JAL-1953 some more comments, moved JalviewBinding

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

diff --git a/src/jalview/ext/treeviewer/TreePanelI.java b/src/jalview/ext/treeviewer/TreePanelI.java
index bfd3211..6871105 100644 (file)
--- a/src/jalview/ext/treeviewer/TreePanelI.java
+++ b/src/jalview/ext/treeviewer/TreePanelI.java
@@ -37,6 +37,13 @@ public interface TreePanelI extends Accessible, MenuContainer
 
   public int getHeight();
 
+  /**
+   * Method for adding a tree node to the Set of nodes that are associated with
+   * some operation outside of the tree, such as nodes belonging to currently
+   * selected Jalview alignment sequences.
+   * 
+   * @param matchedNode
+   */
   public void addToMatchingNodes(TreeNodeI matchedNode);
 
   public abstract Set<Long> getMatchingNodesIds();
@@ -53,6 +60,11 @@ public interface TreePanelI extends Accessible, MenuContainer
 
   public abstract TreeI getTree();
 
+  /**
+   * Gets the File from where the Tree originates.
+   * 
+   * @return
+   */
   public abstract File getTreeFile();
 
   public abstract Rectangle getVisibleArea();
@@ -108,15 +120,13 @@ public interface TreePanelI extends Accessible, MenuContainer
 
   public void setPreferredSize(Dimension preferredSize);
 
-  /**
-   * 
-   * @param file
-   */
   public abstract void setTreeFile(File file);
 
   /**
+   * Checks if the tree has been cut to display just a sub tree.
    * 
-   * @return
+   * @return True if the panel is currently showing only a subtree, otherwise
+   *         false.
    */
   public boolean showingSubTree();