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();
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
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();
*/
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