--- /dev/null
+package jalview.structure;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+/**
+ * A base class holding methods useful to all classes that implement commands
+ * for structure viewers
+ *
+ * @author gmcarstairs
+ *
+ */
+public abstract class StructureCommandsBase implements StructureCommandsI
+{
+ public static final String NAMESPACE_PREFIX = "jv_";
+
+ private static final String CMD_SEPARATOR = ";";
+
+ /**
+ * Returns something that separates concatenated commands
+ *
+ * @return
+ */
+ protected String getCommandSeparator()
+ {
+ return CMD_SEPARATOR;
+ }
+
+ /**
+ * Returns the lowest model number used by the structure viewer
+ *
+ * @return
+ */
+ @Override
+ public int getModelStartNo()
+ {
+ return 0;
+ }
+
+ /**
+ * Helper method to add one contiguous range to the AtomSpec model for the given
+ * value (creating the model if necessary). As used by Jalview, {@code value} is
+ * <ul>
+ * <li>a colour, when building a 'colour structure by sequence' command</li>
+ * <li>a feature value, when building a 'set Chimera attributes from features'
+ * command</li>
+ * </ul>
+ *
+ * @param map
+ * @param value
+ * @param model
+ * @param startPos
+ * @param endPos
+ * @param chain
+ */
+ public static final void addAtomSpecRange(Map<Object, AtomSpecModel> 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.
+ * <p>
+ * The default implementation returns a single command containing one command
+ * per colour, concatenated.
+ *
+ * @param colourMap
+ * @return
+ */
+ @Override
+ public List<StructureCommandI> colourBySequence(
+ Map<Object, AtomSpecModel> colourMap)
+ {
+ List<StructureCommandI> 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<StructureCommandI> colourByResidues(
+ Map<String, Color> colours)
+ {
+ List<StructureCommandI> commands = new ArrayList<>();
+ for (Entry<String, Color> 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<StructureCommandI> setAttributes(
+ Map<String, Map<Object, AtomSpecModel>> featureValues)
+ {
+ // default does nothing, override where this is implemented
+ return null;
+ }
+
+ @Override
+ public List<StructureCommandI> startNotifications(String uri)
+ {
+ return null;
+ }
+
+ @Override
+ public List<StructureCommandI> stopNotifications()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff