X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=6c82bf3aa6a30da7971c5889cf05b6dd9d87cf62;hb=648b167d638390634aa7e1f58c2d1e4feca2d408;hp=45a767c3eb8fe5d9a0ed66bbbdd02cad04669f45;hpb=5dd0323d078fc1f0bab425fcbd4d8bcf1528eb14;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 45a767c..6c82bf3 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,7 +20,7 @@
  */
 package jalview.datamodel;
 
-import jalview.api.DBRefEntryI;
+import jalview.datamodel.features.SequenceFeaturesI;
 
 import java.util.List;
 import java.util.Vector;
@@ -219,8 +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();
 
@@ -266,6 +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
@@ -291,11 +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
@@ -309,6 +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();
@@ -321,7 +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);
 
@@ -444,20 +476,24 @@ public interface SequenceI extends ASequenceI
   public PDBEntry getPDBEntry(String pdbId);
 
   /**
-   * Set the distinct source database, and accession number from which a
-   * sequence and its start-end data were derived from. This is very important
-   * for SIFTS mappings and must be set prior to performing SIFTS mapping.
+   * Get all primary database/accessions for this sequence's data. These
+   * DBRefEntry are expected to resolve to a valid record in the associated
+   * external database, either directly or via a provided 1:1 Mapping.
    * 
-   * @param dbRef
-   *          the source dbRef for the sequence
+   * @return just the primary references (if any) for this sequence, or an empty
+   *         list
    */
-  public void setSourceDBRef(DBRefEntryI dbRef);
+  public List<DBRefEntry> getPrimaryDBRefs();
 
   /**
-   * Get the distinct source database, and accession number from which a
-   * sequence and its start-end data were derived from.
+   * 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
    */
-  public DBRefEntryI getSourceDBRef();
+  List<SequenceFeature> findFeatures(int from, int to, String... types);
 }