X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=c1687fe3dbe812899e70ab9d2081c91a6c6c267c;hb=e2c3b3602486cee3f85dd8dfc7856a5ce6701669;hp=605f6821accf13689fa622773f8162c80cdeb334;hpb=d08df378179f85c2142f69ce63380baad803a0ab;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 605f682..c1687fe 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -22,6 +22,7 @@ package jalview.datamodel;
 
 import jalview.datamodel.features.SequenceFeaturesI;
 
+import java.util.BitSet;
 import java.util.List;
 import java.util.Vector;
 
@@ -118,9 +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();
 
@@ -176,7 +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
@@ -191,16 +192,27 @@ 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 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
    * 
@@ -210,6 +222,13 @@ public interface SequenceI extends ASequenceI
   public int[] gapMap();
 
   /**
+   * Build a bitset corresponding to sequence gaps
+   * 
+   * @return a BitSet where set values correspond to gaps in the sequence
+   */
+  public BitSet gapBitset();
+
+  /**
    * Returns an int array where indices correspond to each position in sequence
    * char array and the element value gives the result of findPosition for that
    * index in the sequence.
@@ -261,12 +280,12 @@ 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
+   * @return
    */
-  public SequenceFeature[] getSequenceFeatures();
+  public List<SequenceFeature> getSequenceFeatures();
 
   /**
    * Answers the object holding features for the sequence
@@ -276,14 +295,13 @@ public interface SequenceI extends ASequenceI
   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!
@@ -348,7 +366,7 @@ 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
@@ -486,13 +504,41 @@ 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 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 type
-   * @param from
-   * @param to
+   * @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(String type, int from, int to);
+  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);
 }