/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.appletgui;
-import jalview.api.FeatureRenderer;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import java.awt.Color;
import java.awt.Font;
this.renderGaps = renderGaps;
}
- @Override
- public Color getResidueBoxColour(SequenceI seq, int i)
+ protected Color getResidueBoxColour(SequenceI seq, int i)
{
allGroups = av.getAlignment().findAllGroups(seq);
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
return resBoxColour;
*
* @param seq
* @param position
- * @param fr
+ * @param finder
* @return
*/
@Override
public Color getResidueColour(final SequenceI seq, int position,
- FeatureRenderer fr)
+ FeatureColourFinder finder)
{
// TODO replace 8 or so code duplications with calls to this method
// (refactored as needed)
Color col = getResidueBoxColour(seq, position);
- if (fr != null)
+ if (finder != null)
{
- col = fr.findFeatureColour(col, seq, position);
+ col = finder.findFeatureColour(col, seq, position);
}
return col;
}
- void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+ void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
- if (cs != null)
+ if (shader.getColourScheme() != null)
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
+ resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ i);
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
}
}
if (currentSequenceGroup.getColourText())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
graphics.setColor(resBoxColour.darker());
}
if (currentSequenceGroup.getShowNonconserved())
if (av.getColourText())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
graphics.setColor(resBoxColour.darker());