/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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
/**
* DOCUMENT ME!
+ *
* @param position
* DOCUMENT ME!
* @param ch
*
* @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
/**
* 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
*
- * @return returns true if the sequence is hidden
- */
- public boolean isHidden();
-
- /**
- *
- * @param hidden
- * visibility status of the sequence
+ * @param pdbId
+ * @return
*/
- public void setHidden(Boolean hidden);
-
+ public PDBEntry getPDBEntry(String pdbId);
}