map,
- Object value,
- int model, int startPos, int endPos, String chain)
+ Object value, String model, int startPos, int endPos,
+ String chain)
{
/*
* Get/initialize map of data for the colour
@@ -198,49 +90,64 @@ public abstract class StructureCommandsBase implements StructureCommandsI
atomSpec = new AtomSpecModel();
map.put(value, atomSpec);
}
-
+
atomSpec.addRange(model, startPos, endPos, chain);
}
/**
- * Returns a colour formatted suitable for use in viewer command syntax
+ * Makes a structure viewer attribute name for a Jalview feature type by
+ * prefixing it with "jv_", and replacing any non-alphanumeric characters with
+ * an underscore
*
- * @param colour
+ * @param featureType
* @return
*/
- protected abstract String getColourString(Color colour);
+ protected 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();
+ return attName;
+ }
/**
* Traverse the map of colours/models/chains/positions to construct a list of
* 'color' commands (one per distinct colour used). The format of each command
* is specific to the structure viewer.
+ *
+ * The default implementation returns a single command containing one command
+ * per colour, concatenated.
*
* @param colourMap
* @return
*/
- public List buildColourCommands(
+ @Override
+ public List colourBySequence(
Map colourMap)
{
- /*
- * This version concatenates all commands into a single String (semi-colon
- * delimited). If length limit issues arise, refactor to return one color
- * command per colour.
- */
- List commands = new ArrayList<>();
- StringBuilder sb = new StringBuilder(256);
- boolean firstColour = true;
+ List commands = new ArrayList<>();
+ StringBuilder sb = new StringBuilder(colourMap.size() * 20);
+ boolean first = true;
for (Object key : colourMap.keySet())
{
Color colour = (Color) key;
- if (!firstColour)
+ final AtomSpecModel colourData = colourMap.get(colour);
+ StructureCommandI command = getColourCommand(colourData, colour);
+ if (!first)
{
- sb.append(getCommandSeparator()).append(" ");
+ sb.append(getCommandSeparator());
}
- firstColour = false;
- final AtomSpecModel colourData = colourMap.get(colour);
- sb.append(getColourCommand(colourData, colour));
+ first = false;
+ sb.append(command.getCommand());
}
- commands.add(sb.toString());
+
+ commands.add(new StructureCommand(sb.toString()));
return commands;
}
@@ -252,10 +159,11 @@ public abstract class StructureCommandsBase implements StructureCommandsI
* @param colour
* @return
*/
- protected String getColourCommand(AtomSpecModel atomSpecModel, Color colour)
+ protected StructureCommandI getColourCommand(AtomSpecModel atomSpecModel,
+ Color colour)
{
- String atomSpec = getAtomSpec(atomSpecModel, false);
- return getColourCommand(atomSpec, colour);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
+ return colourResidues(atomSpec, colour);
}
/**
@@ -266,21 +174,25 @@ public abstract class StructureCommandsBase implements StructureCommandsI
* @param colour
* @return
*/
- protected abstract String getColourCommand(String atomSpec, Color colour);
+ protected abstract StructureCommandI colourResidues(String atomSpec,
+ Color colour);
@Override
- public String colourByResidues(Map colours)
+ public List colourByResidues(
+ Map colours)
{
- StringBuilder cmd = new StringBuilder(12 * colours.size());
-
+ List commands = new ArrayList<>();
for (Entry entry : colours.entrySet())
{
- String residue = entry.getKey();
- String atomSpec = getResidueSpec(residue);
- cmd.append(getColourCommand(atomSpec, entry.getValue()));
- cmd.append(getCommandSeparator());
+ commands.add(colourResidue(entry.getKey(), entry.getValue()));
}
- return cmd.toString();
+ return commands;
+ }
+
+ private StructureCommandI colourResidue(String resName, Color col)
+ {
+ String atomSpec = getResidueSpec(resName);
+ return colourResidues(atomSpec, col);
}
/**
@@ -325,4 +237,42 @@ public abstract class StructureCommandsBase implements StructureCommandsI
* @return
*/
protected abstract String getResidueSpec(String residue);
+
+ @Override
+ public List setAttributes(
+ Map> featureValues)
+ {
+ // default does nothing, override where this is implemented
+ return null;
+ }
+
+ @Override
+ public List startNotifications(String uri)
+ {
+ return null;
+ }
+
+ @Override
+ public List stopNotifications()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ return null;
+ }
}