JAL-2629 removed SequenceI.get/setLastPosition and related code

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 28be85f..e5edc91 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -45,6 +45,10 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
+
   /**
    * Get the display name
    */
@@ -193,13 +197,14 @@ public interface SequenceI extends ASequenceI
   public int findIndex(int pos);
 
   /**
-   * Returns the sequence position for an alignment position.
+   * Returns the sequence position for an alignment (column) position. If at a
+   * gap, returns the position of the next residue to the right. If beyond the
+   * end of the sequence, returns 1 more than the last residue position.
    * 
    * @param i
    *          column index in alignment (from 0..<length)
    * 
-   * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
-   *         ith column
+   * @return
    */
   public int findPosition(int i);
 
@@ -450,17 +455,6 @@ public interface SequenceI extends ASequenceI
   public void transferAnnotation(SequenceI entry, Mapping mp);
 
   /**
-   * @param index
-   *          The sequence index in the MSA
-   */
-  public void setIndex(int index);
-
-  /**
-   * @return The index of the sequence in the alignment
-   */
-  public int getIndex();
-
-  /**
    * @return The RNA of the sequence in the alignment
    */
 
@@ -497,6 +491,16 @@ public interface SequenceI extends ASequenceI
    */
   public List<DBRefEntry> getPrimaryDBRefs();
 
+  public void updateHMMMapping();
+
+  boolean isHMMConsensusSequence();
+
+  void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
+
+  boolean hasHMMAnnotation();
+
+  void setHasInfo(boolean status);
+
   /**
    * Returns a (possibly empty) list of sequence features that overlap the given
    * alignment column range, optionally restricted to one or more specified
@@ -527,6 +531,8 @@ public interface SequenceI extends ASequenceI
    */
   BitSet getInsertionsAsBits();
 
+  void mapToReference(AlignmentAnnotation rf);
+
   /**
    * Replaces every occurrence of c1 in the sequence with c2 and returns the
    * number of characters changed
@@ -534,7 +540,7 @@ public interface SequenceI extends ASequenceI
    * @param c1
    * @param c2
    */
-  public int replace(char c1, char c2);
+  int replace(char c1, char c2);
 
   /**
    * Answers the GeneLociI, or null if not known