JAL-1953 first pass of adding javadoc, some methods renamed

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

diff --git a/src/jalview/ext/treeviewer/LoadedTreeAssociationI.java b/src/jalview/ext/treeviewer/LoadedTreeAssociationI.java
index 19cf834..6252a57 100644 (file)
--- a/src/jalview/ext/treeviewer/LoadedTreeAssociationI.java
+++ b/src/jalview/ext/treeviewer/LoadedTreeAssociationI.java
@@ -5,18 +5,36 @@ import jalview.datamodel.SequenceI;
 import java.util.Map;
 
 /**
- * Interface for associating the leaves of a loaded in (not calculated) tree to
- * the alignment sequences in Jalview.
+ * Interface for associating the nodes of a loaded in (instead of calculated)
+ * tree to the sequences of an alignment in Jalview.
  * 
  * @author kjvanderheide
  *
- * 
  */
 public interface LoadedTreeAssociationI
 {
-  public void associateLeavesToSequences();
+  /**
+   * Tries to match the loaded in tree nodes as best as possible with Jalview
+   * sequences
+   * 
+   * Partially refactored from the old Jalview TreeModel
+   * associateLeavesToSequences method.
+   */
+  public void associateNodesToSequences();
 
+  /**
+   * See
+   * {@link jalview.ext.treeviewer.TreeViewerBindingI#getAlignmentWithNodes()}
+   * 
+   * 
+   */
   public Map<SequenceI, TreeNodeI> getAlignmentWithNodes();
 
+  /**
+   * See
+   * {@link jalview.ext.treeviewer.TreeViewerBindingI#getNodesWithAlignment()}
+   * 
+   * 
+   */
   public Map<TreeNodeI, SequenceI> getNodesWithAlignment();
 }