package jalview.structure;
-import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.util.Comparison;
import java.awt.Color;
import java.util.ArrayList;
-import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
}
@Override
- public String[] setAttributesForFeatures(StructureSelectionManager ssm,
+ public List<StructureCommandI> setAttributesForFeatures(
+ StructureSelectionManager ssm,
String[] files, SequenceI[][] sequence, AlignmentViewPanel avp)
{
// default does nothing, override where this is implemented
* @param chain
*/
public static final void addAtomSpecRange(Map<Object, AtomSpecModel> 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
* @return
*/
@Override
- public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
+ public List<StructureCommandI> colourBySequence(
+ Map<Object, AtomSpecModel> 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.
+ * default implementation creates one command per colour;
+ * override to concatenate colour commands if wanted
*/
- List<String> commands = new ArrayList<>();
- StringBuilder sb = new StringBuilder(256);
- boolean firstColour = true;
+ List<StructureCommandI> commands = new ArrayList<>();
for (Object key : colourMap.keySet())
{
Color colour = (Color) key;
- if (!firstColour)
- {
- sb.append(getCommandSeparator()).append(" ");
- }
- firstColour = false;
final AtomSpecModel colourData = colourMap.get(colour);
- sb.append(getColourCommand(colourData, colour));
+ commands.add(getColourCommand(colourData, colour));
}
- commands.add(sb.toString());
- return commands.toArray(new String[commands.size()]);
+ return commands;
}
/**
* @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);
* @param colour
* @return
*/
- protected abstract String getColourCommand(String atomSpec, Color colour);
+ protected abstract StructureCommandI getColourCommand(String atomSpec,
+ Color colour);
@Override
- public String colourByResidues(Map<String, Color> colours)
+ public List<StructureCommandI> colourByResidues(
+ Map<String, Color> colours)
{
- StringBuilder cmd = new StringBuilder(12 * colours.size());
-
+ List<StructureCommandI> commands = new ArrayList<>();
for (Entry<String, Color> 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 getColourCommand(atomSpec, col);
}
/**