X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=355e27102970e4ae7f9e174d477b5bdc70d48d30;hb=29d4809e01ace4e6ac449ec944bfeec70070ac81;hp=bd193fbd92cf3161877e4f6465f34b7dcdba74ca;hpb=4660fcf0745dbc1f6f6e7241b398301f93edb548;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index bd193fb..355e271 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,18 +20,21 @@
  */
 package jalview.datamodel;
 
+import jalview.api.DBRefEntryI;
+
 import java.util.List;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
- * DOCUMENT ME!
+ * Methods for manipulating a sequence, its metadata and related annotation in
+ * an alignment or dataset.
  * 
  * @author $author$
  * @version $Revision$
  */
-public interface SequenceI
+public interface SequenceI extends ASequenceI
 {
   /**
    * Set the display name for the sequence
@@ -216,6 +219,12 @@ public interface SequenceI
   public int[] findPositionMap();
 
   /**
+   * 
+   * @return true if sequence is composed of amino acid characters
+   */
+  public boolean isProtein();
+
+  /**
    * Delete a range of aligned sequence columns, creating a new dataset sequence
    * if necessary and adjusting start and end positions accordingly.
    * 
@@ -238,6 +247,7 @@ public interface SequenceI
 
   /**
    * DOCUMENT ME!
+   * 
    * @param position
    *          DOCUMENT ME!
    * @param ch
@@ -246,17 +256,20 @@ public interface SequenceI
   public void insertCharAt(int position, int count, char ch);
 
   /**
-   * DOCUMENT ME!
+   * Gets array holding sequence features associated with this sequence. The
+   * array may be held by the sequence's dataset sequence if that is defined.
    * 
-   * @return DOCUMENT ME!
+   * @return hard reference to array
    */
   public SequenceFeature[] getSequenceFeatures();
 
   /**
-   * DOCUMENT ME!
+   * 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
    * 
-   * @param v
-   *          DOCUMENT ME!
+   * @param features
+   *          New array of sequence features
    */
   public void setSequenceFeatures(SequenceFeature[] features);
 
@@ -273,7 +286,7 @@ public interface SequenceI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector<PDBEntry> getPDBId();
+  public Vector<PDBEntry> getAllPDBEntries();
 
   /**
    * add entry to the vector of PDBIds, if it isn't in the list already
@@ -294,9 +307,9 @@ public interface SequenceI
 
   public void setVamsasId(String id);
 
-  public void setDBRef(DBRefEntry[] dbs);
+  public void setDBRefs(DBRefEntry[] dbs);
 
-  public DBRefEntry[] getDBRef();
+  public DBRefEntry[] getDBRefs();
 
   /**
    * add the given entry to the list of DBRefs for this sequence, or replace a
@@ -381,8 +394,8 @@ public interface SequenceI
   /**
    * Transfer any database references or annotation from entry under a sequence
    * mapping. <br/>
-   * <strong>Note: DOES NOT transfer sequence associated alignment
-   * annotation </strong><br/>
+   * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+   * </strong><br/>
    * 
    * @param entry
    * @param mp
@@ -420,16 +433,29 @@ public interface SequenceI
   public List<int[]> getInsertions();
 
   /**
+   * Given a pdbId String, return the equivalent PDBEntry if available in the
+   * given sequence
    * 
-   * @return returns true if the sequence is hidden
+   * @param pdbId
+   * @return
    */
-  public boolean isHidden();
+  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.
    * 
-   * @param hidden
-   *          visibility status of the sequence
+   * @param dbRef
+   *          the source dbRef for the sequence
    */
-  public void setHidden(Boolean hidden);
+  public void setSourceDBRef(DBRefEntryI dbRef);
 
+  /**
+   * Get the distinct source database, and accession number from which a
+   * sequence and its start-end data were derived from.
+   * 
+   * @return
+   */
+  public DBRefEntryI getSourceDBRef();
 }