Merge branch 'develop' into features/mchmmer

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 5fb16d6..d591f42 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -504,8 +504,6 @@ public interface AlignmentI extends AnnotatedCollectionI
    *          - null or specific sequence reference
    * @param groupRef
    *          - null or specific group reference
-   * @param method
-   *          - CalcId for the annotation (must match)
    * 
    * @return existing annotation matching the given attributes
    */
@@ -588,6 +586,16 @@ public interface AlignmentI extends AnnotatedCollectionI
   public void setHiddenColumns(HiddenColumns cols);
 
   /**
+   * Insert a sequence at a position in an alignment
+   * 
+   * @param i
+   *          The index of the position.
+   * @param snew
+   *          The new sequence.
+   */
+  void insertSequenceAt(int i, SequenceI snew);
+
+  /**
    * Set the first sequence as representative and hide its insertions. Typically
    * used when loading JPred files.
    */
@@ -607,5 +615,4 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   public HiddenColumns propagateInsertions(SequenceI profileseq,
           AlignmentView input);
-
 }