+ Hashtable getProperties();
+
+ /**
+ * add a reference to a frame of aligned codons for this alignment
+ *
+ * @param codons
+ */
+ void addCodonFrame(AlignedCodonFrame codons);
+
+ /**
+ * remove a particular codon frame reference from this alignment
+ *
+ * @param codons
+ * @return true if codon frame was removed.
+ */
+ boolean removeCodonFrame(AlignedCodonFrame codons);
+
+ /**
+ * get all codon frames associated with this alignment
+ *
+ * @return
+ */
+ List<AlignedCodonFrame> getCodonFrames();
+
+ /**
+ * Set the codon frame mappings (replacing any existing list).
+ */
+ void setCodonFrames(List<AlignedCodonFrame> acfs);
+
+ /**
+ * get codon frames involving sequenceI
+ */
+ List<AlignedCodonFrame> getCodonFrame(SequenceI seq);
+
+ /**
+ * find sequence with given name in alignment
+ *
+ * @param token
+ * name to find
+ * @param b
+ * true implies that case insensitive matching will <em>also</em> be
+ * tried
+ * @return matched sequence or null
+ */
+ SequenceI findName(String token, boolean b);
+
+ /**
+ * find next sequence with given name in alignment starting after a given
+ * sequence
+ *
+ * @param startAfter
+ * the sequence after which the search will be started (usually the
+ * result of the last call to findName)
+ * @param token
+ * name to find
+ * @param b
+ * true implies that case insensitive matching will <em>also</em> be
+ * tried
+ * @return matched sequence or null
+ */
+ SequenceI findName(SequenceI startAfter, String token, boolean b);
+
+ /**
+ * find first sequence in alignment which is involved in the given search
+ * result object
+ *
+ * @param results
+ * @return -1 or index of sequence in alignment
+ */
+ int findIndex(SearchResultsI results);
+
+ /**
+ * append sequences and annotation from another alignment object to this one.
+ * Note: this is a straight transfer of object references, and may result in
+ * toappend's dependent data being transformed to fit the alignment (changing
+ * gap characters, etc...). If you are uncertain, use the copy Alignment copy
+ * constructor to create a new version which can be appended without side
+ * effect.
+ *
+ * @param toappend
+ * - the alignment to be appended.
+ */
+ void append(AlignmentI toappend);
+
+ /**
+ * Justify the sequences to the left or right by deleting and inserting gaps
+ * before the initial residue or after the terminal residue
+ *
+ * @param right
+ * true if alignment padded to right, false to justify to left
+ * @return true if alignment was changed TODO: return undo object
+ */
+ boolean justify(boolean right);
+
+ /**
+ * add given annotation row at given position (0 is start, -1 is end)
+ *
+ * @param consensus
+ * @param i
+ */
+ void addAnnotation(AlignmentAnnotation consensus, int i);
+
+ /**
+ * search for or create a specific annotation row on the alignment
+ *
+ * @param name
+ * name for annotation (must match)
+ * @param calcId
+ * calcId for the annotation (null or must match)
+ * @param autoCalc
+ * - value of autocalc flag for the annotation
+ * @param seqRef
+ * - null or specific sequence reference
+ * @param groupRef
+ * - null or specific group reference
+ * @param method
+ * - CalcId for the annotation (must match)
+ *
+ * @return existing annotation matching the given attributes
+ */
+ AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
+ boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
+
+ /**
+ * move the given group up or down in the alignment by the given number of
+ * rows. Implementor assumes given group is already present on alignment - no
+ * recalculations are triggered.
+ *
+ * @param sg
+ * @param map
+ * @param up
+ * @param i
+ */
+ void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map<SequenceI, SequenceCollectionI> map, boolean up);
+
+ /**
+ * validate annotation after an edit and update any alignment state flags
+ * accordingly
+ *
+ * @param alignmentAnnotation
+ */
+ void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
+
+ /**
+ * Align this alignment the same as the given one. If both of the same type
+ * (nucleotide/protein) then align both identically. If this is nucleotide and
+ * the other is protein, make 3 gaps for each gap in the protein sequences. If
+ * this is protein and the other is nucleotide, insert a gap for each 3 gaps
+ * (or part thereof) between nucleotide bases. Returns the number of mapped
+ * sequences that were realigned .
+ *
+ * @param al
+ * @return
+ */
+ int alignAs(AlignmentI al);
+
+ /**
+ * Returns the set of distinct sequence names in the alignment.
+ *
+ * @return
+ */
+ Set<String> getSequenceNames();
+
+ /**
+ * Checks if the alignment has at least one sequence with one non-gaped
+ * residue
+ *
+ * @return
+ */
+ public boolean hasValidSequence();
+
+ /**
+ * Update any mappings to 'virtual' sequences to compatible real ones, if
+ * present in the added sequences. Returns a count of mappings updated.
+ *
+ * @param seqs
+ * @return
+ */
+ int realiseMappings(List<SequenceI> seqs);
+
+ /**
+ * Returns the first AlignedCodonFrame that has a mapping between the given
+ * dataset sequences
+ *
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
+
+ public void setHiddenColumns(HiddenColumns cols);
+