X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=b7a291e07c542eef7f53e8998f56413965555e6e;hb=3446323f14bb8a2842cb83f74ed3f41c99b62759;hp=69eb1d43e623c421548fc04907b1cbc4d855db46;hpb=e179e97c0330d1981da7383db497caddd8cad232;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 69eb1d4..b7a291e 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.api.DBRefEntryI;
-
 import java.util.List;
 import java.util.Vector;
 
@@ -219,6 +217,12 @@ public interface SequenceI extends ASequenceI
   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.
    * 
@@ -233,19 +237,21 @@ public interface SequenceI extends ASequenceI
    * DOCUMENT ME!
    * 
    * @param i
-   *          DOCUMENT ME!
+   *          alignment column number
    * @param c
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int i, char c);
 
   /**
-   * DOCUMENT ME!
+   * insert given character at alignment column position
    * 
    * @param position
-   *          DOCUMENT ME!
+   *          alignment column number
+   * @param count
+   *          length of insert
    * @param ch
-   *          DOCUMENT ME!
+   *          character to insert
    */
   public void insertCharAt(int position, int count, char ch);
 
@@ -283,11 +289,18 @@ 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
@@ -435,21 +448,14 @@ 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.
-   * 
-   * @param dbRef
-   *          the source dbRef for the sequence
-   */
-  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.
+   * 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.
    * 
-   * @return
+   * @return just the primary references (if any) for this sequence, or an empty
+   *         list
    */
-  public DBRefEntryI getSourceDBRef();
+  public List<DBRefEntry> getPrimaryDBRefs();
 }