+ List<StructureCommandI> showChains(List<String> toShow);
+
+ /**
+ * Returns a command to superpose structures by closest positioning of
+ * residues in {@code atomSpec} to the corresponding residues in
+ * {@code refAtoms}. If wanted, this may include commands to visually
+ * highlight the residues that were used for the superposition.
+ *
+ * @param refAtoms
+ * @param atomSpec
+ * @param backbone
+ * - superpose based on which kind of atomType
+ * @return
+ */
+ List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
+ AtomSpecModel atomSpec, AtomSpecType backbone);
+
+ /**
+ * Returns a command to open a file of commands at the given path
+ *
+ * @param path
+ * @return
+ */
+ StructureCommandI openCommandFile(String path);
+
+ /**
+ * Returns a command to save the current viewer session state to the given
+ * file
+ *
+ * @param filepath
+ * @return
+ */
+ StructureCommandI saveSession(String filepath);
+
+ enum AtomSpecType
+ {
+ RESIDUE_ONLY, ALPHA, PHOSPHATE
+ };
+
+ /**
+ * Returns a representation of the atom set represented by the model, in
+ * viewer syntax format. If {@code alphaOnly} is true, this is restricted to
+ * Alpha Carbon (peptide) or Phosphorous (rna) only
+ *
+ * @param model
+ * @param specType
+ * @return
+ */
+ String getAtomSpec(AtomSpecModel model, AtomSpecType specType);
+
+ /**
+ * Returns the lowest model number used by the structure viewer (likely 0 or
+ * 1)
+ *
+ * @return
+ */
+ // TODO remove by refactoring so command generation is purely driven by
+ // AtomSpecModel objects derived in the binding classes?
+ int getModelStartNo();
+
+ /**
+ * Returns command(s) to show only the backbone of the peptide (cartoons in
+ * Jmol, chain in Chimera)
+ *
+ * @return
+ */
+ List<StructureCommandI> showBackbone();
+
+ /**
+ * Returns a command to open a file at the given path
+ *
+ * @param file
+ * @return
+ */
+ // refactor if needed to distinguish loading data or session files
+ StructureCommandI loadFile(String file);
+
+ /**
+ * Returns commands to set atom attributes or properties, given a map of
+ * Jalview features as {featureType, {featureValue, AtomSpecModel}}. The
+ * assumption is that one command can be constructed for each feature type and
+ * value combination, to apply it to one or more residues.
+ *
+ * @param featureValues
+ * @return
+ */
+ List<StructureCommandI> setAttributes(
+ Map<String, Map<Object, AtomSpecModel>> featureValues);
+
+ /**
+ * Returns command to open a saved structure viewer session file, or null if
+ * not supported
+ *
+ * @param filepath
+ * @return
+ */
+ StructureCommandI openSession(String filepath);
+
+ /**
+ * Returns command to restore a previously saved version of an existing structure viewer session file.
+ * Default implementation calls 'openSession'
+ * @param filePath
+ * @return
+ */
+ StructureCommandI restoreSession(String filePath);
+
+
+ /**
+ * Returns a command to ask the viewer to close down
+ *
+ * @return
+ */
+ StructureCommandI closeViewer();
+
+ /**
+ * Returns one or more commands to ask the viewer to notify model or selection
+ * changes to the given uri. Returns null if this is not supported by the
+ * structure viewer.
+ *
+ * @param uri
+ * @return
+ */
+ List<StructureCommandI> startNotifications(String uri);
+
+ /**
+ * Returns one or more commands to ask the viewer to stop notifying model or
+ * selection changes. Returns null if this is not supported by the structure
+ * viewer.
+ *
+ * @return
+ */
+ List<StructureCommandI> stopNotifications();
+
+ /**
+ * Returns a command to ask the viewer for its current residue selection, or
+ * null if no such command is supported
+ *
+ * @return
+ */
+ StructureCommandI getSelectedResidues();
+
+ /**
+ * Returns a command to list the unique names of residue attributes, or null
+ * if no such command is supported
+ *
+ * @return
+ */
+ StructureCommandI listResidueAttributes();