Merge branch 'develop' into releases/Release_2_9_1_Branch

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 60040d8..45a767c 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -219,6 +219,12 @@ public interface SequenceI extends ASequenceI
   public int[] findPositionMap();
 
   /**
+   * 
+   * @return true if sequence is composed of amino acid characters
+   */
+  public boolean isProtein();
+
+  /**
    * Delete a range of aligned sequence columns, creating a new dataset sequence
    * if necessary and adjusting start and end positions accordingly.
    * 
@@ -233,19 +239,21 @@ public interface SequenceI extends ASequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *          DOCUMENT ME!
+   *          alignment column number
    * @param c
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int i, char c);
 
   /**
-   * DOCUMENT ME!
+   * insert given character at alignment column position
    * 
    * @param position
-   *          DOCUMENT ME!
+   *          alignment column number
+   * @param count
+   *          length of insert
    * @param ch
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int position, int count, char ch);
 
@@ -435,7 +443,21 @@ public interface SequenceI extends ASequenceI
    */
   public PDBEntry getPDBEntry(String pdbId);
 
+  /**
+   * Set the distinct source database, and accession number from which a
+   * sequence and its start-end data were derived from. This is very important
+   * for SIFTS mappings and must be set prior to performing SIFTS mapping.
+   * 
+   * @param dbRef
+   *          the source dbRef for the sequence
+   */
   public void setSourceDBRef(DBRefEntryI dbRef);
 
+  /**
+   * Get the distinct source database, and accession number from which a
+   * sequence and its start-end data were derived from.
+   * 
+   * @return
+   */
   public DBRefEntryI getSourceDBRef();
 }