JAL-2385 tweak to applet 'switch colour slider context'

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index c15bb99..2df099a 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -41,7 +41,8 @@ public interface AlignmentI extends AnnotatedCollectionI
    * 
    * Calculates the maximum width of the alignment, including gaps.
    * 
-   * @return Greatest sequence length within alignment.
+   * @return Greatest sequence length within alignment, or -1 if no sequences
+   *         present
    */
   @Override
   int getWidth();
@@ -107,11 +108,14 @@ public interface AlignmentI extends AnnotatedCollectionI
    * Used to set a particular index of the alignment with the given sequence.
    * 
    * @param i
-   *          Index of sequence to be updated.
+   *          Index of sequence to be updated. if i>length, sequence will be
+   *          added to end, with no intervening positions.
    * @param seq
-   *          New sequence to be inserted.
+   *          New sequence to be inserted. The existing sequence at position i
+   *          will be replaced.
+   * @return existing sequence (or null if i>current length)
    */
-  void setSequenceAt(int i, SequenceI seq);
+  SequenceI replaceSequenceAt(int i, SequenceI seq);
 
   /**
    * Deletes a sequence from the alignment
@@ -152,15 +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.
@@ -422,7 +427,7 @@ 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.