Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index a1b2683..8f1d160 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -51,7 +51,6 @@ public interface SequenceI extends ASequenceI
   public HiddenMarkovModel getHMM();
 
   public void setHMM(HiddenMarkovModel hmm);
-
   /**
    * Get the display name
    */
@@ -519,7 +518,6 @@ public interface SequenceI extends ASequenceI
    *         list
    */
   public List<DBRefEntry> getPrimaryDBRefs();
-
   /**
    * Answers true if the sequence has annotation for Hidden Markov Model
    * information content, else false
@@ -563,7 +561,7 @@ public interface SequenceI extends ASequenceI
    * @param c1
    * @param c2
    */
-  int replace(char c1, char c2);
+  public int replace(char c1, char c2);
 
   /**
    * Answers the GeneLociI, or null if not known
@@ -593,7 +591,7 @@ public interface SequenceI extends ASequenceI
    *          the iterator to use
    * @return a String corresponding to the sequence
    */
-  String getSequenceStringFromIterator(Iterator<int[]> it);
+  public String getSequenceStringFromIterator(Iterator<int[]> it);
 
   /**
    * Locate the first position in this sequence which is not contained in an
@@ -603,7 +601,6 @@ public interface SequenceI extends ASequenceI
    *          iterator over regions
    * @return first residue not contained in regions
    */
-
   public int firstResidueOutsideIterator(Iterator<int[]> it);