import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
+
+import javax.swing.JTabbedPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
import org.forester.archaeopteryx.MainFrame;
+import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
private AlignmentViewport parentAvport;
+ private JTabbedPane treeTabs;
+
private final StructureSelectionManager ssm;
private Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
parentAvport = jalviewAlignmentViewport;
sequencesBoundToNodes = alignMappedToNodes;
nodesBoundToSequences = nodesMappedToAlign;
+
treeView = archaeopteryx.getMainPanel().getCurrentTreePanel();
+ treeTabs = archaeopteryx.getMainPanel().getTabbedPane();
ssm = parentAvport.getStructureSelectionManager();
+
+ // archaeopteryx.getMainPanel().getControlPanel().setColorBranches(true);
+
ssm.addSelectionListener(this);
treeView.addMouseListener(this);
PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
+
+ treeTabs.addChangeListener(new ChangeListener()
+ {
+
+ @Override
+ public void stateChanged(ChangeEvent e)
+ {
+
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ @Override
+ /**
+ * Resend the selection to the tree view when tabs get switched, this
+ * has to be buried in invokeLater as Forester first resets the tree
+ * view on switching tabs, without invokeLater this would get called
+ * before Forester resets which would nullify the selection.
+ */
+ public void run()
+ {
+ parentAvport.sendSelection();
+ // PaintRefresher.Refresh(treeView,
+ // parentAvport.getSequenceSetId());
+
+ }
+ });
+
+ }
+
+ });
+
}
@Override
@Override
public void mouseClicked(MouseEvent e)
{
+ SwingUtilities.invokeLater(new Runnable() {
+
+ @Override
+ /**
+ * invokeLater so that this always runs after Forester's mouseClicked
+ */
+ public void run()
+ {
+ final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
+ if (node != null)
+ {
+ if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
+ // selection if shift
+ // IS NOT pressed
+ {
+ parentAvport.setSelectionGroup(null);
+ treeView.setFoundNodes0(null);
+
+ }
+ showNodeSelectionOnAlign(node);
+ }
+ else
+ {
+ partitionTree(e);
+
+
+ }
+
+ }
+ });
+
+
}
@Override
public void mousePressed(final MouseEvent e)
{
- showNodeSelectionOnAlign(e);
- }
+ }
@Override
public void mouseReleased(MouseEvent e)
{
}
+ /**
+ * Partially refactored from TreeCanvas
+ */
+ public void partitionTree(final MouseEvent e)
+ {
+ int x = e.getX();
+ int lineLength = treeView.getHeight();
+
+ Phylogeny tree = treeView.getPhylogeny();
+ double treeHeight = tree.calculateHeight(true);
+
+
+
+ if (treeHeight != 0)
+ {
+ int viewWidth = treeView.getWidth();
+
+ // treeView.validate();
+
+ // System.out.println("selection");
+ // System.out.println(x);
+ // System.out.println("-------------");
+ // System.out.println("width");
+ // System.out.println(viewWidth);
+
+ }
+
+
+ }
+
+
@Override
- public void showNodeSelectionOnAlign(final MouseEvent e)
+ public void showNodeSelectionOnAlign(final PhylogenyNode node)
{
- final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
- if (node != null)
+ if (treeView.getFoundNodes0() == null)
{
- if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
- // selection if shift
- // IS NOT pressed
- {
- parentAvport.setSelectionGroup(null);
- }
+ treeView.setFoundNodes0(new HashSet<Long>());
+ }
if (node.isInternal())
{
{
showMatchingSequence(node);
}
-
+ treeView.repaint();
+ PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
}
- }
+
SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
if (matchingSequence != null)
{
+ long nodeId = nodeToMatch.getId();
+ addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
treeSelectionChanged(matchingSequence);
- parentAvport.sendSelection();
- PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
+ // parentAvport.sendSelection(); // this shouldn't be needed
+
}
}
List<PhylogenyNode> childNodes = PhylogenyMethods
.getAllDescendants(parentNode);
+
for (PhylogenyNode childNode : childNodes)
{
+ // childNode.getBranchData().setBranchColor(new BranchColor(Color.BLUE));
SequenceI matchingSequence = nodesBoundToSequences.get(childNode);
if (matchingSequence != null)
{
+ long nodeId = childNode.getId();
+ addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
+
treeSelectionChanged(matchingSequence);
}
+
}
+ // parentAvport.sendSelection(); // this shouldn't be needed
+
- parentAvport.sendSelection();
- PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
}
/**
@Override
public void treeSelectionChanged(final SequenceI sequence)
{
- SequenceGroup selected = parentAvport.getSelectionGroup();
-
- if (selected == null)
+ if (!parentAvport.isClosed()) // alignment view could be closed
{
- selected = new SequenceGroup();
- parentAvport.setSelectionGroup(selected);
- }
+ SequenceGroup selected = parentAvport.getSelectionGroup();
- selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
- selected.addOrRemove(sequence, true);
+ if (selected == null)
+ {
+ selected = new SequenceGroup();
+ parentAvport.setSelectionGroup(selected);
+ }
- }
+ selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
+ selected.addOrRemove(sequence, true);
+ }
- public AlignmentViewport getParentAvport()
- {
- return parentAvport;
}
+ public void sortByTree_actionPerformed() {
+ // parentAvport.mirrorCommand(command, undo, ssm, source);
- public void setParentAvport(final AlignmentViewport parentAvport)
- {
- this.parentAvport = parentAvport;
+ // alignFrame
+ // .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+
}
- // av.setCurrentTree(tree);
+
+
+ /**
+ * sort the associated alignment view by the current tree.
+ *
+ * @param e
+ */
+ // @Override
+ // public void sortByTree_actionPerformed()// modify for Aptx
+ // {
+ //
+ // // if (treeCanvas.applyToAllViews)
+ //
+ // final ArrayList<CommandI> commands = new ArrayList<>();
+ // for (AlignmentPanel ap : PaintRefresher
+ // .getAssociatedPanels(parentAvport.getSequenceSetId()))
+ // {
+ // commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
+ // }
+ // av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+ // {
//
- // /*
- // * isPopupTrigger is set for mousePressed (Mac)
- // * or mouseReleased (Windows)
- // */
- // if (e.isPopupTrigger())
+ // @Override
+ // public void undoCommand(AlignmentI[] views)
// {
- // if (highlightNode != null)
+ // for (CommandI tsort : commands)
// {
- // chooseSubtreeColour();
+ // tsort.undoCommand(views);
// }
- // return;
// }
//
- // /*
- // * defer right-click handling on Windows to
- // * mouseClicked; note isRightMouseButton
- // * also matches Cmd-click on Mac which should do
- // * nothing here
- // */
- // if (SwingUtilities.isRightMouseButton(e))
+ // @Override
+ // public int getSize()
// {
- // return;
+ // return commands.size();
// }
//
- // int x = e.getX();
- // int y = e.getY();
- //
- // Object ob = findElement(x, y);
- //
- // if (ob instanceof SequenceI)
+ // @Override
+ // public String getDescription()
// {
- // treeSelectionChanged((Sequence) ob);
- // PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
- // repaint();
- // av.sendSelection();
- // return;
+ // return "Tree Sort (many views)";
// }
- // else if (!(ob instanceof SequenceNode))
- // {
- // // Find threshold
- // if (tree.getMaxHeight() != 0)
- // {
- // threshold = (float) (x - offx)
- // / (float) (getWidth() - labelLength - (2 * offx));
//
- // List<SequenceNode> groups = tree.groupNodes(threshold);
- // setColor(tree.getTopNode(), Color.black);
- //
- // AlignmentPanel[] aps = getAssociatedPanels();
- //
- // // TODO push calls below into a single AlignViewportI method?
- // // see also AlignViewController.deleteGroups
- // for (int a = 0; a < aps.length; a++)
+ // @Override
+ // public void doCommand(AlignmentI[] views)
// {
- // aps[a].av.setSelectionGroup(null);
- // aps[a].av.getAlignment().deleteAllGroups();
- // aps[a].av.clearSequenceColours();
- // if (aps[a].av.getCodingComplement() != null)
+ //
+ // for (CommandI tsort : commands)
// {
- // aps[a].av.getCodingComplement().setSelectionGroup(null);
- // aps[a].av.getCodingComplement().getAlignment()
- // .deleteAllGroups();
- // aps[a].av.getCodingComplement().clearSequenceColours();
+ // tsort.doCommand(views);
// }
// }
- // colourGroups(groups);
+ // });
+ // for (AlignmentPanel ap : PaintRefresher
+ // .getAssociatedPanels(av.getSequenceSetId()))
+ // {
+ // // ensure all the alignFrames refresh their GI after adding an undo item
+ // ap.alignFrame.updateEditMenuBar();
// }
- //
- // PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
- // repaint();
// }
+ // else
+ // {
+ // treeCanvas.ap.alignFrame
+ // .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+ // }
+
+
+
+ /**
+ * TO BE MOVED
+ *
+ * @param set
+ * @param objectToCheck
+ */
+ public static <E> void addOrRemoveInSet(Set<E> set, E objectToCheck)
+ {
+ if (set.contains(objectToCheck))
+ {
+ set.remove(objectToCheck);
+ }
+ else
+ {
+ set.add(objectToCheck);
+ }
+
+ }
+
+ public AlignmentViewport getParentAvport()
+ {
+ return parentAvport;
+ }
+
+ public void setParentAvport(final AlignmentViewport parentAvport)
+ {
+ this.parentAvport = parentAvport;
+ }
}
git://source.jalview.org / jalview.git / blobdiff