private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
@Override
- public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
- {
- List<String> colourCommands = buildColourCommands(colourMap);
-
- return colourCommands.toArray(new String[colourCommands.size()]);
- }
-
- @Override
public String getColourCommand(String atomSpec, Color colour)
{
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
* @param colour
* @return
*/
- @Override
protected String getColourString(Color colour)
{
return ColorUtils.toTkCode(colour);
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
ssm, files, seqs, viewPanel);
- List<String> commands = buildSetAttributeCommands(featureMap);
-
- return commands.toArray(new String[commands.size()]);
+ return setAttributes(featureMap);
}
/**
* @param featureMap
* @return
*/
- protected List<String> buildSetAttributeCommands(
+ protected String[] setAttributes(
Map<String, Map<Object, AtomSpecModel>> featureMap)
{
List<String> commands = new ArrayList<>();
AtomSpecModel atomSpecModel = values.get(value);
String featureValue = value.toString();
featureValue = featureValue.replaceAll("\\'", "'");
- String cmd = getSetAttributeCommand(attributeName, featureValue,
+ String cmd = setAttribute(attributeName, featureValue,
atomSpecModel);
commands.add(cmd);
}
}
- return commands;
+ return commands.toArray(new String[commands.size()]);
}
/**
* @param atomSpecModel
* @return
*/
- protected String getSetAttributeCommand(String attributeName,
+ protected String setAttribute(String attributeName,
String attributeValue,
AtomSpecModel atomSpecModel)
{