X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=2f3e92580756a8a839ad4e6af97d9194e81d6ddd;hb=2b4cc5fb6217217761b4a8bd2529e51b4775a57d;hp=e81553b9e18c7ccce8a63ffed813249dd79dac8e;hpb=39d49ec61c046327da8a35a5fddfd1ade1ff6d7a;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index e81553b..2f3e925 100755
--- 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;
 
@@ -116,9 +119,9 @@ public interface SequenceI extends ASequenceI
   public String getSequenceAsString(int start, int end);
 
   /**
-   * Get the sequence as a character array
+   * Answers a copy of the sequence as a character array
    * 
-   * @return seqeunce and any gaps
+   * @return
    */
   public char[] getSequence();
 
@@ -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
@@ -189,17 +192,28 @@ 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);
 
   /**
+   * Returns the from-to sequence positions (start..) for the given column
+   * positions (1..), or null if no residues are included in the range
+   * 
+   * @param fromColum
+   * @param toColumn
+   * @return
+   */
+  public Range findPositions(int fromColum, int toColumn);
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -260,22 +274,28 @@ 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
+   */
+  public List<SequenceFeature> getSequenceFeatures();
+
+  /**
+   * Answers the object holding features for the sequence
    * 
-   * @return hard reference to array
+   * @return
    */
-  public SequenceFeature[] getSequenceFeatures();
+  SequenceFeaturesI getFeatures();
 
   /**
-   * 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
+   * 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!
@@ -340,7 +360,7 @@ 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
@@ -430,17 +450,6 @@ 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
    */
 
@@ -476,4 +485,43 @@ public interface SequenceI extends ASequenceI
    *         list
    */
   public List<DBRefEntry> getPrimaryDBRefs();
+
+  /**
+   * Returns a (possibly empty) list of sequence features that overlap the given
+   * alignment column range, optionally restricted to one or more specified
+   * feature types. If the range is all gaps, then features which enclose it are
+   * included (but not contact features).
+   * 
+   * @param fromCol
+   *          start column of range inclusive (1..)
+   * @param toCol
+   *          end column of range inclusive (1..)
+   * @param types
+   *          optional feature types to restrict results to
+   * @return
+   */
+  List<SequenceFeature> findFeatures(int fromCol, int toCol, 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();
+
+  /**
+   * Replaces every occurrence of c1 in the sequence with c2 and returns the
+   * number of characters changed
+   * 
+   * @param c1
+   * @param c2
+   */
+  public int replace(char c1, char c2);
 }