+ * 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 (from 1..) 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 the range of sequence positions included in the given alignment
+ * position range. If no positions are included (the range is entirely gaps),
+ * then returns null.
+ *
+ * <pre>
+ * Example:
+ * >Seq/8-13
+ * ABC--DE-F
+ * findPositions(1, 4) returns Range(9, 9) // B only
+ * findPositions(3, 4) returns null // all gaps
+ * findPositions(2, 6) returns Range(10, 12) // CDE
+ * findPositions(3, 7) returns Range(11,12) // DE
+ * </pre>
+ *
+ * @param fromCol
+ * first aligned column position (base 0, inclusive)
+ * @param toCol
+ * last aligned column position (base 0, inclusive)
+ *
+ * @return
+ */
+ public Range findPositions(int fromCol, int toCol);
+
+ /**
+ * 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();
+
+ /**
+ * 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
+ */
+ public boolean isProtein();
+
+ /**
+ * 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
+ * alignment column number
+ * @param c
+ * character to insert
+ */
+ public void insertCharAt(int i, char c);
+
+ /**
+ * insert given character at alignment column position
+ *
+ * @param position
+ * alignment column number
+ * @param count
+ * length of insert
+ * @param ch
+ * character to insert
+ */
+ public void insertCharAt(int position, int count, char ch);
+
+ /**
+ * Answers a list of all sequence features associated with this sequence. The
+ * list may be held by the sequence's dataset sequence if that is defined.
+ *
+ * @return hard reference to array
+ */
+ public List<SequenceFeature> getSequenceFeatures();
+
+ /**
+ * Answers the object holding features for the sequence
+ *
+ * @return
+ */
+ SequenceFeaturesI getFeatures();
+
+ /**
+ * Replaces the sequence features associated with this sequence with the given
+ * features. If this sequence has a dataset sequence, then this method will
+ * update the dataset sequence's features instead.
+ *
+ * @param features
+ */
+ public void setSequenceFeatures(List<SequenceFeature> features);
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id
+ * DOCUMENT ME!
+ */
+ public void setPDBId(Vector<PDBEntry> ids);
+
+ /**
+ * Returns a list
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector<PDBEntry> getAllPDBEntries();
+
+ /**
+ * 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 boolean addPDBId(PDBEntry entry);
+
+ /**
+ * update the list of PDBEntrys to include any DBRefEntrys citing structural
+ * databases
+ *
+ * @return true if PDBEntry list was modified