import java.awt.Color;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
public class ChimeraCommands
{
+ public static final String NAMESPACE_PREFIX = "jv_";
+
/**
- * utility to construct the commands to colour chains by the given alignment
- * for passing to Chimera
- *
- * @returns Object[] { Object[] { <model being coloured>,
+ * Constructs Chimera commands to colour residues as per the Jalview alignment
*
+ * @param ssm
+ * @param files
+ * @param sequence
+ * @param sr
+ * @param fr
+ * @param alignment
+ * @return
*/
public static StructureMappingcommandSet getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
}
/**
- * Constructs and returns a set of Chimera commands to set attributes on
- * residues corresponding to features in Jalview
+ * 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
StructureSelectionManager ssm, String[] files,
SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
{
- Map<String, AtomSpecModel> featureMap = buildFeaturesMap(
+ Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
ssm, files, seqs, fr, alignment);
List<String> commands = buildSetAttributeCommands(featureMap);
}
/**
- * Helper method to build a map of { featureType, AtomSpecModel }
+ * <pre>
+ * Helper method to build a map of
+ * { featureType, { feature value, AtomSpecModel } }
+ * </pre>
*
* @param ssm
* @param files
* @param alignment
* @return
*/
- protected static Map<String, AtomSpecModel> buildFeaturesMap(
+ protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
StructureSelectionManager ssm, String[] files,
SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
{
- Map<String, AtomSpecModel> theMap = new LinkedHashMap<String, AtomSpecModel>();
+ Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
if (visibleFeatures.isEmpty())
*/
protected static void scanSequenceFeatures(List<String> visibleFeatures,
StructureMapping mapping, SequenceI seq,
- Map<String, AtomSpecModel> theMap, int modelNumber)
+ Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
SequenceFeature[] sfs = seq.getSequenceFeatures();
if (sfs == null)
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
- if (!visibleFeatures.contains(type))
+
+ /*
+ * Only copy visible features, don't copy any which originated
+ * from Chimera, and suppress uninteresting ones (e.g. RESNUM)
+ */
+ boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+ .equals(sf.getFeatureGroup());
+ if (isFromViewer || !visibleFeatures.contains(type))
{
continue;
}
if (!mappedRanges.isEmpty())
{
- AtomSpecModel atomSpec = theMap.get(type);
- if (atomSpec == null)
+ String value = sf.getDescription();
+ if (value == null || value.length() == 0)
{
- atomSpec = new AtomSpecModel();
- theMap.put(type, atomSpec);
+ value = type;
+ }
+ float score = sf.getScore();
+ if (score != 0f && !Float.isNaN(score))
+ {
+ value = Float.toString(score);
+ }
+ Map<Object, AtomSpecModel> featureValues = theMap.get(type);
+ if (featureValues == null)
+ {
+ featureValues = new HashMap<Object, AtomSpecModel>();
+ theMap.put(type, featureValues);
}
for (int[] range : mappedRanges)
{
- atomSpec.addRange(modelNumber, range[0], range[1],
+ addRange(featureValues, value, modelNumber, range[0], range[1],
mapping.getChain());
}
}
}
/**
- * Traverse the map of features/models/chains/positions to construct a list of
- * 'setattr' commands (one per feature type). The format of each command is
+ * 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 " " #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
* </blockquote>
* </pre>
- * <p>
- * Note we are not (currently) setting attribute values, only the type
- * (presence) of each attribute. This is to avoid overloading the Chimera REST
- * interface by sending too many distinct commands. Analysis by feature values
- * may still be performed in Jalview, on selections created in Chimera.
*
* @param featureMap
* @return
*/
protected static List<String> buildSetAttributeCommands(
- Map<String, AtomSpecModel> featureMap)
+ Map<String, Map<Object, AtomSpecModel>> featureMap)
{
List<String> commands = new ArrayList<String>();
for (String featureType : featureMap.keySet())
{
- StringBuilder sb = new StringBuilder(128);
- String sanitised = featureType.replace(" ", "_").replace("-", "_");
- sb.append("setattr r jv_").append(sanitised).append(" \" \" ");
- sb.append(featureMap.get(featureType).getAtomSpec());
- commands.add(sb.toString());
+ 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
+ */
+ StringBuilder sb = new StringBuilder(128);
+ sb.append("setattr r ").append(attributeName).append(" \"")
+ .append(value.toString()).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.
+ *
+ * @param featureType
+ * @return <pre>
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+ * </pre>
+ */
+ protected static 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();
+
+ /*
+ * Chimera treats an attribute name ending in 'color' as colour-valued;
+ * Jalview doesn't, so prevent this by appending an underscore
+ */
+ if (attName.toUpperCase().endsWith("COLOR"))
+ {
+ attName += "_";
+ }
+
+ return attName;
+ }
+
}