+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.renderer;
import static org.testng.AssertJUnit.assertEquals;
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;
}