assertEquals(Color.WHITE, ccs.applyConservation(colour, 4));
assertEquals(Color.WHITE, ccs.applyConservation(colour, 5));
assertEquals(Color.WHITE, ccs.applyConservation(colour, 6));
- assertEquals(new Color(235, 225, 215), ccs.applyConservation(colour, 7));
- assertEquals(new Color(215, 195, 175), ccs.applyConservation(colour, 8));
- assertEquals(new Color(195, 165, 135), ccs.applyConservation(colour, 9));
+ assertEquals(new Color(235, 225, 215),
+ ccs.applyConservation(colour, 7));
+ assertEquals(new Color(215, 195, 175),
+ ccs.applyConservation(colour, 8));
+ assertEquals(new Color(195, 165, 135),
+ ccs.applyConservation(colour, 9));
assertEquals(colour, ccs.applyConservation(colour, 10));
assertEquals(colour, ccs.applyConservation(colour, 11));
assertEquals(Color.WHITE, ccs.applyConservation(colour, 12));
colours[23] = Color.red; // gap colour
ColourSchemeI cs = new UserColourScheme(colours);
rs = new ResidueShader(cs);
-
+
assertEquals(Color.red, rs.findColour(' ', 7, null));
assertEquals(Color.blue, rs.findColour('Q', 7, null));
-
+
/*
* stub Conservation to return a given consensus string
*/
}
};
rs.setConservation(cons);
-
+
/*
* with 0% threshold, there should be no fading
*/
rs.setConservationInc(0);
assertEquals(Color.red, rs.findColour(' ', 7, null));
assertEquals(Color.blue, rs.findColour('Q', 7, null));
-
+
/*
* with 40% threshold, 'fade factor' is
* (11-score)/10 * 40/20 = (11-score)/5
protected ProfilesI getStubConsensus(final String modalResidue,
final float pid)
{
- ProfilesI consensus = new ProfilesI() {
+ ProfilesI consensus = new ProfilesI()
+ {
@Override
public ProfileI get(int i)
{
- return new ProfileI() {
+ return new ProfileI()
+ {
@Override
public void setCounts(ResidueCount residueCounts)
{
public int getNonGapped()
{
return 0;
- }};
+ }
+ };
}
@Override
{
return 0;
}
-
+
};
return consensus;
}