X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Ftreeviewer%2FTreeViewerBindingI.java;h=afbceab5fbd867d8888aeeb08453e1ae2938cdb6;hb=2605483ebb517c8b31e821f192c95557145f9c2d;hp=8642703dbe099c865543cce08a986f487dd887c6;hpb=46d18401c788a01ef8ad5340547d0209cbf2186d;p=jalview.git

diff --git a/src/jalview/ext/treeviewer/TreeViewerBindingI.java b/src/jalview/ext/treeviewer/TreeViewerBindingI.java
index 8642703..afbceab 100644
--- a/src/jalview/ext/treeviewer/TreeViewerBindingI.java
+++ b/src/jalview/ext/treeviewer/TreeViewerBindingI.java
@@ -66,8 +66,22 @@ public interface TreeViewerBindingI
    */
   public void partitionTree(final int x);
 
+  /**
+   * Looks up the given TreeNodeI in the tree and highlights Jalview sequences
+   * that belong to it or its descendants.
+   * 
+   * @param parentNode
+   *          node from where the descendants should get matched, this node
+   *          should be internal.
+   */
   public void showMatchingChildSequences(TreeNodeI parentNode);
 
+  /**
+   * Highlights the Jalview sequence belonging to the given TreeNodeI (if
+   * possible).
+   * 
+   * @param nodeToMatch
+   */
   public void showMatchingSequence(TreeNodeI nodeToMatch);
 
   /**
@@ -82,13 +96,25 @@ public interface TreeViewerBindingI
    * tree.
    * 
    * @param alignPanel
-   *          Panel containing the alignment to be sorted.
+   *          panel containing the alignment to be sorted.
    * @return the sorting Command
    */
   public CommandI sortAlignmentIn(AlignmentPanel alignPanel);
 
+  /**
+   * This should be triggered when the user wants to sort the Jalview alignment
+   * by the sequence order of the tree.
+   */
   public void sortByTree_actionPerformed();
 
+  /**
+   * If the nodes that should be matched have changed (different one selected by
+   * the user), this method notifies the Jalview alignment view that the
+   * matching sequences have changed as well.
+   * 
+   * @param sequence
+   *          the new SequenceI that should be matched.
+   */
   public void treeSelectionChanged(SequenceI sequence);
 
 }