import jalview.gui.Desktop;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
*/
public class ChimeraXCommands extends ChimeraCommands
{
- public static final String NAMESPACE_PREFIX = "jv_";
-
private static final String CMD_COLOUR_BY_CHARGE = "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow";
/**
* Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and
- * builds a Chimera format atom spec
+ * builds a ChimeraX format atom spec
*
* @param modelAndChainRanges
*/
}
/**
- * 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
- */
- protected static void addAtomSpecRange(Map<Object, AtomSpecModel> map,
- Object value, int 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);
- }
-
- /**
- * Constructs and returns Chimera commands to set attributes on residues
- * corresponding to features in Jalview. Attribute names are the Jalview
- * feature type, with a "jv_" prefix.
- *
- * @param ssm
- * @param files
- * @param seqs
- * @param viewPanel
- * @return
- */
- public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
- StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
- AlignmentViewPanel viewPanel)
- {
- Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
- ssm, files, seqs, viewPanel);
-
- List<String> commands = buildSetAttributeCommands(featureMap);
-
- StructureMappingcommandSet cs = new StructureMappingcommandSet(
- ChimeraXCommands.class, null,
- commands.toArray(new String[commands.size()]));
-
- return cs;
- }
-
- /**
* <pre>
* Helper method to build a map of
* { featureType, { feature value, AtomSpecModel } }
}
/**
- * Traverse the map of features/values/models/chains/positions to construct a
- * list of 'setattr' commands (one per distinct feature type and value).
- * <p>
- * The format of each command is
- *
- * <pre>
- * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
- * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
- * </blockquote>
- * </pre>
- *
- * @param featureMap
- * @return
- */
- protected static List<String> buildSetAttributeCommands(
- Map<String, Map<Object, AtomSpecModel>> featureMap)
- {
- List<String> commands = new ArrayList<>();
- for (String featureType : featureMap.keySet())
- {
- String attributeName = makeAttributeName(featureType);
-
- /*
- * clear down existing attributes for this feature
- */
- // 'problem' - sets attribute to None on all residues - overkill?
- // commands.add("~setattr r " + attributeName + " :*");
-
- Map<Object, AtomSpecModel> values = featureMap.get(featureType);
- for (Object value : values.keySet())
- {
- /*
- * for each distinct value recorded for this feature type,
- * add a command to set the attribute on the mapped residues
- * Put values in single quotes, encoding any embedded single quotes
- */
- StringBuilder sb = new StringBuilder(128);
- String featureValue = value.toString();
- featureValue = featureValue.replaceAll("\\'", "'");
- sb.append("setattr r ").append(attributeName).append(" '")
- .append(featureValue).append("' ");
- sb.append(values.get(value).getAtomSpec());
- commands.add(sb.toString());
- }
- }
-
- return commands;
- }
-
- /**
* Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
* for a 'Jalview' namespace, and any non-alphanumeric character is converted
* to an underscore.
return "view";
}
+ /**
+ * {@inheritDoc}
+ *
+ * @return
+ */
+ protected static int getModelStartNo()
+ {
+ return 1;
+ }
+
+ /**
+ * Returns a viewer command to set the given residue attribute value on
+ * residues specified by the AtomSpecModel, for example
+ *
+ * <pre>
+ * setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
+ * </pre>
+ *
+ * @param attributeName
+ * @param attributeValue
+ * @param atomSpecModel
+ * @return
+ */
+ @Override
+ protected String getSetAttributeCommand(String attributeName,
+ String attributeValue, AtomSpecModel atomSpecModel)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ sb.append("setattr ").append(atomSpecModel.getAtomSpecX());
+ sb.append(" res ").append(attributeName).append(" '")
+ .append(attributeValue).append("'");
+ sb.append(" create true");
+ return sb.toString();
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff