*/
package jalview.ext.rbvi.chimera;
+import jalview.api.AlignViewportI;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureMapping;
* @param sequence
* @param sr
* @param fr
- * @param alignment
+ * @param viewport
* @return
*/
public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ AlignViewportI viewport)
{
Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
- sequence, sr, fr, alignment);
+ sequence, sr, fr, viewport);
List<String> colourCommands = buildColourCommands(colourMap);
/**
* <pre>
- * Build a data structure which maps contiguous subsequences for each colour.
- * This generates a data structure from which we can easily generate the
- * Chimera command for colour by sequence.
+ * Build a data structure which records contiguous subsequences for each colour.
+ * From this we can easily generate the Chimera command for colour by sequence.
* Color
* Model number
* Chain
protected static Map<Object, AtomSpecModel> buildColoursMap(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ AlignViewportI viewport)
{
+ ColumnSelection cs = viewport.getColumnSelection();
+ AlignmentI al = viewport.getAlignment();
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
Color lastColour = null;
+
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
{
final SequenceI seq = sequence[pdbfnum][s];
if (mapping[m].getSequence() == seq
- && (sp = alignment.findIndex(seq)) > -1)
+ && (sp = al.findIndex(seq)) > -1)
{
- SequenceI asp = alignment.getSequenceAt(sp);
+ SequenceI asp = al.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
}
Color colour = sr.getResidueColour(seq, r, fr);
+
+ /*
+ * darker colour for hidden regions
+ */
+ if (!cs.isVisible(r))
+ {
+ // colour = ColorUtils.darkerThan(colour);
+ colour = Color.GRAY;
+ }
+
final String chain = mapping[m].getChain();
/*
*/
StringBuilder sb = new StringBuilder(128);
String featureValue = value.toString();
- featureValue.replaceAll("'", "'");
+ featureValue = featureValue.replaceAll("\\'", "'");
sb.append("setattr r ").append(attributeName).append(" '")
.append(featureValue).append("' ");
sb.append(values.get(value).getAtomSpec());