+ * exclusive index of last position in segment to be returned.
+ *
+ * @return char[max(0,end-start)];
+ */
+ public char[] getSequence(int start, int end);
+
+ /**
+ * create a new sequence object with a subsequence of this one but sharing the
+ * same dataset sequence
+ *
+ * @param start
+ * int index for start position (base 0, inclusive)
+ * @param end
+ * int index for end position (base 0, exclusive)
+ *
+ * @return SequenceI
+ * @note implementations may use getSequence to get the sequence data
+ */
+ public SequenceI getSubSequence(int start, int end);
+
+ /**
+ * get the i'th character in this sequence's local reference frame (ie from
+ * 0-number of characters lying from start-end)
+ *
+ * @param i
+ * index
+ * @return character or ' '
+ */
+ public char getCharAt(int i);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param desc
+ * DOCUMENT ME!
+ */
+ public void setDescription(String desc);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDescription();
+
+ /**
+ * Return the alignment column for a sequence position
+ *
+ * @param pos
+ * lying from start to end
+ *
+ * @return aligned column for residue (0 if residue is upstream from
+ * alignment, -1 if residue is downstream from alignment) note.
+ * Sequence object returns sequence.getEnd() for positions upstream
+ * currently. TODO: change sequence for
+ * assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
+ *
+ */
+ public int findIndex(int pos);
+
+ /**
+ * Returns the sequence position for an alignment position
+ *
+ * @param i
+ * column index in alignment (from 0..<length)
+ *
+ * @return residue number for residue (left of and) nearest ith column
+ */
+ public int findPosition(int i);
+
+ /**
+ * Returns an int array where indices correspond to each residue in the
+ * sequence and the element value gives its position in the alignment
+ *
+ * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
+ * residues in SequenceI object
+ */
+ public int[] gapMap();
+
+ /**
+ * Returns an int array where indices correspond to each position in sequence
+ * char array and the element value gives the result of findPosition for that
+ * index in the sequence.
+ *
+ * @return int[SequenceI.getLength()]
+ */
+ public int[] findPositionMap();
+
+ /**
+ * Delete a range of aligned sequence columns, creating a new dataset sequence
+ * if necessary and adjusting start and end positions accordingly.
+ *
+ * @param i
+ * first column in range to delete (inclusive)
+ * @param j
+ * last column in range to delete (exclusive)
+ */
+ public void deleteChars(int i, int j);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param c
+ * DOCUMENT ME!
+ */
+ public void insertCharAt(int i, char c);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param position
+ * DOCUMENT ME!
+ * @param ch
+ * DOCUMENT ME!
+ */
+ public void insertCharAt(int position, int count, char ch);
+
+ /**
+ * 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 hard reference to array
+ */
+ public SequenceFeature[] getSequenceFeatures();
+
+ /**
+ * 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 features
+ * New array of sequence features
+ */
+ public void setSequenceFeatures(SequenceFeature[] features);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
+ */
+ public void setPDBId(Vector<PDBEntry> ids);
+
+ /**
+ * Returns a list
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector<PDBEntry> getAllPDBEntries();
+
+ /**
+ * add entry to the vector of PDBIds, if it isn't in the list already
+ *
+ * @param entry
+ */
+ public void addPDBId(PDBEntry entry);
+
+ /**
+ * update the list of PDBEntrys to include any DBRefEntrys citing structural
+ * databases
+ *
+ * @return true if PDBEntry list was modified
+ */
+ public boolean updatePDBIds();
+
+ public String getVamsasId();
+
+ public void setVamsasId(String id);
+
+ public void setDBRefs(DBRefEntry[] dbs);
+
+ public DBRefEntry[] getDBRefs();
+
+ /**
+ * add the given entry to the list of DBRefs for this sequence, or replace a
+ * similar one if entry contains a map object and the existing one doesnt.
+ *
+ * @param entry
+ */
+ public void addDBRef(DBRefEntry entry);
+
+ public void addSequenceFeature(SequenceFeature sf);
+
+ public void deleteFeature(SequenceFeature sf);
+
+ public void setDatasetSequence(SequenceI seq);
+
+ public SequenceI getDatasetSequence();
+
+ /**
+ * Returns a new array containing this sequence's annotations, or null.
+ */
+ public AlignmentAnnotation[] getAnnotation();
+
+ /**
+ * Returns true if this sequence has the given annotation (by object
+ * identity).
+ */
+ public boolean hasAnnotation(AlignmentAnnotation ann);
+
+ /**
+ * Add the given annotation, if not already added, and set its sequence ref to
+ * be this sequence. Does nothing if this sequence's annotations already
+ * include this annotation (by identical object reference).
+ */
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation);
+
+ public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
+
+ /**
+ * Derive a sequence (using this one's dataset or as the dataset)
+ *
+ * @return duplicate sequence with valid dataset sequence