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);
146 treeView.setFoundNodes0(null);
149 showNodeSelectionOnAlign(node);
165 public void mousePressed(final MouseEvent e)
170 public void mouseReleased(MouseEvent e)
175 public void mouseEntered(MouseEvent e)
180 public void mouseExited(MouseEvent e)
186 public void selection(final SequenceGroup seqsel,
187 final ColumnSelection colsel, final HiddenColumns hidden,
188 final SelectionSource source)
190 if (source == parentAvport) // check if source is alignment from where the
193 treeView.setFoundNodes0(
194 new HashSet<Long>(seqsel.getSequences().size()));
196 for (SequenceI selectedSequence : seqsel.getSequences())
198 PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence);
199 if (matchingNode != null)
201 treeView.getFoundNodes0().add(matchingNode.getId());
205 PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
213 * Partially refactored from TreeCanvas
215 public void partitionTree(final MouseEvent e)
219 Phylogeny tree = treeView.getPhylogeny();
220 double treeHeight = tree.calculateHeight(true);
225 int viewWidth = treeView.getWidth();
227 // treeView.validate();
229 // System.out.println("selection");
230 // System.out.println(x);
231 // System.out.println("-------------");
232 // System.out.println("width");
233 // System.out.println(viewWidth);
242 public void showNodeSelectionOnAlign(final PhylogenyNode node)
244 if (treeView.getFoundNodes0() == null)
246 treeView.setFoundNodes0(new HashSet<Long>());
249 if (node.isInternal())
251 showMatchingChildSequences(node);
256 showMatchingSequence(node);
259 PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
267 public void showMatchingSequence(final PhylogenyNode nodeToMatch)
269 SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
270 if (matchingSequence != null)
272 long nodeId = nodeToMatch.getId();
273 addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
274 treeSelectionChanged(matchingSequence);
275 // parentAvport.sendSelection(); // this shouldn't be needed
281 public void showMatchingChildSequences(final PhylogenyNode parentNode)
283 List<PhylogenyNode> childNodes = PhylogenyMethods
284 .getAllDescendants(parentNode);
287 for (PhylogenyNode childNode : childNodes)
289 // childNode.getBranchData().setBranchColor(new BranchColor(Color.BLUE));
291 SequenceI matchingSequence = nodesBoundToSequences.get(childNode);
292 if (matchingSequence != null)
294 long nodeId = childNode.getId();
295 addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
297 treeSelectionChanged(matchingSequence);
302 // parentAvport.sendSelection(); // this shouldn't be needed
308 * Refactored from TreeCanvas.
311 * of the node selected in the tree viewer.
314 public void treeSelectionChanged(final SequenceI sequence)
316 if (!parentAvport.isClosed()) // alignment view could be closed
318 SequenceGroup selected = parentAvport.getSelectionGroup();
320 if (selected == null)
322 selected = new SequenceGroup();
323 parentAvport.setSelectionGroup(selected);
326 selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
327 selected.addOrRemove(sequence, true);
336 * @param objectToCheck
338 public <E> void addOrRemoveInSet(Set<E> set, E objectToCheck)
340 if (set.contains(objectToCheck))
342 set.remove(objectToCheck);
346 set.add(objectToCheck);
351 public AlignmentViewport getParentAvport()
356 public void setParentAvport(final AlignmentViewport parentAvport)
358 this.parentAvport = parentAvport;