import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
import jalview.util.Comparison;
import java.awt.Color;
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getViewportColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
return resBoxColour;
/**
* DOCUMENT ME!
*
- * @param collectionColourSchemeI
+ * @param shader
* DOCUMENT ME!
* @param seq
* DOCUMENT ME!
* @param i
* DOCUMENT ME!
*/
- void getBoxColour(CollectionColourSchemeI collectionColourSchemeI,
- SequenceI seq, int i)
+ void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
- if (collectionColourSchemeI != null)
+ if (shader != null)
{
- resBoxColour = collectionColourSchemeI.findColour(seq.getCharAt(i),
+ resBoxColour = shader.findColour(seq.getCharAt(i),
i, seq);
}
else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getViewportColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
}
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.getViewportColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
{
if (!getboxColour)
{
- getBoxColour(av.getViewportColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()