X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Farchaeopteryx%2FJalviewBinding.java;h=54b92252e18e33fa1676046d827afe37ef804c9d;hb=f7c1fd8a0f220e1e896414b1aa905bd30138c26a;hp=3f69299cb0f546283548a66248676772d1379a97;hpb=f7ef599318242d5d63dbe1e9679224534f7b6aa3;p=jalview.git diff --git a/src/jalview/ext/archaeopteryx/JalviewBinding.java b/src/jalview/ext/archaeopteryx/JalviewBinding.java index 3f69299..54b9225 100644 --- a/src/jalview/ext/archaeopteryx/JalviewBinding.java +++ b/src/jalview/ext/archaeopteryx/JalviewBinding.java @@ -1,30 +1,49 @@ package jalview.ext.archaeopteryx; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.Conservation; +import jalview.api.AlignViewportI; +import jalview.commands.CommandI; +import jalview.commands.OrderCommand; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.ext.treeviewer.ExternalTreeViewerBindingI; +import jalview.ext.treeviewer.TreeFrameI; +import jalview.ext.treeviewer.TreeI; +import jalview.ext.treeviewer.TreeNodeI; +import jalview.ext.treeviewer.TreePanelI; +import jalview.ext.treeviewer.TreeViewerBindingI; +import jalview.ext.treeviewer.TreeViewerUtils; +import jalview.ext.treeviewer.LoadedTreeSequenceAssociation; +import jalview.gui.AlignViewport; +import jalview.gui.AlignmentPanel; +import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.PaintRefresher; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.UserColourScheme; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; +import jalview.util.MappingUtils; +import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import java.awt.Color; +import java.awt.Rectangle; import java.awt.event.ActionEvent; import java.awt.event.InputEvent; import java.awt.event.MouseEvent; +import java.util.ArrayList; 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.PhylogenyMethods; -import org.forester.phylogeny.PhylogenyNode; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; /** * Class for binding the Archaeopteryx tree viewer to the Jalview alignment that @@ -35,19 +54,29 @@ import org.forester.phylogeny.PhylogenyNode; * */ public final class JalviewBinding - implements ExternalTreeViewerBindingI + implements TreeViewerBindingI { - private org.forester.archaeopteryx.TreePanel treeView; + private final TreeFrameI aptxFrame; - private AlignmentViewport parentAvport; + private TreePanelI treeView; - private JTabbedPane treeTabs; + private AlignmentViewport parentAvport; private final StructureSelectionManager ssm; - private Map sequencesBoundToNodes; + private AlignmentPanel[] associatedPanels; + + private Map sequencesBoundToNodes; + + private Map nodesBoundToSequences; + + private float rootX; + + private float furthestNodeX; - private Map nodesBoundToSequences; + private int nrTreeGroups = 0; + + private boolean applyToAllViews = false; /** * @@ -64,75 +93,180 @@ public final class JalviewBinding * map with tree nodes and matching sequences used to calculate the * tree as key, value pair respectively. */ - public JalviewBinding(final MainFrame archaeopteryx, + public JalviewBinding(final TreeFrameI archaeopteryx, final AlignmentViewport jalviewAlignmentViewport, - final Map alignMappedToNodes, - final Map nodesMappedToAlign) + final Map alignMappedToNodes, + final Map nodesMappedToAlign) { + + if (archaeopteryx.getNumberOfTrees() > 1) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.getString("label.tabs_detected_archaeopteryx"), + MessageManager.getString("label.problem_reading_tree_file"), + JvOptionPane.WARNING_MESSAGE); + + } + // deal with/prohibit null values here as that will cause problems + aptxFrame = archaeopteryx; parentAvport = jalviewAlignmentViewport; sequencesBoundToNodes = alignMappedToNodes; nodesBoundToSequences = nodesMappedToAlign; - treeView = archaeopteryx.getMainPanel().getCurrentTreePanel(); - treeTabs = archaeopteryx.getMainPanel().getTabbedPane(); + treeView = archaeopteryx.getTreePanel(); ssm = parentAvport.getStructureSelectionManager(); - - // archaeopteryx.getMainPanel().getControlPanel().setColorBranches(true); ssm.addSelectionListener(this); treeView.addMouseListener(this); - PaintRefresher.Register(treeView, parentAvport.getSequenceSetId()); - + treeView.registerWithPaintRefresher( + parentAvport.getSequenceSetId()); + associatedPanels = PaintRefresher + .getAssociatedPanels(parentAvport.getSequenceSetId()); - treeTabs.addChangeListener(new ChangeListener() + aptxFrame.addFrameListener(new InternalFrameAdapter() { @Override - public void stateChanged(ChangeEvent e) + public void internalFrameClosed(InternalFrameEvent 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()); - - } - }); - + TreeViewerUtils.getActiveTreeViews().remove(aptxFrame); + ssm.removeSelectionListener(JalviewBinding.this); } - + }); + // 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() + // { + // treeView = archaeopteryx.getMainPanel().getCurrentTreePanel(); + // parentAvport.sendSelection(); + // // PaintRefresher.Refresh(treeView, + // // parentAvport.getSequenceSetId()); + // + // } + // }); + // + // } + // + // }); + } @Override public void actionPerformed(ActionEvent e) { + // reset hidden sequences first + parentAvport.showAllHiddenSeqs(); + + if (treeView.showingSubTree()) + { + LoadedTreeSequenceAssociation bindAptxNodes = new LoadedTreeSequenceAssociation( + parentAvport.getAlignment().getSequencesArray(), + treeView.getTree()); + bindAptxNodes.associateLeavesToSequences(); + sequencesBoundToNodes = bindAptxNodes.getAlignmentWithNodes(); + nodesBoundToSequences = bindAptxNodes.getNodesWithAlignment(); + TreeViewerUtils.associateNodesWithJalviewSequences(aptxFrame, parentAvport, + sequencesBoundToNodes, nodesBoundToSequences); + + + for (SequenceI seq : parentAvport.getAlignment().getSequencesArray()) + { + if (!sequencesBoundToNodes.containsKey(seq)) + { + parentAvport.hideSequence(new SequenceI[] { seq }); + } + } + } + + else + { + + Rectangle visibleView = treeView.getVisibleArea(); + + for (TreeNodeI node : treeView.getTree().getRoot() + .getAllDescendants()) + { + if (!(node.getXcoord() > visibleView.getMinX() + && node.getXcoord() < visibleView.getMaxX() + && node.getYcoord() > visibleView.getMinY() + && node.getYcoord() < visibleView.getMaxY())) + { + parentAvport + .hideSequence(new SequenceI[] + { nodesBoundToSequences.get(node) }); + } + } + + } + + + } @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 TreeNodeI 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.getX()); + } + treeView.notifyPaintRefresher(parentAvport.getSequenceSetId(), + false, false); + treeView.repaint(); + + + + } + }); + + } @Override public void mousePressed(final MouseEvent e) { - showNodeSelectionOnAlign(e); - } + } @Override public void mouseReleased(MouseEvent e) { @@ -157,39 +291,251 @@ public final class JalviewBinding if (source == parentAvport) // check if source is alignment from where the // tree originates { - treeView.setFoundNodes0( + treeView.setMatchingNodes( new HashSet(seqsel.getSequences().size())); + for (SequenceI selectedSequence : seqsel.getSequences()) { - PhylogenyNode matchingNode = sequencesBoundToNodes.get(selectedSequence); + TreeNodeI matchingNode = sequencesBoundToNodes + .get(selectedSequence); if (matchingNode != null) { - treeView.getFoundNodes0().add(matchingNode.getId()); + treeView.getMatchingNodes().add(matchingNode.getId()); + + + // if (!matchingNode.getBranchData().isHasBranchColor()) + // { + // // Color foundNodesColour = treeView.getTreeColorSet() + // // .getFoundColor0(); + // // matchingNode.getBranchData() + // // .setBranchColor(new BranchColor(foundNodesColour)); + // + // } + } } - PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId()); + treeView.repaint(); } } + /** + * Partially refactored from TreeCanvas + */ + public void partitionTree(final int x) + { + TreeI tree = treeView.getTree(); - @Override - public void showNodeSelectionOnAlign(final MouseEvent e) + if (!tree.isEmpty()) + { + // should be calculated on each partition as the tree can theoretically + // change in the meantime + TreeNodeI furthestNode = tree.getFurthestNode(); + furthestNodeX = furthestNode.getXcoord(); + rootX = tree.getRoot().getXcoord(); + + // don't bother if 0 distance tree or clicked x lies outside of tree + if (furthestNodeX != rootX && !(x > furthestNodeX)) + { + float threshold = (x - rootX) / (furthestNodeX - rootX); + List foundNodes = getNodesAboveThreshold( + threshold, + tree.getRoot()); + + } + } + + + } + + public List getNodesAboveThreshold(double threshold, + TreeNodeI node) + { + + List nodesAboveThreshold = new ArrayList<>(); + + parentAvport.setSelectionGroup(null); + parentAvport.getAlignment().deleteAllGroups(); + parentAvport.clearSequenceColours(); + if (parentAvport.getCodingComplement() != null) + { + parentAvport.getCodingComplement().setSelectionGroup(null); + parentAvport.getCodingComplement().getAlignment().deleteAllGroups(); + parentAvport.getCodingComplement().clearSequenceColours(); + } + + + colourNodesAboveThreshold(nodesAboveThreshold, threshold, + node); + return nodesAboveThreshold; + + } + + /** + * Partially refactored from TreeCanvas colourGroups (can be made nicer). + * + * @param nodeList + * @param threshold + * @param treeLength + * @param node + * @return + */ + private List colourNodesAboveThreshold( + List nodeList, double threshold, + TreeNodeI node) + { + + for (TreeNodeI childNode : node.getDirectChildren()) + { + childNode.setBranchColor(Color.black); + float nodeCutoff = (childNode.getXcoord() - rootX) + / (furthestNodeX - rootX); + + if (nodeCutoff > threshold) + { + nodeList.add(childNode); + + Color randomColour = new Color((int) (Math.random() * 255), + (int) (Math.random() * 255), (int) (Math.random() * 255)); + childNode.setBranchColor(randomColour); + + List groupSeqs = new ArrayList<>(); + SequenceI seq = nodesBoundToSequences.get(childNode); + if (seq != null) + { + groupSeqs.add(seq); + parentAvport.setSequenceColour(seq, randomColour); + } + + List descendantNodes = childNode + .getAllDescendants(); + // .forEach instead? + for (TreeNodeI descNode : descendantNodes) + { + seq = nodesBoundToSequences.get(descNode); + if (seq != null) + { + groupSeqs.add(seq); + parentAvport.setSequenceColour(seq, randomColour); + } + + descNode.setBranchColor(randomColour); + } + + if (groupSeqs != null) + { + nrTreeGroups++; + groupThresholdSequences(groupSeqs, randomColour); + }} + + else + { + colourNodesAboveThreshold(nodeList, threshold, childNode); + } + } + + + for (AlignmentPanel associatedPanel : associatedPanels) { + + associatedPanel.updateAnnotation(); + + final AlignViewportI codingComplement = associatedPanel.getAlignViewport() + .getCodingComplement(); + if (codingComplement != null) + { + // GROSS + ((AlignViewport) codingComplement).getAlignPanel() + .updateAnnotation(); + } + } + + + return nodeList; + } + + public void groupThresholdSequences(List groupedSeqs, + Color groupColour) { - final PhylogenyNode node = treeView.findNode(e.getX(), e.getY()); - if (node != null) + SequenceGroup treeGroup = new SequenceGroup(groupedSeqs, null, null, + true, true, false, 0, + parentAvport.getAlignment().getWidth() - 1); + + ColourSchemeI cs = null; + if (parentAvport.getGlobalColourScheme() != null) { - if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous - // selection if shift - // IS NOT pressed + if (parentAvport.getGlobalColourScheme() instanceof UserColourScheme) + { + cs = new UserColourScheme( + ((UserColourScheme) parentAvport.getGlobalColourScheme()) + .getColours()); + } + else + { + cs = ColourSchemeProperty.getColourScheme(treeGroup, + ColourSchemeProperty.getColourName( + parentAvport.getGlobalColourScheme())); + } + + } + treeGroup.setColourScheme(cs); + treeGroup.getGroupColourScheme().setThreshold( + parentAvport.getResidueShading().getThreshold(), + parentAvport.isIgnoreGapsConsensus()); + + treeGroup.setName("Tree Group " + nrTreeGroups); + treeGroup.setIdColour(groupColour); + + for (AlignmentPanel associatedPanel : associatedPanels) + { + AlignViewportI altViewport = associatedPanel + .getAlignViewport(); + + if (altViewport.getGlobalColourScheme() != null + && altViewport.getResidueShading() + .conservationApplied()) { - parentAvport.setSelectionGroup(null); + Conservation conserv = new Conservation(treeGroup.getName(), + treeGroup.getSequences(null), treeGroup.getStartRes(), + treeGroup.getEndRes()); + conserv.calculate(); + conserv.verdict(false, altViewport.getConsPercGaps()); + treeGroup.getGroupColourScheme().setConservation(conserv); } + altViewport.getAlignment().addGroup(treeGroup); + // TODO can we push all of the below into AlignViewportI? + final AlignViewportI codingComplement = altViewport + .getCodingComplement(); + if (codingComplement != null) + { + SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(treeGroup, + parentAvport, codingComplement); + if (mappedGroup.getSequences().size() > 0) + { + codingComplement.getAlignment().addGroup(mappedGroup); + for (SequenceI seq : mappedGroup.getSequences()) + { + codingComplement.setSequenceColour(seq, groupColour.brighter()); + } + } + } + + } + + } + + /** + * may or may not need an extra repaint on the alignment view (check what kira + * does) + */ + @Override + public void showNodeSelectionOnAlign(final TreeNodeI node) + { + if (node.isInternal()) { showMatchingChildSequences(node); @@ -200,43 +546,53 @@ public final class JalviewBinding showMatchingSequence(node); } + } - } + @Override - public void showMatchingSequence(final PhylogenyNode nodeToMatch) + public void showMatchingSequence(final TreeNodeI nodeToMatch) { SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch); if (matchingSequence != null) { + long nodeId = nodeToMatch.getId(); + addOrRemoveInSet(treeView.getMatchingNodes(), nodeId); treeSelectionChanged(matchingSequence); parentAvport.sendSelection(); - PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId()); // redundant? + } } @Override - public void showMatchingChildSequences(final PhylogenyNode parentNode) + public void showMatchingChildSequences(final TreeNodeI parentNode) { - List childNodes = PhylogenyMethods - .getAllDescendants(parentNode); + // redundancy here, Forester already iterates through tree to get all + // descendants + List childNodes = parentNode.getAllDescendants(); + - for (PhylogenyNode childNode : childNodes) + for (TreeNodeI childNode : childNodes) { // childNode.getBranchData().setBranchColor(new BranchColor(Color.BLUE)); SequenceI matchingSequence = nodesBoundToSequences.get(childNode); if (matchingSequence != null) { + long nodeId = childNode.getId(); + addOrRemoveInSet(treeView.getMatchingNodes(), nodeId); + treeSelectionChanged(matchingSequence); } + } parentAvport.sendSelection(); - PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId()); // redundant? + + } /** @@ -248,16 +604,128 @@ public final class JalviewBinding @Override public void treeSelectionChanged(final SequenceI sequence) { - SequenceGroup selected = parentAvport.getSelectionGroup(); + if (!parentAvport.isClosed()) // alignment view could be closed + { + SequenceGroup selected = parentAvport.getSelectionGroup(); + + if (selected == null) + { + selected = new SequenceGroup(); + parentAvport.setSelectionGroup(selected); + } - if (selected == null) + selected.setEndRes(parentAvport.getAlignment().getWidth() - 1); + selected.addOrRemove(sequence, true); + } + + } + + @Override + public void sortByTree_actionPerformed()// modify for Aptx + { + + // if (treeCanvas.applyToAllViews) + // { + // final ArrayList commands = new ArrayList<>(); + // for (AlignmentPanel ap : PaintRefresher + // .getAssociatedPanels(parentAvport.getSequenceSetId())) + // { + // commands.add(sortAlignmentIn(ap.av.getAlignPanel())); + // } + // parentAvport.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)); + // } + + } + + @Override + public CommandI sortAlignmentIn(AlignmentPanel ap) + { + // TODO: move to alignment view controller + + AlignmentViewport viewport = ap.av; + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + try + { + AlignmentSorter.sortByTree(viewport.getAlignment(), + nodesBoundToSequences, + treeView.getTree()); + CommandI undo; + undo = new OrderCommand("Tree Sort", oldOrder, + viewport.getAlignment()); + + ap.paintAlignment(true, false); + return undo; + + } catch (Exception e) { - selected = new SequenceGroup(); - parentAvport.setSelectionGroup(selected); + System.err.println(e.getMessage()); } + return null; + + } + - selected.setEndRes(parentAvport.getAlignment().getWidth() - 1); - selected.addOrRemove(sequence, true); + + /** + * TO BE MOVED + * + * @param set + * @param objectToCheck + */ + public static void addOrRemoveInSet(Set set, E objectToCheck) + { + if (set.contains(objectToCheck)) + { + set.remove(objectToCheck); + } + else + { + set.add(objectToCheck); + } } @@ -270,6 +738,17 @@ public final class JalviewBinding { this.parentAvport = parentAvport; } + + public AlignmentPanel[] getAssociatedPanels() + { + return associatedPanels; + } + + public void setAssociatedPanels(AlignmentPanel[] associatedPanels) + { + this.associatedPanels = associatedPanels; + } + }