import static org.testng.Assert.assertEquals;
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-import java.awt.Color;
-
-import org.testng.annotations.Test;
-
public class PIDColourSchemeTest
{
static final Color white = Color.white;
/*
* doesn't use column or sequence
+ * we assume consensus residue is computed as upper case
*/
assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
assertEquals(scheme.findColour('A', 0, null, "KFV", 100f), white);
assertEquals(scheme.findColour('a', 0, null, "A", 80f), over60);
- assertEquals(scheme.findColour('A', 0, null, "a", 80f), over60);
- assertEquals(scheme.findColour('a', 0, null, "a", 80f), over60);
assertEquals(scheme.findColour('A', 0, null, "AC", 80f), over60);
assertEquals(scheme.findColour('A', 0, null, "KCA", 80f), over60);
}
* first column PID is 50%, or 67% ignoring gaps
*/
String seqs = ">seq1\nAAAAA\n>seq2\nAAAAA\n>seq3\n-CCCC\n>seq4\nFFFFF\n";
+
+ /*
+ * load data and wait for consensus to be computed
+ */
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
DataSourceType.PASTE);
AlignViewport viewport = af.getViewport();
viewport.setIgnoreGapsConsensus(false, af.alignPanel);
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ } while (af.getViewport().getCalcManager().isWorking());
af.changeColour_actionPerformed(JalviewColourScheme.PID.toString());
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
* including gaps, A should be coloured for 50% consensus
*/
Color c = viewport
- .getViewportColourScheme().findColour('A', 0, seq);
+ .getResidueShading().findColour('A', 0, seq);
assertEquals(c, over40);
/*
*/
viewport.setIgnoreGapsConsensus(true, af.alignPanel);
c = viewport
- .getViewportColourScheme().findColour('A', 0, seq);
+ .getResidueShading().findColour('A', 0, seq);
assertEquals(c, over60);
}
}