javadoc and new method to get alignment sequence index using a SearchResults object

[jalview.git] / src / jalview / datamodel / AlignmentI.java

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index b4075a0..af5b7c4 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -122,7 +122,7 @@ public interface AlignmentI
    * @param s
    *                Sequence to look for.
    * 
-   * @return Index of sequence within the alignment.
+   * @return Index of sequence within the alignment or -1 if not found
    */
   public int findIndex(SequenceI s);
 
@@ -359,4 +359,11 @@ public interface AlignmentI
    */
   public SequenceI findName(SequenceI startAfter, String token, boolean b);
 
+  /**
+   * find first sequence in alignment which is involved in the given search result object
+   * @param results
+   * @return -1 or index of sequence in alignment
+   */
+  public int findIndex(SearchResults results);
+
 }