1 package jalview.ext.archaeopteryx;
3 import jalview.datamodel.ColumnSelection;
4 import jalview.datamodel.HiddenColumns;
5 import jalview.datamodel.SequenceGroup;
6 import jalview.datamodel.SequenceI;
7 import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
8 import jalview.gui.PaintRefresher;
9 import jalview.structure.SelectionSource;
10 import jalview.structure.StructureSelectionManager;
11 import jalview.viewmodel.AlignmentViewport;
13 import java.awt.event.ActionEvent;
14 import java.awt.event.InputEvent;
15 import java.awt.event.MouseEvent;
16 import java.util.HashSet;
17 import java.util.List;
21 import javax.swing.JTabbedPane;
22 import javax.swing.SwingUtilities;
23 import javax.swing.event.ChangeEvent;
24 import javax.swing.event.ChangeListener;
26 import org.forester.archaeopteryx.MainFrame;
27 import org.forester.phylogeny.Phylogeny;
28 import org.forester.phylogeny.PhylogenyMethods;
29 import org.forester.phylogeny.PhylogenyNode;
32 * Class for binding the Archaeopteryx tree viewer to the Jalview alignment that
33 * it originates from, meaning that selecting sequences in the tree viewer also
34 * selects them in the alignment view and vice versa.
36 * @author kjvanderheide
39 public final class JalviewBinding
40 implements ExternalTreeViewerBindingI<PhylogenyNode>
42 private org.forester.archaeopteryx.TreePanel treeView;
44 private AlignmentViewport parentAvport;
46 private JTabbedPane treeTabs;
48 private final StructureSelectionManager ssm;
50 private Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
52 private Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
56 * @param archaeopteryx
58 * @param jalviewAlignmentViewport
59 * alignment viewport from which the tree was calculated.
61 * @param alignMappedToNodes
62 * map with sequences used to calculate the tree and matching tree
63 * nodes as key, value pair respectively.
65 * @param nodesMappedToAlign
66 * map with tree nodes and matching sequences used to calculate the
67 * tree as key, value pair respectively.
69 public JalviewBinding(final MainFrame archaeopteryx,
70 final AlignmentViewport jalviewAlignmentViewport,
71 final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
72 final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
74 // deal with/prohibit null values here as that will cause problems
75 parentAvport = jalviewAlignmentViewport;
76 sequencesBoundToNodes = alignMappedToNodes;
77 nodesBoundToSequences = nodesMappedToAlign;
79 treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
80 treeTabs = archaeopteryx.getMainPanel().getTabbedPane();
81 ssm = parentAvport.getStructureSelectionManager();
83 // archaeopteryx.getMainPanel().getControlPanel().setColorBranches(true);
85 ssm.addSelectionListener(this);
86 treeView.addMouseListener(this);
87 PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
90 treeTabs.addChangeListener(new ChangeListener()
94 public void stateChanged(ChangeEvent e)
97 SwingUtilities.invokeLater(new Runnable()
102 * Resend the selection to the tree view when tabs get switched, this
103 * has to be buried in invokeLater as Forester first resets the tree
104 * view on switching tabs, without invokeLater this would get called
105 * before Forester resets which would nullify the selection.
109 parentAvport.sendSelection();
110 // PaintRefresher.Refresh(treeView,
111 // parentAvport.getSequenceSetId());
123 public void actionPerformed(ActionEvent e)
128 public void mouseClicked(MouseEvent e)
130 SwingUtilities.invokeLater(new Runnable() {
134 * invokeLater so that this always runs after Forester's mouseClicked
138 final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
141 if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
142 // selection if shift
145 parentAvport.setSelectionGroup(null);
148 showNodeSelectionOnAlign(node);
164 public void mousePressed(final MouseEvent e)
169 public void mouseReleased(MouseEvent e)
174 public void mouseEntered(MouseEvent e)
179 public void mouseExited(MouseEvent e)
185 public void selection(final SequenceGroup seqsel,
186 final ColumnSelection colsel, final HiddenColumns hidden,
187 final SelectionSource source)
189 if (source == parentAvport) // check if source is alignment from where the
192 treeView.setFoundNodes0(
193 new HashSet<Long>(seqsel.getSequences().size()));
195 for (SequenceI selectedSequence : seqsel.getSequences())
197 PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence);
198 if (matchingNode != null)
200 treeView.getFoundNodes0().add(matchingNode.getId());
212 * Partially refactored from TreeCanvas
214 public void partitionTree(final MouseEvent e)
217 int lineLength = treeView.getHeight();
219 Phylogeny tree = treeView.getPhylogeny();
220 double treeHeight = tree.calculateHeight(true);
226 int viewWidth = treeView.getWidth();
228 // treeView.validate();
230 // System.out.println("selection");
231 // System.out.println(x);
232 // System.out.println("-------------");
233 // System.out.println("width");
234 // System.out.println(viewWidth);
244 public void showNodeSelectionOnAlign(final PhylogenyNode node)
247 if (node.isInternal())
249 showMatchingChildSequences(node);
254 showMatchingSequence(node);
264 public void showMatchingSequence(final PhylogenyNode nodeToMatch)
266 SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
267 if (matchingSequence != null)
269 long nodeId = nodeToMatch.getId();
270 addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
271 treeSelectionChanged(matchingSequence);
272 parentAvport.sendSelection();
278 public void showMatchingChildSequences(final PhylogenyNode parentNode)
280 List<PhylogenyNode> childNodes = PhylogenyMethods
281 .getAllDescendants(parentNode);
284 for (PhylogenyNode childNode : childNodes)
286 // childNode.getBranchData().setBranchColor(new BranchColor(Color.BLUE));
288 SequenceI matchingSequence = nodesBoundToSequences.get(childNode);
289 if (matchingSequence != null)
291 long nodeId = childNode.getId();
292 addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
294 treeSelectionChanged(matchingSequence);
299 parentAvport.sendSelection();
305 * Refactored from TreeCanvas.
308 * of the node selected in the tree viewer.
311 public void treeSelectionChanged(final SequenceI sequence)
313 if (!parentAvport.isClosed()) // alignment view could be closed
315 SequenceGroup selected = parentAvport.getSelectionGroup();
317 if (selected == null)
319 selected = new SequenceGroup();
320 parentAvport.setSelectionGroup(selected);
323 selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
324 selected.addOrRemove(sequence, true);
328 public void sortByTree_actionPerformed() {
329 // parentAvport.mirrorCommand(command, undo, ssm, source);
332 // .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
338 * sort the associated alignment view by the current tree.
343 // public void sortByTree_actionPerformed()// modify for Aptx
346 // // if (treeCanvas.applyToAllViews)
348 // final ArrayList<CommandI> commands = new ArrayList<>();
349 // for (AlignmentPanel ap : PaintRefresher
350 // .getAssociatedPanels(parentAvport.getSequenceSetId()))
352 // commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
354 // av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
358 // public void undoCommand(AlignmentI[] views)
360 // for (CommandI tsort : commands)
362 // tsort.undoCommand(views);
367 // public int getSize()
369 // return commands.size();
373 // public String getDescription()
375 // return "Tree Sort (many views)";
379 // public void doCommand(AlignmentI[] views)
382 // for (CommandI tsort : commands)
384 // tsort.doCommand(views);
388 // for (AlignmentPanel ap : PaintRefresher
389 // .getAssociatedPanels(av.getSequenceSetId()))
391 // // ensure all the alignFrames refresh their GI after adding an undo item
392 // ap.alignFrame.updateEditMenuBar();
397 // treeCanvas.ap.alignFrame
398 // .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
407 * @param objectToCheck
409 public static <E> void addOrRemoveInSet(Set<E> set, E objectToCheck)
411 if (set.contains(objectToCheck))
413 set.remove(objectToCheck);
417 set.add(objectToCheck);
422 public AlignmentViewport getParentAvport()
427 public void setParentAvport(final AlignmentViewport parentAvport)
429 this.parentAvport = parentAvport;