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 db45d1b..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
    */
@@ -580,18 +578,41 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
+  /**
+   * Set the hidden columns collection on the alignment
+   * 
+   * @param cols
+   */
   public void setHiddenColumns(HiddenColumns cols);
 
   /**
    * Insert a sequence at a position in an alignment
    * 
    * @param i
-   *          The idnex of the position.
+   *          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.
+   */
+  public void setupJPredAlignment();
 
+  /**
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   *          sequence in al which sequences are aligned to
+   * @param input
+   *          alignment view where sequence corresponding to profileseq is first
+   *          entry
+   * @return new HiddenColumns for new alignment view, with insertions into
+   *         profileseq marked as hidden.
+   */
+  public HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentView input);
 }