Merge branch 'patch/JAL-3874_newJmolAndGradleDedup' into develop

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 5a3aafd..7c3eb41 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -114,9 +114,11 @@ public interface SequenceI extends ASequenceI
    * get a range on the sequence as a string
    * 
    * @param start
-   *          position relative to start of sequence including gaps (from 0)
+   *          (inclusive) position relative to start of sequence including gaps
+   *          (from 0)
    * @param end
-   *          position relative to start of sequence including gaps (from 0)
+   *          (exclusive) position relative to start of sequence including gaps
+   *          (from 0)
    * 
    * @return String containing all gap and symbols in specified range
    */
@@ -218,7 +220,7 @@ public interface SequenceI extends ASequenceI
    *          - last column, base 1
    * @return
    */
-  public Range findPositions(int fromColum, int toColumn);
+  public ContiguousI findPositions(int fromColum, int toColumn);
 
   /**
    * Returns an int array where indices correspond to each residue in the
@@ -444,6 +446,17 @@ public interface SequenceI extends ASequenceI
           String label);
 
   /**
+   * Returns a (possibly empty) list of any annotations that match on given
+   * calcId (source), label (type) and description (observation instance).
+   * Null values do not match.
+   * 
+   * @param calcId
+   * @param label
+   * @param description
+   */
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description);
+  /**
    * create a new dataset sequence (if necessary) for this sequence and sets
    * this sequence to refer to it. This call will move any features or
    * references on the sequence onto the dataset. It will also make a duplicate