public class OverviewResColourFinder extends ResidueColourFinder
{
- final Color GAP_COLOUR;
+ final Color GAP_COLOUR; // default colour to use at gaps
- final Color RESIDUE_COLOUR;
+ final Color RESIDUE_COLOUR; // default colour to use at residues
- final Color HIDDEN_COLOUR;
+ 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()
{
- GAP_COLOUR = Color.lightGray; // new Color(240, 240, 240);
- RESIDUE_COLOUR = Color.white;
- HIDDEN_COLOUR = Color.DARK_GRAY.darker();
+ 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)
{
// settings
if (shader.getColourScheme() != null)
{
- if (!shader.getColourScheme().hasGapColour()
- && Comparison.isGap(currentChar))
+ if (Comparison.isGap(currentChar)
+ && (!shader.getColourScheme().hasGapColour()))
{
resBoxColour = GAP_COLOUR;
}
*/
@Override
protected Color getResidueBoxColour(boolean showBoxes,
- ResidueShaderI shader,
- SequenceGroup[] allGroups, SequenceI seq, int i)
+ ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
+ int i)
{
ResidueShaderI currentShader;
SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
return getBoxColour(currentShader, seq, i);
}
+ /**
+ * Supply hidden colour
+ *
+ * @return colour of hidden regions
+ */
protected Color getHiddenColour()
{
return HIDDEN_COLOUR;