JAL-1953 some more comments, moved JalviewBinding

[jalview.git] / src / jalview / ext / treeviewer / TreeViewerBindingI.java

diff --git a/src/jalview/ext/treeviewer/TreeViewerBindingI.java b/src/jalview/ext/treeviewer/TreeViewerBindingI.java
index bb6eb19..afbceab 100644 (file)
--- a/src/jalview/ext/treeviewer/TreeViewerBindingI.java
+++ b/src/jalview/ext/treeviewer/TreeViewerBindingI.java
@@ -59,14 +59,29 @@ public interface TreeViewerBindingI
   public Map<TreeNodeI, SequenceI> getNodesWithAlignment();
 
   /**
+   * Triggers a tree partition from the specified x coordinate.
    * 
    * @param x
-   *          coordinate that functions as the clustering threshold
+   * 
    */
   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);
 
   /**
@@ -81,13 +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);
 
 }