+++ /dev/null
-package jalview.ext.archaeopteryx;
-
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
-import jalview.gui.PaintRefresher;
-import jalview.structure.SelectionSource;
-import jalview.structure.StructureSelectionManager;
-import jalview.viewmodel.AlignmentViewport;
-
-import java.awt.event.ActionEvent;
-import java.awt.event.InputEvent;
-import java.awt.event.MouseEvent;
-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;
-
-/**
- * Class for binding the Archaeopteryx tree viewer to the Jalview alignment that
- * it originates from, meaning that selecting sequences in the tree viewer also
- * selects them in the alignment view and vice versa.
- *
- * @author kjvanderheide
- *
- */
-public final class JalviewBinding
- implements ExternalTreeViewerBindingI<PhylogenyNode>
-{
- private org.forester.archaeopteryx.TreePanel treeView;
-
- private AlignmentViewport parentAvport;
-
- private JTabbedPane treeTabs;
-
- private final StructureSelectionManager ssm;
-
- private Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
-
- private Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
-
- /**
- *
- * @param archaeopteryx
- *
- * @param jalviewAlignmentViewport
- * alignment viewport from which the tree was calculated.
- *
- * @param alignMappedToNodes
- * map with sequences used to calculate the tree and matching tree
- * nodes as key, value pair respectively.
- *
- * @param nodesMappedToAlign
- * map with tree nodes and matching sequences used to calculate the
- * tree as key, value pair respectively.
- */
- public JalviewBinding(final MainFrame archaeopteryx,
- final AlignmentViewport jalviewAlignmentViewport,
- final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
- final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
- {
- // deal with/prohibit null values here as that will cause problems
- 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
- public void actionPerformed(ActionEvent e)
- {
- }
-
- @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);
-
- }
- showNodeSelectionOnAlign(node);
- }
- else
- {
- partitionTree(e);
-
-
- }
-
- }
- });
-
-
- }
-
- @Override
- public void mousePressed(final MouseEvent e)
- {
-
- }
- @Override
- public void mouseReleased(MouseEvent e)
- {
- }
-
- @Override
- public void mouseEntered(MouseEvent e)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- }
-
-
- @Override
- public void selection(final SequenceGroup seqsel,
- final ColumnSelection colsel, final HiddenColumns hidden,
- final SelectionSource source)
- {
- if (source == parentAvport) // check if source is alignment from where the
- // tree originates
- {
- treeView.setFoundNodes0(
- new HashSet<Long>(seqsel.getSequences().size()));
-
- for (SequenceI selectedSequence : seqsel.getSequences())
- {
- PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence);
- if (matchingNode != null)
- {
- treeView.getFoundNodes0().add(matchingNode.getId());
- }
-
- }
- treeView.repaint();
-
- }
-
-
- }
-
- /**
- * 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 PhylogenyNode node)
- {
-
- if (node.isInternal())
- {
- showMatchingChildSequences(node);
- }
-
- else
- {
- showMatchingSequence(node);
- }
-
- }
-
-
-
-
-
- @Override
- public void showMatchingSequence(final PhylogenyNode nodeToMatch)
- {
- SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
- if (matchingSequence != null)
- {
- long nodeId = nodeToMatch.getId();
- addOrRemoveInSet(treeView.getFoundNodes0(), nodeId);
- treeSelectionChanged(matchingSequence);
- parentAvport.sendSelection();
-
- }
- }
-
- @Override
- public void showMatchingChildSequences(final PhylogenyNode parentNode)
- {
- 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();
-
-
- }
-
- /**
- * Refactored from TreeCanvas.
- *
- * @param sequence
- * of the node selected in the tree viewer.
- */
- @Override
- public void treeSelectionChanged(final SequenceI sequence)
- {
- if (!parentAvport.isClosed()) // alignment view could be closed
- {
- SequenceGroup selected = parentAvport.getSelectionGroup();
-
- if (selected == null)
- {
- selected = new SequenceGroup();
- parentAvport.setSelectionGroup(selected);
- }
-
- selected.setEndRes(parentAvport.getAlignment().getWidth() - 1);
- selected.addOrRemove(sequence, true);
- }
-
- }
- public void sortByTree_actionPerformed() {
- // parentAvport.mirrorCommand(command, undo, ssm, source);
-
- // alignFrame
- // .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
-
- }
-
-
- /**
- * 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()
- // {
- //
- // @Override
- // public void undoCommand(AlignmentI[] views)
- // {
- // for (CommandI tsort : commands)
- // {
- // tsort.undoCommand(views);
- // }
- // }
- //
- // @Override
- // public int getSize()
- // {
- // return commands.size();
- // }
- //
- // @Override
- // public String getDescription()
- // {
- // return "Tree Sort (many views)";
- // }
- //
- // @Override
- // public void doCommand(AlignmentI[] views)
- // {
- //
- // for (CommandI tsort : commands)
- // {
- // tsort.doCommand(views);
- // }
- // }
- // });
- // for (AlignmentPanel ap : PaintRefresher
- // .getAssociatedPanels(av.getSequenceSetId()))
- // {
- // // ensure all the alignFrames refresh their GI after adding an undo item
- // ap.alignFrame.updateEditMenuBar();
- // }
- // }
- // 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