--- /dev/null
+package jalview.structure;
+
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Methods that generate commands that can be sent to a molecular structure
+ * viewer program (e.g. Jmol, Chimera, ChimeraX)
+ *
+ * @author gmcarstairs
+ *
+ */
+public interface StructureCommandsI
+{
+ /**
+ * Returns the command to colour by chain
+ *
+ * @return
+ */
+ StructureCommandI colourByChain();
+
+ /**
+ * Returns the command to colour residues using a charge-based scheme:
+ * <ul>
+ * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
+ * <li>Lysine and Arginine (positive charge) blue</li>
+ * <li>Cysteine - yellow</li>
+ * <li>all others - white</li>
+ * </ul>
+ *
+ * @return
+ */
+ List<StructureCommandI> colourByCharge();
+
+ /**
+ * Returns the command to colour residues with the colours provided in the
+ * map, one per three letter residue code
+ *
+ * @param colours
+ * @return
+ */
+ List<StructureCommandI> colourByResidues(Map<String, Color> colours);
+
+ /**
+ * Returns the command to set the background colour of the structure viewer
+ *
+ * @param col
+ * @return
+ */
+ StructureCommandI setBackgroundColour(Color col);
+
+ /**
+ * Returns commands to colour mapped residues of structures according to
+ * Jalview's colouring (including feature colouring if applied). Parameter is
+ * a map from Color to a model of all residues assigned that colour.
+ *
+ * @param colourMap
+ * @return
+ */
+
+ List<StructureCommandI> colourBySequence(
+ Map<Object, AtomSpecModel> colourMap);
+
+ /**
+ * Returns a command to centre the display in the structure viewer
+ *
+ * @return
+ */
+ StructureCommandI focusView();
+
+ /**
+ * Returns a command to show only the selected chains. The items in the input
+ * list should be formatted as "modelid:chainid".
+ *
+ * @param toShow
+ * @return
+ */
+ 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
+ * @return
+ */
+ List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
+ AtomSpecModel atomSpec);
+
+ /**
+ * 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);
+
+ /**
+ * 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 alphaOnly
+ * @return
+ */
+ String getAtomSpec(AtomSpecModel model, boolean alphaOnly);
+
+ /**
+ * 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 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();
+
+ /**
+ * Returns a command to list residues with an attribute of the given name,
+ * with attribute value, or null if no such command is supported
+ *
+ * @return
+ */
+ StructureCommandI getResidueAttributes(String attName);
+}
git://source.jalview.org / jalview.git / blobdiff