X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=a0b3ff1a0696fdac5c26d9f107e725b03642de9d;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=2209f87c76aca24a23863528a5d83492c544a9fd;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2209f87..a0b3ff1 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -156,15 +156,16 @@ public interface AlignmentI extends AnnotatedCollectionI
   int findIndex(SequenceI s);
 
   /**
-   * Finds group that given sequence is part of.
+   * Returns the first group (in the order in which groups were added) that
+   * includes the given sequence and aligned position (base 0), or null if none
+   * found
    * 
-   * @param s
-   *          Sequence in alignment.
+   * @param seq
+   * @param position
    * 
-   * @return First group found for sequence. WARNING : Sequences may be members
-   *         of several groups. This method is incomplete.
+   * @return
    */
-  SequenceGroup findGroup(SequenceI s);
+  SequenceGroup findGroup(SequenceI seq, int position);
 
   /**
    * Finds all groups that a given sequence is part of.
@@ -298,12 +299,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   boolean hasRNAStructure();
 
   /**
-   * Set alignment to be a nucleotide sequence
-   * 
-   */
-  void setNucleotide(boolean b);
-
-  /**
    * Get the associated dataset for the alignment.
    * 
    * @return Alignment containing dataset sequences or null of this is a
@@ -426,7 +421,7 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @param results
    * @return -1 or index of sequence in alignment
    */
-  int findIndex(SearchResults results);
+  int findIndex(SearchResultsI results);
 
   /**
    * append sequences and annotation from another alignment object to this one.