JAL-2480 include sequenceFeatureStore in createDatasetSequence

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index ec7520b..6c82bf3 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.features.SequenceFeaturesI;
+
 import java.util.List;
 import java.util.Vector;
 
@@ -217,8 +219,11 @@ 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();
 
@@ -264,6 +269,13 @@ public interface SequenceI extends ASequenceI
   public SequenceFeature[] getSequenceFeatures();
 
   /**
+   * Answers the object holding features for the sequence
+   * 
+   * @return
+   */
+  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
@@ -289,11 +301,18 @@ public interface SequenceI extends ASequenceI
   public Vector<PDBEntry> getAllPDBEntries();
 
   /**
-   * add entry to the vector of PDBIds, if it isn't in the list already
+   * Adds the entry to the *normalised* list of PDBIds.
+   * 
+   * 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 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
@@ -307,6 +326,14 @@ 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();
@@ -319,7 +346,14 @@ 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);
 
@@ -441,7 +475,6 @@ 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
@@ -451,4 +484,16 @@ public interface SequenceI extends ASequenceI
    *         list
    */
   public List<DBRefEntry> getPrimaryDBRefs();
+
+  /**
+   * 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 from
+   * @param to
+   * @param types
+   * @return
+   */
+  List<SequenceFeature> findFeatures(int from, int to, String... types);
 }