+
+ /**
+ * {@inheritDoc} In the overview, the showBoxes setting is ignored, as the
+ * overview displays the colours regardless.
+ */
+ @Override
+ protected Color getResidueBoxColour(boolean showBoxes,
+ ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
+ int i)
+ {
+ ResidueShaderI currentShader;
+ SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
+ i);
+ if (currentSequenceGroup != null)
+ {
+ currentShader = currentSequenceGroup.getGroupColourScheme();
+ }
+ else
+ {
+ currentShader = shader;
+ }
+
+ return getBoxColour(currentShader, seq, i);
+ }
+
+ /**
+ * Returns the colour used for hidden regions
+ *
+ * @return
+ */
+ public Color getHiddenColour()
+ {
+ return hiddenColour;
+ }
+
+ /**
+ * Returns the colour used for gaps, if not overridden by the alignment colour
+ * scheme
+ *
+ * @return
+ */
+ public Color getGapColour()
+ {
+ return gapColour;
+ }
+
+ /**
+ * Returns the colour used for residues (before applying any feature
+ * colouring) if there is no alignment colour scheme
+ *
+ * @return
+ */
+ public Color getResidueColour()
+ {
+ return residueColour;
+ }