map,
+ Object value, String model, int startPos, int endPos,
+ String chain)
+ {
+ /*
+ * Get/initialize map of data for the colour
+ */
+ AtomSpecModel atomSpec = map.get(value);
+ if (atomSpec == null)
+ {
+ atomSpec = new AtomSpecModel();
+ map.put(value, atomSpec);
+ }
+
+ atomSpec.addRange(model, startPos, endPos, chain);
+ }
+
+ /**
+ * Makes a structure viewer attribute name for a Jalview feature type by
+ * prefixing it with "jv_", and replacing any non-alphanumeric characters with
+ * an underscore
+ *
+ * @param featureType
+ * @return
+ */
+ protected String makeAttributeName(String featureType)
+ {
+ StringBuilder sb = new StringBuilder();
+ if (featureType != null)
+ {
+ for (char c : featureType.toCharArray())
+ {
+ sb.append(Character.isLetterOrDigit(c) ? c : '_');
+ }
+ }
+ String attName = NAMESPACE_PREFIX + sb.toString();
+ return attName;
+ }
+
+ /**
+ * Traverse the map of colours/models/chains/positions to construct a list of
+ * 'color' commands (one per distinct colour used). The format of each command
+ * is specific to the structure viewer.
+ *
+ * The default implementation returns a single command containing one command
+ * per colour, concatenated.
+ *
+ * @param colourMap
+ * @return
+ */
+ @Override
+ public List colourBySequence(
+ Map colourMap)
+ {
+ List commands = new ArrayList<>();
+ StringBuilder sb = new StringBuilder(colourMap.size() * 20);
+ boolean first = true;
+ for (Object key : colourMap.keySet())
+ {
+ Color colour = (Color) key;
+ final AtomSpecModel colourData = colourMap.get(colour);
+ StructureCommandI command = getColourCommand(colourData, colour);
+ if (!first)
+ {
+ sb.append(getCommandSeparator());
+ }
+ first = false;
+ sb.append(command.getCommand());
+ }
+
+ commands.add(new StructureCommand(sb.toString()));
+ return commands;
+ }
+
+ /**
+ * Returns a command to colour the atoms represented by {@code atomSpecModel}
+ * with the colour specified by {@code colourCode}.
+ *
+ * @param atomSpecModel
+ * @param colour
+ * @return
+ */
+ protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
+ Color colour)
+ {
+ String atomSpec = getAtomSpec(atomSpecModel, false);
+ return colourResidues(atomSpec, colour);
+ }
+
+ /**
+ * Returns a command to colour the atoms described (in viewer command syntax)
+ * by {@code atomSpec} with the colour specified by {@code colourCode}
+ *
+ * @param atomSpec
+ * @param colour
+ * @return
+ */
+ protected abstract StructureCommandI colourResidues(String atomSpec,
+ Color colour);
+
+ @Override
+ public List colourByResidues(
+ Map colours)
+ {
+ List commands = new ArrayList<>();
+ for (Entry entry : colours.entrySet())
+ {
+ commands.add(colourResidue(entry.getKey(), entry.getValue()));
+ }
+ return commands;
+ }
+
+ private StructureCommandI colourResidue(String resName, Color col)
+ {
+ String atomSpec = getResidueSpec(resName);
+ return colourResidues(atomSpec, col);
+ }
+
+ /**
+ * Helper method to append one start-end range to an atomspec string
+ *
+ * @param sb
+ * @param start
+ * @param end
+ * @param chain
+ * @param firstPositionForModel
+ */
+ protected void appendRange(StringBuilder sb, int start, int end,
+ String chain, boolean firstPositionForModel, boolean isChimeraX)
+ {
+ if (!firstPositionForModel)
+ {
+ sb.append(",");
+ }
+ if (end == start)
+ {
+ sb.append(start);
+ }
+ else
+ {
+ sb.append(start).append("-").append(end);
+ }
+
+ if (!isChimeraX)
+ {
+ sb.append(".");
+ if (!" ".equals(chain))
+ {
+ sb.append(chain);
+ }
+ }
+ }
+
+ /**
+ * Returns the atom specifier meaning all occurrences of the given residue
+ *
+ * @param residue
+ * @return
+ */
+ protected abstract String getResidueSpec(String residue);
+
+ @Override
+ public List setAttributes(
+ Map> featureValues)
+ {
+ // default does nothing, override where this is implemented
+ return null;
+ }
+
+ @Override
+ public List startNotifications(String uri)
+ {
+ return null;
+ }
+
+ @Override
+ public List stopNotifications()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ return null;
+ }
+}