package jalview.structure;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.SequenceI;
-
import java.awt.Color;
import java.util.ArrayList;
import java.util.List;
public abstract class StructureCommandsBase implements StructureCommandsI
{
private static final String CMD_SEPARATOR = ";";
+ public static final String NAMESPACE_PREFIX = "jv_";
/**
* Returns something that separates concatenated commands
return CMD_SEPARATOR;
}
- @Override
- public List<StructureCommandI> setAttributesForFeatures(
- StructureSelectionManager ssm,
- String[] files, SequenceI[][] sequence, AlignmentViewPanel avp)
- {
- // default does nothing, override where this is implemented
- return null;
- }
-
/**
* Returns the lowest model number used by the structure viewer
*
}
/**
+ * 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 featureType
+ * @return
+ */
+ 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.
+ * <p>
+ * The default implementation returns a single command containing one command
+ * per colour, concatenated.
*
* @param colourMap
* @return
public List<StructureCommandI> colourBySequence(
Map<Object, AtomSpecModel> colourMap)
{
- /*
- * default implementation creates one command per colour;
- * override to concatenate colour commands if wanted
- */
List<StructureCommandI> commands = new ArrayList<>();
+ StringBuilder sb = new StringBuilder(colourMap.size() * 20);
+ boolean first = true;
for (Object key : colourMap.keySet())
{
Color colour = (Color) key;
final AtomSpecModel colourData = colourMap.get(colour);
- commands.add(getColourCommand(colourData, colour));
+ StructureCommandI command = getColourCommand(colourData, colour);
+ if (!first)
+ {
+ sb.append(getCommandSeparator());
+ }
+ first = false;
+ sb.append(command.getCommand());
}
+ commands.add(new StructureCommand(sb.toString()));
return commands;
}
Color colour)
{
String atomSpec = getAtomSpec(atomSpecModel, false);
- return getColourCommand(atomSpec, colour);
+ return colourResidues(atomSpec, colour);
}
/**
* @param colour
* @return
*/
- protected abstract StructureCommandI getColourCommand(String atomSpec,
+ protected abstract StructureCommandI colourResidues(String atomSpec,
Color colour);
@Override
private StructureCommandI colourResidue(String resName, Color col)
{
String atomSpec = getResidueSpec(resName);
- return getColourCommand(atomSpec, col);
+ return colourResidues(atomSpec, col);
}
/**
* @return
*/
protected abstract String getResidueSpec(String residue);
+
+ @Override
+ public List<StructureCommandI> setAttributes(
+ Map<String, Map<Object, AtomSpecModel>> featureValues)
+ {
+ // default does nothing, override where this is implemented
+ return null;
+ }
+
+ @Override
+ public List<StructureCommandI> startNotifications(String uri)
+ {
+ return null;
+ }
+
+ @Override
+ public List<StructureCommandI> stopNotifications()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return null;
+ }
}