featureValues = theMap.get(type);
if (featureValues == null)
{
featureValues = new HashMap<>();
theMap.put(type, featureValues);
}
for (int[] range : mappedRanges)
{
addAtomSpecRange(featureValues, value, modelNumber, range[0],
range[1], mapping.getChain());
}
}
}
}
/**
* Traverse the map of features/values/models/chains/positions to construct a
* list of 'setattr' commands (one per distinct feature type and value).
*
* The format of each command is
*
*
* setattr r " " #modelnumber:range.chain
* e.g. setattr r jv:chain #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
*
*
*
* @param featureMap
* @param binding
* @return
*/
protected static List buildSetAttributeCommands(
Map> featureMap,
AAStructureBindingModel binding)
{
List 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 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(getAtomSpec(values.get(value), binding));
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
*
*
* @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
*
*/
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;
}
/**
* Returns the range(s) formatted as a Chimera atomspec
*
* @return
*/
public static String getAtomSpec(AtomSpecModel atomSpec,
AAStructureBindingModel binding)
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
for (Integer model : atomSpec.getModels())
{
if (!firstModel)
{
sb.append("|");
}
firstModel = false;
sb.append(binding.getModelSpec(model)).append(":");
boolean firstPositionForModel = true;
for (String chain : atomSpec.getChains(model))
{
chain = " ".equals(chain) ? chain : chain.trim();
List rangeList = atomSpec.getRanges(model, chain);
String chainToken = " ".equals(chain) ? "." : "." + chain;
appendResidueRange(sb, rangeList, chainToken,
firstPositionForModel);
firstPositionForModel = false;
}
}
return sb.toString();
}
/**
* Chimera atomspec requires chain to be specified for each start-end residue
* range, otherwise it will apply to all chains
*
* @param sb
* @param chain
*/
protected static void appendChainToRange(StringBuilder sb, String chain)
{
sb.append(".");
if (!" ".equals(chain))
{
sb.append(chain);
}
}
}