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

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

diff --git a/src/jalview/ext/treeviewer/LoadedTreeSequenceAssociation.java b/src/jalview/ext/treeviewer/LoadedTreeSequenceAssociation.java
index 479e450..c05a57c 100644 (file)
--- a/src/jalview/ext/treeviewer/LoadedTreeSequenceAssociation.java
+++ b/src/jalview/ext/treeviewer/LoadedTreeSequenceAssociation.java
@@ -8,6 +8,14 @@ import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
 
+/**
+ * Generic implementation of {@link LoadedTreeAssociationI } that tries to
+ * associate tree nodes based on comparing Jalview's sequence IDs to tree node
+ * names.
+ * 
+ * @author kjvanderheide
+ *
+ */
 public class LoadedTreeSequenceAssociation
         implements LoadedTreeAssociationI
 {
@@ -29,18 +37,8 @@ public class LoadedTreeSequenceAssociation
 
   }
 
-  /**
-   * Tries to match sequences from Jalview with tree nodes in Archaeopteryx and
-   * fills in the tree node with sequence data if a match is found.
-   * 
-   * Partially refactored from the old Jalview TreeModel
-   * associateLeavesToSequences method.
-   *
-   * @param seqs
-   * @param aptxTree
-   */
   @Override
-  public void associateLeavesToSequences()
+  public void associateNodesToSequences()
 
   {
     SequenceIdMatcher algnIds = new SequenceIdMatcher(alignSequences);