)) // don't
 289                                                                        // bother
 290                                                                        // if 0
 291                                                        // distance tree or
 292                                                        // clicked x lies outside
 293                                                        // of tree
 294       {
 295
 296         float threshold = (x - rootX) / (furthestNodeX - rootX);
 297         List<PhylogenyNode> foundNodes = getNodesAboveThreshold(threshold,
 298                 tree.getRoot());
 299
 300       }
 301     }
 302
 303
 304   }
 305
 306   public List<PhylogenyNode> getNodesAboveThreshold(double threshold,
 307           PhylogenyNode node)
 308   {
 309
 310     List<PhylogenyNode> nodesAboveThreshold = new ArrayList<>();
 311
 312     parentAvport.setSelectionGroup(null);
 313     parentAvport.getAlignment().deleteAllGroups();
 314     parentAvport.clearSequenceColours();
 315     if (parentAvport.getCodingComplement() != null)
 316     {
 317       parentAvport.getCodingComplement().setSelectionGroup(null);
 318       parentAvport.getCodingComplement().getAlignment().deleteAllGroups();
 319       parentAvport.getCodingComplement().clearSequenceColours();
 320     }
 321
 322
 323     colourNodesAboveThreshold(nodesAboveThreshold, threshold,
 324             node);
 325     return nodesAboveThreshold;
 326
 327   }
 328
 329   /**
 330    * Partially refactored from TreeCanvas colourGroups (can be made nicer).
 331    *
 332    * @param nodeList
 333    * @param threshold
 334    * @param treeLength
 335    * @param node
 336    * @return
 337    */
 338   private List<PhylogenyNode> colourNodesAboveThreshold(
 339           List<PhylogenyNode> nodeList, double threshold,
 340           PhylogenyNode node)
 341   {
 342
 343     for (PhylogenyNode childNode : node.getDescendants())
 344     {
 345       childNode.getBranchData()
 346               .setBranchColor(new BranchColor(Color.black));
 347       float nodeCutoff = (childNode.getXcoord() - rootX)
 348               / (furthestNodeX - rootX);
 349
 350       if (nodeCutoff > threshold)
 351       {
 352         nodeList.add(childNode);
 353
 354         Color randomColour = new Color((int) (Math.random() * 255),
 355                 (int) (Math.random() * 255), (int) (Math.random() * 255));
 356         childNode.getBranchData()
 357                 .setBranchColor(new BranchColor(randomColour));
 358
 359         List<SequenceI> groupSeqs = new ArrayList<>();
 360         SequenceI seq = nodesBoundToSequences.get(childNode);
 361         if (seq != null)
 362         {
 363           groupSeqs.add(seq);
 364           parentAvport.setSequenceColour(seq, randomColour);
 365         }
 366
 367         List<PhylogenyNode> descendantNodes = PhylogenyMethods
 368                 .getAllDescendants(childNode);
 369         // .forEach instead?
 370         for (PhylogenyNode descNode : descendantNodes)
 371         {
 372           seq = nodesBoundToSequences.get(descNode);
 373           if (seq != null)
 374           {
 375             groupSeqs.add(seq);
 376             parentAvport.setSequenceColour(seq, randomColour);
 377           }
 378
 379           descNode.getBranchData()
 380                   .setBranchColor(new BranchColor(randomColour));
 381         }
 382
 383         if (groupSeqs != null)
 384         {
 385           nrTreeGroups++;
 386           groupThresholdSequences(groupSeqs, randomColour);
 387         }}
 388
 389       else
 390       {
 391         colourNodesAboveThreshold(nodeList, threshold, childNode);
 392       }
 393     }
 394
 395
 396         for (AlignmentPanel associatedPanel : associatedPanels) {
 397
 398         associatedPanel.updateAnnotation();
 399
 400         final AlignViewportI codingComplement = associatedPanel.getAlignViewport()
 401                 .getCodingComplement();
 402         if (codingComplement != null)
 403         {
 404           // GROSS
 405           ((AlignViewport) codingComplement).getAlignPanel()
 406                   .updateAnnotation();
 407         }
 408       }
 409
 410
 411     return nodeList;
 412   }
 413
 414   public void groupThresholdSequences(List<SequenceI> groupedSeqs,
 415           Color groupColour)
 416   {
 417     SequenceGroup treeGroup = new SequenceGroup(groupedSeqs, null, null,
 418             true, true, false, 0,
 419             parentAvport.getAlignment().getWidth() - 1);
 420
 421     ColourSchemeI cs = null;
 422     if (parentAvport.getGlobalColourScheme() != null)
 423     {
 424       if (parentAvport.getGlobalColourScheme() instanceof UserColourScheme)
 425       {
 426         cs = new UserColourScheme(
 427                 ((UserColourScheme) parentAvport.getGlobalColourScheme())
 428                         .getColours());
 429       }
 430       else
 431       {
 432         cs = ColourSchemeProperty.getColourScheme(treeGroup,
 433                 ColourSchemeProperty.getColourName(
 434                         parentAvport.getGlobalColourScheme()));
 435       }
 436
 437     }
 438     treeGroup.setColourScheme(cs);
 439     treeGroup.getGroupColourScheme().setThreshold(
 440             parentAvport.getResidueShading().getThreshold(),
 441             parentAvport.isIgnoreGapsConsensus());
 442
 443     treeGroup.setName("Tree Group " + nrTreeGroups);
 444     treeGroup.setIdColour(groupColour);
 445
 446     for (AlignmentPanel associatedPanel : associatedPanels)
 447     {
 448       AlignViewportI altViewport = associatedPanel
 449               .getAlignViewport();
 450
 451       if (altViewport.getGlobalColourScheme() != null
 452               && altViewport.getResidueShading()
 453                       .conservationApplied())
 454       {
 455         Conservation conserv = new Conservation(treeGroup.getName(),
 456                 treeGroup.getSequences(null), treeGroup.getStartRes(),
 457                 treeGroup.getEndRes());
 458         conserv.calculate();
 459         conserv.verdict(false, altViewport.getConsPercGaps());
 460         treeGroup.getGroupColourScheme().setConservation(conserv);
 461       }
 462
 463       altViewport.getAlignment().addGroup(treeGroup);
 464       // TODO can we push all of the below into AlignViewportI?
 465       final AlignViewportI codingComplement = altViewport
 466               .getCodingComplement();
 467       if (codingComplement != null)
 468       {
 469         SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(treeGroup,
 470                 parentAvport, codingComplement);
 471         if (mappedGroup.getSequences().size() > 0)
 472         {
 473           codingComplement.getAlignment().addGroup(mappedGroup);
 474           for (SequenceI seq : mappedGroup.getSequences())
 475           {
 476             codingComplement.setSequenceColour(seq, groupColour.brighter());
 477           }
 478         }
 479       }
 480
 481     }
 482
 483   }
 484
 485   /**
 486    * may or may not need an extra repaint on the alignment view (check what kira
 487    * does)
 488    */
 489   @Override
 490   public void showNodeSelectionOnAlign(final PhylogenyNode node)
 491   {
 492
 493       if (node.isInternal())
 494       {
 495         showMatchingChildSequences(node);
 496       }
 497
 498       else
 499       {
 500         showMatchingSequence(node);
 501       }
 502
 503
 504     }
 505
 506
 507
 508
 509
 510   @Override
 511   public void showMatchingSequence(final PhylogenyNode nodeToMatch)
 512   {
 513     SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
 514     if (matchingSequence != null)
 515     {
 516       long nodeId = nodeToMatch.getId();
 517       addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
 518       treeSelectionChanged(matchingSequence);
 519       parentAvport.sendSelection();
 520
 521     }
 522   }
 523
 524   @Override
 525   public void showMatchingChildSequences(final PhylogenyNode parentNode)
 526   {
 527     List<PhylogenyNode> childNodes = PhylogenyMethods
 528             .getAllDescendants(parentNode);
 529
 530
 531     for (PhylogenyNode childNode : childNodes)
 532     {
 533       // childNode.getBranchData().setBranchColor(new BranchColor(Color.BLUE));
 534
 535       SequenceI matchingSequence = nodesBoundToSequences.get(childNode);
 536       if (matchingSequence != null)
 537       {
 538         long nodeId = childNode.getId();
 539         addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
 540
 541         treeSelectionChanged(matchingSequence);
 542
 543       }
 544
 545     }
 546     parentAvport.sendSelection();
 547
 548
 549   }
 550
 551   /**
 552    * Refactored from TreeCanvas.
 553    *
 554    * @param sequence
 555    *          of the node selected in the tree viewer.
 556    */
 557   @Override
 558   public void treeSelectionChanged(final SequenceI sequence)
 559   {
 560     if (!parentAvport.isClosed()) // alignment view could be closed
 561     {
 562       SequenceGroup selected = parentAvport.getSelectionGroup();
 563
 564       if (selected == null)
 565       {
 566         selected = new SequenceGroup();
 567         parentAvport.setSelectionGroup(selected);
 568       }
 569
 570       selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
 571         selected.addOrRemove(sequence, true);
 572     }
 573
 574   }
 575   public void sortByTree_actionPerformed() {
 576
 577   }
 578
 579
 580
 581   /**
 582    * TO BE MOVED
 583    *
 584    * @param set
 585    * @param objectToCheck
 586    */
 587   public static <E> void addOrRemoveInSet(Set<E> set, E objectToCheck)
 588   {
 589     if (set.contains(objectToCheck))
 590     {
 591       set.remove(objectToCheck);
 592     }
 593     else
 594     {
 595       set.add(objectToCheck);
 596     }
 597
 598   }
 599
 600   public AlignmentViewport getParentAvport()
 601   {
 602     return parentAvport;
 603   }
 604
 605   public void setParentAvport(final AlignmentViewport parentAvport)
 606   {
 607     this.parentAvport = parentAvport;
 608   }
 609
 610   public AlignmentPanel[] getAssociatedPanels()
 611   {
 612     return associatedPanels;
 613   }
 614
 615   public void setAssociatedPanels(AlignmentPanel[] associatedPanels)
 616   {
 617     this.associatedPanels = associatedPanels;
 618   }
 619
 620 }
 621
 622
 623