package jalview.gui;
import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueColourFinder;
ResidueColourFinder resColourFinder;
+ private boolean colourGaps;
+ private Color gapColour=Color.white;
+
/**
* Creates a new SequenceRenderer object
*
}
/**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
+ * initialise state for a render
+ * @param renderGaps - whether gap symbols are shown
+ * @param colourGaps - whether boxes for gaps are to be coloured
*/
- public void prepare(Graphics g, boolean renderGaps)
+ public void prepare(Graphics g, boolean renderGaps, boolean colourGaps)
{
graphics = g;
fm = g.getFontMetrics();
&& av.getCharWidth() == dwidth);
this.renderGaps = renderGaps;
+ this.colourGaps = colourGaps;
+ this.gapColour = Color.white;
+ if (colourGaps)
+ {
+ this.gapColour = Cache.getDefaultColour(Preferences.GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+ }
+ resColourFinder = new ResidueColourFinder(gapColour);
}
/**
public synchronized void drawBoxes(SequenceI seq, int start, int end,
int y1)
{
- Color resBoxColour = Color.white;
+ Color resBoxColour = gapColour;
if (seq == null)
{
resBoxColour = resColourFinder
.getBoxColour(av.getResidueShading(), seq, i);
}
+ } else {
+ resBoxColour = gapColour;
}
if (resBoxColour != tempColour)