featureValues = theMap.get(type);
if (featureValues == null)
{
featureValues = new HashMap<>();
theMap.put(type, featureValues);
}
for (int[] range : mappedRanges)
{
addColourRange(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;
// todo use JalviewChimeraBinding.getModelSpec(model)
// which means this cannot be static
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);
/*
* sort ranges into ascending start position order
*/
Collections.sort(rangeList, IntRangeComparator.ASCENDING);
int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
Iterator iterator = rangeList.iterator();
while (iterator.hasNext())
{
int[] range = iterator.next();
if (range[0] <= end + 1)
{
/*
* range overlaps or is contiguous with the last one
* - so just extend the end position, and carry on
* (unless this is the last in the list)
*/
end = Math.max(end, range[1]);
}
else
{
/*
* we have a break so append the last range
*/
appendRange(sb, start, end, chain, firstPositionForModel);
firstPositionForModel = false;
start = range[0];
end = range[1];
}
}
/*
* and append the last range
*/
if (!rangeList.isEmpty())
{
appendRange(sb, start, end, chain, firstPositionForModel);
firstPositionForModel = false;
}
}
}
return sb.toString();
}
/**
* A helper method that appends one start-end range to a Chimera atomspec
*
* @param sb
* @param start
* @param end
* @param chain
* @param firstPositionForModel
*/
static void appendRange(StringBuilder sb, int start, int end,
String chain, boolean firstPositionForModel)
{
if (!firstPositionForModel)
{
sb.append(",");
}
if (end == start)
{
sb.append(start);
}
else
{
sb.append(start).append("-").append(end);
}
sb.append(".");
if (!" ".equals(chain))
{
sb.append(chain);
}
}
}