*/
package jalview.renderer;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
public class OverviewResColourFinder extends ResidueColourFinder
{
+ final Color GAP_COLOUR; // default colour to use at gaps
+
+ final Color RESIDUE_COLOUR; // default colour to use at residues
+
+ final Color HIDDEN_COLOUR; // colour for hidden regions
+
+ boolean useLegacy = false;
+
+ public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+
+ public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+
+ public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+ .darker();
+
+ /**
+ * Constructor without colour settings (used by applet)
+ */
+ public OverviewResColourFinder()
+ {
+ this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN);
+ }
+
+ /**
+ * Constructor with colour settings
+ *
+ * @param useLegacyColouring
+ * whether to use legacy gap colouring (white gaps, grey residues)
+ * @param gapCol
+ * gap colour if not legacy
+ * @param hiddenCol
+ * hidden region colour (transparency applied by rendering code)
+ */
+ public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,
+ Color hiddenCol)
+ {
+ if (useLegacyColouring)
+ {
+ GAP_COLOUR = Color.white;
+ RESIDUE_COLOUR = Color.lightGray;
+ HIDDEN_COLOUR = hiddenCol;
+ }
+ else
+ {
+ GAP_COLOUR = gapCol;
+ RESIDUE_COLOUR = Color.white;
+ HIDDEN_COLOUR = hiddenCol;
+ }
+ }
+
@Override
public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
- Color resBoxColour = Color.white;
+ Color resBoxColour = RESIDUE_COLOUR;
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 (Comparison.isGap(currentChar)
- && !shader.getColourScheme().hasGapColour())
+ && (!shader.getColourScheme().hasGapColour()))
{
- resBoxColour = Color.lightGray;
+ resBoxColour = GAP_COLOUR;
}
else
{
}
else if (Comparison.isGap(currentChar))
{
- resBoxColour = Color.lightGray;
+ 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);
+ }
+
+ /**
+ * Supply hidden colour
+ *
+ * @return colour of hidden regions
+ */
+ protected Color getHiddenColour()
+ {
+ return HIDDEN_COLOUR;
+ }
}