+ * (exclusive) position relative to start of sequence including gaps
+ * (from 0)
+ *
+ * @return String containing all gap and symbols in specified range
+ */
+ public String getSequenceAsString(int start, int end);
+
+ /**
+ * Answers a copy of the sequence as a character array
+ *
+ * @return
+ */
+ public char[] getSequence();
+
+ /**
+ * get stretch of sequence characters in an array
+ *
+ * @param start
+ * absolute index into getSequence()
+ * @param end
+ * 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 (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 (column) position. If at a
+ * gap, returns the position of the next residue to the right. If beyond the
+ * end of the sequence, returns 1 more than the last residue position.
+ *
+ * @param i
+ * column index in alignment (from 0..<length)
+ *
+ * @return
+ */
+ public int findPosition(int i);
+
+ /**
+ * Returns the sequence positions for first and last residues lying within the
+ * given column positions [fromColum,toColumn] (where columns are numbered
+ * from 1), or null if no residues are included in the range
+ *
+ * @param fromColum
+ * - first column base 1. (0 and negative positions are rounded up)
+ * @param toColumn
+ * - last column, base 1
+ * @return null if fromColum>toColumn
+ */
+ public ContiguousI findPositions(int fromColum, int toColumn);
+
+ /**
+ * 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();
+
+ /**
+ * Build a bitset corresponding to sequence gaps
+ *
+ * @return a BitSet where set values correspond to gaps in the sequence
+ */
+ public BitSet gapBitset();
+
+ /**
+ * 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
+ */
+ 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
+ */
+ public boolean updatePDBIds();
+
+ public String getVamsasId();
+
+ 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();
+
+ /**
+ * 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);
+
+ /**
+ * Adds the given sequence feature and returns true, or returns false if it is
+ * already present on the sequence, or if the feature type is null.
+ *
+ * @param sf
+ * @return
+ */
+ public boolean 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
+ */
+ public SequenceI deriveSequence();
+
+ /**
+ * set the array of associated AlignmentAnnotation for this sequenceI
+ *
+ * @param revealed
+ */
+ public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
+
+ /**
+ * Get one or more alignment annotations with a particular label.
+ *
+ * @param label
+ * string which each returned annotation must have as a label.
+ * @return null or array of annotations.
+ */
+ public AlignmentAnnotation[] getAnnotation(String label);
+
+ /**
+ * Returns a (possibly empty) list of any annotations that match on given
+ * calcId (source) and label (type). Null values do not match.
+ *
+ * @param calcId
+ * @param label
+ */
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label);
+
+ /**
+ * create a new dataset sequence (if necessary) for this sequence and sets
+ * this sequence to refer to it. This call will move any features or
+ * references on the sequence onto the dataset. It will also make a duplicate
+ * of existing annotation rows for the dataset sequence, rather than relocate
+ * them in order to preserve external references (since 2.8.2).
+ *
+ * @return dataset sequence for this sequence
+ */
+ public SequenceI createDatasetSequence();
+
+ /**
+ * Transfer any database references or annotation from entry under a sequence
+ * mapping. <br/>
+ * <strong>Note: DOES NOT transfer sequence associated alignment annotation
+ * </strong><br/>
+ *
+ * @param entry
+ * @param mp
+ * null or mapping from entry's numbering to local start/end