--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.renderer;
+
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+
+public class OverviewResColourFinder extends ResidueColourFinder
+{
+ final Color GAP_COLOUR = new Color(240, 240, 240);
+
+ @Override
+ public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+ {
+ Color resBoxColour = Color.white;
+ char currentChar = seq.getCharAt(i);
+
+ // In the overview window, gaps are coloured grey, unless the colour scheme
+ // specifies a gap colour, in which case gaps honour the colour scheme
+ // settings
+ if (shader.getColourScheme() != null)
+ {
+ if (!shader.getColourScheme().hasGapColour()
+ && Comparison.isGap(currentChar))
+ {
+ resBoxColour = GAP_COLOUR;
+ }
+ else
+ {
+ resBoxColour = shader.findColour(currentChar, i, seq);
+ }
+ }
+ else if (Comparison.isGap(currentChar))
+ {
+ resBoxColour = GAP_COLOUR;
+ }
+
+ return resBoxColour;
+ }
+
+ /**
+ * {@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);
+ }
+}