Merge branch 'features/JAL-2446NCList' into

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 7ecb4ed..38be37f 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,9 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.features.SequenceFeaturesI;
+
+import java.util.BitSet;
 import java.util.List;
 import java.util.Vector;
 
@@ -174,7 +177,7 @@ public interface SequenceI extends ASequenceI
   public String getDescription();
 
   /**
-   * Return the alignment column for a sequence position
+   * Return the alignment column (from 1..) for a sequence position
    * 
    * @param pos
    *          lying from start to end
@@ -189,16 +192,41 @@ 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 position.
    * 
    * @param i
    *          column index in alignment (from 0..<length)
    * 
-   * @return residue number for residue (left of and) nearest ith column
+   * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
+   *         ith column
    */
   public int findPosition(int i);
 
   /**
+   * Returns the range of sequence positions included in the given alignment
+   * position range. If no positions are included (the range is entirely gaps),
+   * then returns null.
+   * 
+   * <pre>
+   * Example: 
+   * >Seq/8-13
+   * ABC--DE-F
+   * findPositions(1, 4) returns Range(9, 9) // B only
+   * findPositions(3, 4) returns null // all gaps
+   * findPositions(2, 6) returns Range(10, 12) // CDE
+   * findPositions(3, 7) returns Range(11,12) // DE
+   * </pre>
+   * 
+   * @param fromCol
+   *          first aligned column position (base 0, inclusive)
+   * @param toCol
+   *          last aligned column position (base 0, inclusive)
+   * 
+   * @return
+   */
+  public Range findPositions(int fromCol, int toCol);
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -259,22 +287,28 @@ public interface SequenceI extends ASequenceI
   public void insertCharAt(int position, int count, char ch);
 
   /**
-   * Gets array holding sequence features associated with this sequence. The
-   * array may be held by the sequence's dataset sequence if that is defined.
+   * Answers a list of all sequence features associated with this sequence. The
+   * list may be held by the sequence's dataset sequence if that is defined.
    * 
    * @return hard reference to array
    */
-  public SequenceFeature[] getSequenceFeatures();
+  public List<SequenceFeature> getSequenceFeatures();
 
   /**
-   * 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
+   * Answers the object holding features for the sequence
+   * 
+   * @return
+   */
+  SequenceFeaturesI getFeatures();
+
+  /**
+   * Replaces the sequence features associated with this sequence with the given
+   * features. If this sequence has a dataset sequence, then this method will
+   * update the dataset sequence's features instead.
    * 
    * @param features
-   *          New array of sequence features
    */
-  public void setSequenceFeatures(SequenceFeature[] features);
+  public void setSequenceFeatures(List<SequenceFeature> features);
 
   /**
    * DOCUMENT ME!
@@ -339,7 +373,7 @@ public interface SequenceI extends ASequenceI
 
   /**
    * Adds the given sequence feature and returns true, or returns false if it is
-   * already present on the sequence
+   * already present on the sequence, or if the feature type is null.
    * 
    * @param sf
    * @return
@@ -477,13 +511,28 @@ public interface SequenceI extends ASequenceI
   public List<DBRefEntry> getPrimaryDBRefs();
 
   /**
-   * Returns a (possibly empty) list of sequence features of the given type that
-   * overlap the range from-to (inclusive)
+   * Returns a (possibly empty) list of sequence features that overlap the range
+   * from-to (inclusive), optionally restricted to one or more specified feature
+   * types
    * 
-   * @param type
    * @param from
    * @param to
+   * @param types
    * @return
    */
-  List<SequenceFeature> findFeatures(String type, int from, int to);
+  List<SequenceFeature> findFeatures(int from, int to, String... types);
+
+  /**
+   * Method to call to indicate that the sequence (characters or alignment/gaps)
+   * has been modified. Provided to allow any cursors on residue/column
+   * positions to be invalidated.
+   */
+  void sequenceChanged();
+  
+  /**
+   * 
+   * @return BitSet corresponding to index [0,length) where Comparison.isGap()
+   *         returns true.
+   */
+  BitSet getInsertionsAsBits();
 }