X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Farchaeopteryx%2FJalviewAptxBinding.java;h=e0a143ce1b41484ce0977ee50a820fb40ad3615b;hb=b6c5f18ed142f770c8ff9bbe4a5000dbb277080e;hp=755828dee147f223f604245e16902e2e8940e6ed;hpb=efbac0c57e4f0cfed3ff952606afe5d3009f4e86;p=jalview.git

diff --git a/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java b/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
index 755828d..e0a143c 100644
--- a/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
@@ -13,28 +13,54 @@ 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 org.forester.archaeopteryx.MainFrame;
+import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 
-public class JalviewAptxBinding implements JalviewTreeViewerBindingI
+/**
+ * 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 JalviewAptxBinding implements JalviewTreeViewerBindingI
 {
-  org.forester.archaeopteryx.TreePanel treeView;
+  private org.forester.archaeopteryx.TreePanel treeView;
 
-  AlignmentViewport parentAvport;
+  private AlignmentViewport parentAvport;
 
-  StructureSelectionManager ssm;
+  private final StructureSelectionManager ssm;
 
-  Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
+  private Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
 
-  Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
+  private Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
 
-  public JalviewAptxBinding(MainFrame archaeopteryx,
-          AlignmentViewport jalviewAlignmentViewport,
-          Map<SequenceI, PhylogenyNode> alignMappedToNodes,
-          Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
+  /**
+   * 
+   * @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 JalviewAptxBinding(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;
@@ -43,6 +69,7 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
     ssm.addSelectionListener(this);
     treeView.addMouseListener(this);
     PaintRefresher.Register(treeView, parentAvport.getSequenceSetId());
+
   }
 
   @Override
@@ -56,7 +83,7 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
   }
 
   @Override
-  public void mousePressed(MouseEvent e)
+  public void mousePressed(final MouseEvent e)
   {
     showNodeSelectionOnAlign(e);
   }
@@ -76,12 +103,14 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
   {
   }
 
+
   @Override
-  public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          HiddenColumns hidden, SelectionSource source)
+  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
+    // tree originates
     {
       treeView.setFoundNodes0(
               new HashSet<Long>(seqsel.getSequences().size()));
@@ -103,47 +132,76 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
   }
 
   /**
-   * Note that this currently only checks external nodes
+   * If a node is selected in the tree panel this method highlights the
+   * corresponding sequence in the Jalview alignment view. If an internal node
+   * is selected all child sequences get highlighted as well.
    */
   @Override
-  public void showNodeSelectionOnAlign(MouseEvent e)
+  public void showNodeSelectionOnAlign(final MouseEvent e)
   {
     final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
     if (node != null)
     {
-      SequenceI matchingSequence = nodesBoundToSequences.get(node);
-      if (matchingSequence != null)
+      if ((e.getModifiers() & InputEvent.SHIFT_MASK) == 0) // clear previous
+      // selection if shift
+      // IS NOT pressed
       {
+        parentAvport.setSelectionGroup(null);
+      }
 
-        if ((e.getModifiers() & InputEvent.SHIFT_MASK) != 0) // shift is pressed
-        // (so multiple nodes
-        // can be selected)
-        {
-          // something?
+      if (node.isInternal())
+      {
+        showMatchingChildSequences(node);
 
-        }
-        else
-        {
-          parentAvport.setSelectionGroup(null); // reset selection if shift
-                                                // isn't
-          // pressed
-        }
+      }
+      else
+      {
+        showMatchingSequence(node);
 
-        treeSelectionChanged(matchingSequence);
-        parentAvport.sendSelection(); // not actually needed?
+      }
 
-        PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
+    }
+  }
+
+
+
+
+  public void showMatchingSequence(final PhylogenyNode nodeToMatch)
+  {
+    SequenceI matchingSequence = nodesBoundToSequences.get(nodeToMatch);
+    if (matchingSequence != null)
+    {
+      treeSelectionChanged(matchingSequence);
+      parentAvport.sendSelection();
+      PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
+    }
+  }
+
+  public void showMatchingChildSequences(final PhylogenyNode parentNode)
+  {
+    final List<PhylogenyNode> childNodes = PhylogenyMethods
+            .getAllDescendants(parentNode);
+
+    for (PhylogenyNode childNode : childNodes)
+    {
+      SequenceI matchingSequence = nodesBoundToSequences.get(childNode);
+      if (matchingSequence != null)
+      {
+        treeSelectionChanged(matchingSequence);
       }
     }
 
+    parentAvport.sendSelection();
+    PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
   }
 
   /**
-   * Refactored from TreeCanvas
+   * Refactored from TreeCanvas.
    * 
    * @param sequence
+   *          of the node selected in the tree viewer.
    */
-  public void treeSelectionChanged(SequenceI sequence)
+  public void treeSelectionChanged(final SequenceI sequence)
   {
     SequenceGroup selected = parentAvport.getSelectionGroup();
 
@@ -163,7 +221,7 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
     return parentAvport;
   }
 
-  public void setParentAvport(AlignmentViewport parentAvport)
+  public void setParentAvport(final AlignmentViewport parentAvport)
   {
     this.parentAvport = parentAvport;
   }