X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;fp=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=2f365e6e113c7c8fc4b4d28082afa7f075f8772c;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=7c3eb41fa8f4a598d9a8ea4daf2e333d1c2f2bf6;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 7c3eb41..2f365e6 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -357,12 +357,13 @@ public interface SequenceI extends ASequenceI
   /**
    * set the array of Database references for the sequence.
    * 
-   * BH 2019.02.04 changes param to DBModlist 
+   * BH 2019.02.04 changes param to DBModlist
    * 
    * @param dbs
    * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
    *             set are not normalised.
-   * @throws InvalidArgumentException if the is not one created by Sequence itself
+   * @throws InvalidArgumentException
+   *           if the is not one created by Sequence itself
    */
   @Deprecated
   public void setDBRefs(DBModList<DBRefEntry> dbs);
@@ -447,8 +448,8 @@ public interface SequenceI extends ASequenceI
 
   /**
    * 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.
+   * calcId (source), label (type) and description (observation instance). Null
+   * values do not match.
    * 
    * @param calcId
    * @param label
@@ -456,6 +457,7 @@ public interface SequenceI extends ASequenceI
    */
   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
@@ -530,7 +532,8 @@ public interface SequenceI extends ASequenceI
    *          optional feature types to restrict results to
    * @return
    */
-  List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
+  List<SequenceFeature> findFeatures(int fromCol, int toCol,
+          String... types);
 
   /**
    * Method to call to indicate that the sequence (characters or alignment/gaps)
@@ -538,7 +541,7 @@ public interface SequenceI extends ASequenceI
    * positions to be invalidated.
    */
   void sequenceChanged();
-  
+
   /**
    * 
    * @return BitSet corresponding to index [0,length) where Comparison.isGap()
@@ -570,9 +573,8 @@ public interface SequenceI extends ASequenceI
    * @param chromosomeId
    * @param map
    */
-  void setGeneLoci(String speciesId, String assemblyId,
-          String chromosomeId, MapList map);
-
+  void setGeneLoci(String speciesId, String assemblyId, String chromosomeId,
+          MapList map);
 
   /**
    * Returns the sequence string constructed from the substrings of a sequence
@@ -595,6 +597,4 @@ public interface SequenceI extends ASequenceI
    */
   public int firstResidueOutsideIterator(Iterator<int[]> it);
 
-
 }
-