JAL-1953 first pass of adding javadoc, some methods renamed
[jalview.git] / src / jalview / ext / archaeopteryx / JalviewBinding.java
index 61171b3..f0c2866 100644 (file)
@@ -1,12 +1,22 @@
 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.AlignmentI;
 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.LoadedTreeSequenceAssociation;
+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.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
@@ -22,6 +32,7 @@ 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;
@@ -31,19 +42,10 @@ 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 javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
-import org.forester.archaeopteryx.MainFrame;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.BranchColor;
-
 /**
  * Class for binding the Archaeopteryx tree viewer to the Jalview alignment that
  * it originates from, meaning that selecting sequences in the tree viewer also
@@ -53,21 +55,19 @@ import org.forester.phylogeny.data.BranchColor;
  *
  */
 public final class JalviewBinding
-        implements ExternalTreeViewerBindingI<PhylogenyNode>
+        implements TreeViewerBindingI
 {
-  private org.forester.archaeopteryx.TreePanel treeView;
+  private final TreeFrameI aptxFrame;
 
-  private AlignmentViewport parentAvport;
+  private TreePanelI treeView;
 
-  private final JTabbedPane treeTabs;
+  private AlignmentViewport parentAvport;
 
   private final StructureSelectionManager ssm;
 
-  private AlignmentPanel[] associatedPanels;
-
-  private Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
+  private Map<SequenceI, TreeNodeI> sequencesBoundToNodes;
 
-  private Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
+  private Map<TreeNodeI, SequenceI> nodesBoundToSequences;
 
   private float rootX;
 
@@ -92,83 +92,130 @@ 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<SequenceI, PhylogenyNode> alignMappedToNodes,
-          final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
+          final Map<SequenceI, TreeNodeI> alignMappedToNodes,
+          final Map<TreeNodeI, SequenceI> nodesMappedToAlign)
   {
 
-    if (archaeopteryx.getMainPanel().getTabbedPane().getTabCount() > 1)
+    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();
     
+    aptxFrame.setViewBinding(this);
     ssm.addSelectionListener(this);
     treeView.addMouseListener(this);
-    PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
-    associatedPanels = PaintRefresher
-            .getAssociatedPanels(parentAvport.getSequenceSetId());
+    treeView.registerWithPaintRefresher(
+            parentAvport.getSequenceSetId());
 
-    archaeopteryx.addInternalFrameListener(new InternalFrameAdapter()
+    aptxFrame.addFrameListener(new InternalFrameAdapter()
     {
 
       @Override
       public void internalFrameClosed(InternalFrameEvent e)
       {
-        AptxInit.getAllAptxFrames().remove(archaeopteryx);
+        TreeViewerUtils.getActiveTreeViews().remove(aptxFrame);
+        ssm.removeSelectionListener(JalviewBinding.this);
       }
 
     });
 
-    treeTabs.addChangeListener(new ChangeListener()
-    {
+    // 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 stateChanged(ChangeEvent e)
-      {
+  }
 
-        SwingUtilities.invokeLater(new Runnable()
+  @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.associateNodesToSequences();
+      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 });
+        }
+      }
+    }
 
-          @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());
+    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 actionPerformed(ActionEvent e)
-  {
   }
 
   @Override
@@ -182,7 +229,8 @@ public final class JalviewBinding
        */
       public void run()
       {
-        final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
+        final TreeNodeI node = treeView.findNode(e.getX(),
+                e.getY());
         if (node != null)
         {
           if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
@@ -199,7 +247,8 @@ public final class JalviewBinding
 
           partitionTree(e.getX());
       }
-        PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
+        treeView.notifyPaintRefresher(parentAvport.getSequenceSetId(),
+                false, false);
         treeView.repaint();
 
 
@@ -239,25 +288,27 @@ public final class JalviewBinding
     if (source == parentAvport) // check if source is alignment from where the
     // tree originates
     {
-      treeView.setFoundNodes0(
+      treeView.setMatchingNodes(
               new HashSet<Long>(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));
 
-          }
+          // if (!matchingNode.getBranchData().isHasBranchColor())
+          // {
+          // // Color foundNodesColour = treeView.getTreeColorSet()
+          // // .getFoundColor0();
+          // // matchingNode.getBranchData()
+          // // .setBranchColor(new BranchColor(foundNodesColour));
+          //
+          // }
 
         }
 
@@ -274,40 +325,35 @@ public final class JalviewBinding
    */
   public void partitionTree(final int x)
   {
-    Phylogeny tree = treeView.getPhylogeny();
+    TreeI tree = treeView.getTree();
 
     if (!tree.isEmpty())
     {
       // should be calculated on each partition as the tree can theoretically
       // change in the meantime
-      PhylogenyNode furthestNode = PhylogenyMethods
-              .calculateNodeWithMaxDistanceToRoot(tree);
+      TreeNodeI furthestNode = tree.getFurthestNode();
       furthestNodeX = furthestNode.getXcoord();
       rootX = tree.getRoot().getXcoord();
 
-      if (furthestNodeX != rootX && !(x < rootX || x > furthestNodeX)) // don't
-                                                                       // bother
-                                                                       // if 0
-                                                       // distance tree or
-                                                       // clicked x lies outside
-                                                       // of tree
-      {
+      // 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<PhylogenyNode> foundNodes = getNodesAboveThreshold(threshold,
+        List<TreeNodeI> foundNodes = getNodesAboveThreshold(
+                threshold,
                 tree.getRoot());
 
-      }
+
     }
 
 
   }
 
-  public List<PhylogenyNode> getNodesAboveThreshold(double threshold,
-          PhylogenyNode node)
+  public List<TreeNodeI> getNodesAboveThreshold(float threshold,
+          TreeNodeI node)
   {
 
-    List<PhylogenyNode> nodesAboveThreshold = new ArrayList<>();
+    List<TreeNodeI> nodesAboveThreshold = new ArrayList<>();
 
     parentAvport.setSelectionGroup(null);
     parentAvport.getAlignment().deleteAllGroups();
@@ -335,15 +381,14 @@ public final class JalviewBinding
    * @param node
    * @return
    */
-  private List<PhylogenyNode> colourNodesAboveThreshold(
-          List<PhylogenyNode> nodeList, double threshold,
-          PhylogenyNode node)
+  private List<TreeNodeI> colourNodesAboveThreshold(
+          List<TreeNodeI> nodeList, float threshold,
+          TreeNodeI node)
   {
 
-    for (PhylogenyNode childNode : node.getDescendants())
+    for (TreeNodeI childNode : node.getDirectChildren())
     {
-      childNode.getBranchData()
-              .setBranchColor(new BranchColor(Color.black));
+      childNode.setBranchColor(Color.black);
       float nodeCutoff = (childNode.getXcoord() - rootX)
               / (furthestNodeX - rootX);
 
@@ -353,8 +398,7 @@ public final class JalviewBinding
 
         Color randomColour = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
-        childNode.getBranchData()
-                .setBranchColor(new BranchColor(randomColour));
+        childNode.setBranchColor(randomColour);
 
         List<SequenceI> groupSeqs = new ArrayList<>();
         SequenceI seq = nodesBoundToSequences.get(childNode);
@@ -364,10 +408,10 @@ public final class JalviewBinding
           parentAvport.setSequenceColour(seq, randomColour);
         }
 
-        List<PhylogenyNode> descendantNodes = PhylogenyMethods
-                .getAllDescendants(childNode);
+        List<TreeNodeI> descendantNodes = childNode
+                .getAllDescendants();
         // .forEach instead?
-        for (PhylogenyNode descNode : descendantNodes)
+        for (TreeNodeI descNode : descendantNodes)
         {
           seq = nodesBoundToSequences.get(descNode);
           if (seq != null)
@@ -376,8 +420,7 @@ public final class JalviewBinding
             parentAvport.setSequenceColour(seq, randomColour);
           }
 
-          descNode.getBranchData()
-                  .setBranchColor(new BranchColor(randomColour));
+          descNode.setBranchColor(randomColour);
         }
 
         if (groupSeqs != null)
@@ -392,8 +435,8 @@ public final class JalviewBinding
       }
     }
 
-
-        for (AlignmentPanel associatedPanel : associatedPanels) {
+    for (AlignmentPanel associatedPanel : getAssociatedPanels())
+    {
 
         associatedPanel.updateAnnotation();
 
@@ -443,7 +486,7 @@ public final class JalviewBinding
     treeGroup.setName("Tree Group " + nrTreeGroups);
     treeGroup.setIdColour(groupColour);
 
-    for (AlignmentPanel associatedPanel : associatedPanels)
+    for (AlignmentPanel associatedPanel : getAssociatedPanels())
     {
       AlignViewportI altViewport = associatedPanel
               .getAlignViewport();
@@ -482,12 +525,9 @@ public final class JalviewBinding
 
   }
 
-  /**
-   * may or may not need an extra repaint on the alignment view (check what kira
-   * does)
-   */
+
   @Override
-  public void showNodeSelectionOnAlign(final PhylogenyNode node)
+  public void showNodeSelectionOnAlign(final TreeNodeI node)
   {
 
       if (node.isInternal())
@@ -508,13 +548,13 @@ public final class JalviewBinding
 
 
   @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.getFoundNodes0(), nodeId);
+      addOrRemoveInSet(treeView.getMatchingNodes(), nodeId);
       treeSelectionChanged(matchingSequence);
       parentAvport.sendSelection();
 
@@ -522,21 +562,20 @@ public final class JalviewBinding
   }
 
   @Override
-  public void showMatchingChildSequences(final PhylogenyNode parentNode)
+  public void showMatchingChildSequences(final TreeNodeI parentNode)
   {
-    List<PhylogenyNode> childNodes = PhylogenyMethods
-            .getAllDescendants(parentNode);
+    // redundancy here, Forester already iterates through tree to get all
+    // descendants
+    List<TreeNodeI> 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.getFoundNodes0(), nodeId);
+        addOrRemoveInSet(treeView.getMatchingNodes(), nodeId);
 
         treeSelectionChanged(matchingSequence);
 
@@ -548,12 +587,7 @@ public final class JalviewBinding
 
   }
 
-  /**
-   * Refactored from TreeCanvas.
-   * 
-   * @param sequence
-   *          of the node selected in the tree viewer.
-   */
+
   @Override
   public void treeSelectionChanged(final SequenceI sequence)
   {
@@ -572,7 +606,85 @@ public final class JalviewBinding
     }
 
   }
-  public void sortByTree_actionPerformed() {
+
+  @Override
+  public void sortByTree_actionPerformed()
+  {
+
+    // if (applyToAllViews)
+
+      final ArrayList<CommandI> commands = new ArrayList<>();
+      for (AlignmentPanel ap : PaintRefresher
+              .getAssociatedPanels(parentAvport.getSequenceSetId()))
+      {
+        commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
+        ap.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);
+            }
+          }
+        });
+
+        ap.alignFrame.updateEditMenuBar();
+      }
+    }
+  // else
+  // {
+  // alignPanel.alignFrame.addHistoryItem(sortAlignmentIn(alignPanel));
+  // }
+
+
+
+  @Override
+  public CommandI sortAlignmentIn(AlignmentPanel ap)
+  {
+    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)
+    {
+      System.err.println(e.getMessage());
+    }
+    return null;
 
   }
   
@@ -609,14 +721,23 @@ public final class JalviewBinding
 
   public AlignmentPanel[] getAssociatedPanels()
   {
-    return associatedPanels;
+    return PaintRefresher
+            .getAssociatedPanels(parentAvport.getSequenceSetId());
+  }
+
+  @Override
+  public Map<SequenceI, TreeNodeI> getAlignmentWithNodes()
+  {
+    return sequencesBoundToNodes;
   }
 
-  public void setAssociatedPanels(AlignmentPanel[] associatedPanels)
+  @Override
+  public Map<TreeNodeI, SequenceI> getNodesWithAlignment()
   {
-    this.associatedPanels = associatedPanels;
+    return nodesBoundToSequences;
   }
 
+
 }