X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=6992a8db9aee7b69bea20bed1fa2fd1189569bc4;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=55c59db27ec69e5ec73202893e5e3b153e4ce9e1;hpb=c06a9af4331b34a8537b28b5e749c442e1bc1682;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 55c59db..6992a8d 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;
 
@@ -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
@@ -189,12 +192,13 @@ 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);
 
@@ -217,8 +221,11 @@ public interface SequenceI extends ASequenceI
   public int[] findPositionMap();
 
   /**
+   * Answers true if the sequence is composed of amino acid characters. Note
+   * that implementations may use heuristic methods which are not guaranteed to
+   * give the biologically 'right' answer.
    * 
-   * @return true if sequence is composed of amino acid characters
+   * @return
    */
   public boolean isProtein();
 
@@ -256,22 +263,28 @@ 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!
@@ -289,16 +302,18 @@ public interface SequenceI extends ASequenceI
   public Vector<PDBEntry> getAllPDBEntries();
 
   /**
-   * add entry to the *normalised* vector of PDBIds.
+   * Adds the entry to the *normalised* list of PDBIds.
    * 
-   * If a PDBEntry is passed with an entry.getID() string, as one already in the
-   * list, or one is added that appears to be the same but has a chain ID
+   * If a PDBEntry is passed with the same entry.getID() string as one already
+   * in the list, or one is added that appears to be the same but has a chain ID
    * appended, then the existing PDBEntry will be updated with the new
-   * attributes.
+   * attributes instead, unless the entries have distinct chain codes or
+   * associated structure files.
    * 
    * @param entry
+   * @return true if the entry was added, false if updated
    */
-  public void addPDBId(PDBEntry entry);
+  public boolean addPDBId(PDBEntry entry);
 
   /**
    * update the list of PDBEntrys to include any DBRefEntrys citing structural
@@ -312,6 +327,14 @@ public interface SequenceI extends ASequenceI
 
   public void setVamsasId(String id);
 
+  /**
+   * set the array of Database references for the sequence.
+   * 
+   * @param dbs
+   * @deprecated - use is discouraged since side-effects may occur if DBRefEntry
+   *             set are not normalised.
+   */
+  @Deprecated
   public void setDBRefs(DBRefEntry[] dbs);
 
   public DBRefEntry[] getDBRefs();
@@ -324,7 +347,14 @@ public interface SequenceI extends ASequenceI
    */
   public void addDBRef(DBRefEntry entry);
 
-  public void addSequenceFeature(SequenceFeature sf);
+  /**
+   * Adds the given sequence feature and returns true, or returns false if it is
+   * already present on the sequence, or if the feature type is null.
+   * 
+   * @param sf
+   * @return
+   */
+  public boolean addSequenceFeature(SequenceFeature sf);
 
   public void deleteFeature(SequenceFeature sf);
 
@@ -446,7 +476,6 @@ public interface SequenceI extends ASequenceI
    */
   public PDBEntry getPDBEntry(String pdbId);
 
-
   /**
    * Get all primary database/accessions for this sequence's data. These
    * DBRefEntry are expected to resolve to a valid record in the associated
@@ -456,4 +485,34 @@ 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();
 }