* The format of each command is * *
** * @param featureMap * @return */ @Override public Listsetattr r*" " #modelnumber:range.chain * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,... *
* setatr res jv_chain 'primary' #1:12-34,48-55.B ** * @param attributeName * @param attributeValue * @param atomSpecModel * @return */ protected StructureCommandI setAttribute(String attributeName, String attributeValue, AtomSpecModel atomSpecModel) { StringBuilder sb = new StringBuilder(128); sb.append("setattr res ").append(attributeName).append(" '") .append(attributeValue).append("' "); sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY)); return new StructureCommand(sb.toString()); } /** * 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 */ @Override protected String makeAttributeName(String featureType) { String attName = super.makeAttributeName(featureType); /* * Chimera treats an attribute name ending in 'color' as colour-valued; * Jalview doesn't, so prevent this by appending an underscore */ if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR")) { attName += "_"; } return attName; } @Override public StructureCommandI colourByChain() { return COLOUR_BY_CHAIN; } @Override public List
* #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A ** * where *
*
* @param model
* @param specType
* @return
* @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
*/
@Override
public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
for (String model : atomSpec.getModels())
{
if (!firstModel)
{
sb.append("|");
}
firstModel = false;
appendModel(sb, model, atomSpec, specType);
}
return sb.toString();
}
/**
* A helper method to append an atomSpec string for atoms in the given model
*
* @param sb
* @param model
* @param atomSpec
* @param alphaOnly
*/
protected void appendModel(StringBuilder sb, String model,
AtomSpecModel atomSpec, AtomSpecType specType)
{
sb.append("#").append(model).append(":");
boolean firstPositionForModel = true;
for (String chain : atomSpec.getChains(model))
{
chain = " ".equals(chain) ? chain : chain.trim();
List rangeList = atomSpec.getRanges(model, chain);
for (int[] range : rangeList)
{
appendRange(sb, range[0], range[1], chain, firstPositionForModel,
false);
firstPositionForModel = false;
}
}
if (specType == AtomSpecType.ALPHA)
{
/*
* restrict to alpha carbon, no alternative locations
* (needed to ensuring matching atom counts for superposition)
*/
sb.append("@CA").append(NO_ALTLOCS);
}
if (specType == AtomSpecType.PHOSPHATE)
{
sb.append("@P").append(NO_ALTLOCS);
}
}
@Override
public List showBackbone()
{
return Arrays.asList(SHOW_BACKBONE);
}
@Override
public StructureCommandI loadFile(String file)
{
return new StructureCommand("open " + file);
}
@Override
public StructureCommandI openSession(String filepath)
{
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
// this version of the command has no dependency on file extension
return new StructureCommand("open chimera:" + filepath);
}
@Override
public StructureCommandI closeViewer()
{
return CLOSE_CHIMERA;
}
@Override
public List startNotifications(String uri)
{
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
List cmds = new ArrayList<>();
cmds.add(new StructureCommand("listen start models url " + uri));
cmds.add(new StructureCommand(
"listen start select prefix SelectionChanged url " + uri));
return cmds;
}
@Override
public List stopNotifications()
{
List cmds = new ArrayList<>();
cmds.add(STOP_NOTIFY_MODELS);
cmds.add(STOP_NOTIFY_SELECTION);
return cmds;
}
@Override
public StructureCommandI getSelectedResidues()
{
return GET_SELECTION;
}
@Override
public StructureCommandI listResidueAttributes()
{
return LIST_RESIDUE_ATTRIBUTES;
}
@Override
public StructureCommandI getResidueAttributes(String attName)
{
// this alternative command
// list residues spec ':*/attName' attr attName
// doesn't report 'None' values (which is good), but
// fails for 'average.bfactor' (which is bad):
return new StructureCommand("list residues attr '" + attName + "'");
}
@Override
public List centerViewOn(List residues)
{
// TODO Auto-generated method stub
return null;
}
}