*/
package jalview.datamodel;
+import jalview.api.DBRefEntryI;
+
import java.util.List;
import java.util.Vector;
/**
* DOCUMENT ME!
+ *
* @param position
* DOCUMENT ME!
* @param ch
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);
*
* @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
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
/**
* 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
*/
public List<int[]> getInsertions();
+ /**
+ * Given a pdbId String, return the equivalent PDBEntry if available in the
+ * given sequence
+ *
+ * @param pdbId
+ * @return
+ */
+ 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.
+ *
+ * @return
+ */
+ public DBRefEntryI getSourceDBRef();
}