JAL-2110 SequenceI.isProtein method

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 50f88f3..355e271 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.
    * 
@@ -250,17 +256,20 @@ public interface SequenceI extends ASequenceI
   public void insertCharAt(int position, int count, char ch);
 
   /**
-   * DOCUMENT ME!
+   * Gets array holding sequence features associated with this sequence. The
+   * array may be held by the sequence's dataset sequence if that is defined.
    * 
-   * @return DOCUMENT ME!
+   * @return hard reference to array
    */
   public SequenceFeature[] getSequenceFeatures();
 
   /**
-   * DOCUMENT ME!
+   * Replaces the array of sequence features associated with this sequence with
+   * a new array reference. If this sequence has a dataset sequence, then this
+   * method will update the dataset sequence's feature array
    * 
-   * @param v
-   *          DOCUMENT ME!
+   * @param features
+   *          New array of sequence features
    */
   public void setSequenceFeatures(SequenceFeature[] features);
 
@@ -298,7 +307,7 @@ public interface SequenceI extends ASequenceI
 
   public void setVamsasId(String id);
 
-  public void setDBRef(DBRefEntry[] dbs);
+  public void setDBRefs(DBRefEntry[] dbs);
 
   public DBRefEntry[] getDBRefs();
 
@@ -432,7 +441,21 @@ 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();
 }