public class OverviewResColourFinder extends ResidueColourFinder
{
- final Color GAP_COLOUR = new Color(240, 240, 240);
+ public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
- @Override
- public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+ public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+
+ public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+ .darker();
+
+ final Color gapColour; // colour to use for gaps
+
+ final int gapColourInt; // RGB value of gapColour
+
+ final Color residueColour; // colour to use for uncoloured residues
+
+ final Color hiddenColour; // colour for hidden regions
+
+ boolean useLegacy = false;
+
+ /**
+ * Constructor without colour settings (used by applet)
+ */
+ public OverviewResColourFinder()
{
- Color resBoxColour = Color.white;
- char currentChar = seq.getCharAt(i);
+ this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN);
+ }
- // 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)
+ /**
+ * 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)
{
- if (Comparison.isGap(currentChar)
- && !shader.getColourScheme().hasGapColour())
- {
- resBoxColour = GAP_COLOUR;
- }
- else
- {
- resBoxColour = shader.findColour(currentChar, i, seq);
- }
+ gapColour = Color.white;
+ residueColour = Color.lightGray;
}
- else if (Comparison.isGap(currentChar))
+ else
{
- resBoxColour = GAP_COLOUR;
+ gapColour = gapCol;
+ residueColour = Color.WHITE;
}
+ gapColourInt = gapColour.getRGB();
+ hiddenColour = hiddenCol;
+ }
- return resBoxColour;
+ /**
+ * Overrides the method to return the currently configured Overview colours
+ * for gaps, or residues with no colour scheme set. A custom colour scheme
+ * which specifies a colour for gaps overrides the normal gap colour.
+ */
+ @Override
+ public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+ {
+ char currentChar = seq.getCharAt(i);
+ boolean isGap = Comparison.isGap(currentChar);
+ if (shader.getColourScheme() == null)
+ {
+ return (isGap ? gapColour : residueColour);
+ }
+ return (isGap && !shader.getColourScheme().hasGapColour() ? gapColour
+ : shader.findColour(currentChar, i, seq));
}
/**
- * {@inheritDoc} In the overview, the showBoxes setting is ignored, as the
- * overview displays the colours regardless.
+ * 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 shader, SequenceGroup[] allGroups, SequenceI seq,
+ int i)
{
- ResidueShaderI currentShader;
SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
i);
- if (currentSequenceGroup != null)
- {
- currentShader = currentSequenceGroup.getGroupColourScheme();
- }
- else
- {
- currentShader = shader;
- }
-
+ ResidueShaderI currentShader = (currentSequenceGroup == null ? shader
+ : currentSequenceGroup.getGroupColourScheme());
return getBoxColour(currentShader, seq, i);
}
+
+ /**
+ * Returns the coloured configured for hidden regions in the Overview
+ *
+ * @return
+ */
+ protected Color getHiddenColour()
+ {
+ return hiddenColour;
+ }
}