package jalview.ext.jmol;
import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
*/
public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignViewportI viewport)
+ SequenceI[][] sequence, SequenceRenderer sr,
+ AlignmentViewPanel viewPanel)
{
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
ColumnSelection cs = viewport.getColumnSelection();
AlignmentI al = viewport.getAlignment();
List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
lastPos = pos;
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-
- if (fr != null)
- {
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
- }
+ Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+ finder);
/*
* shade hidden regions darker
*/
if (!cs.isVisible(r))
{
- // col = ColorUtils.darkerThan(col);
col = Color.GRAY;
}