+/*
+ * 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.gui;
-import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.Assert.assertEquals;
+import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ZappoColourScheme;
import java.awt.Color;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class SequenceRendererTest
{
+ AlignmentI al;
+ AlignViewport av;
- @Test(groups ={ "Functional" })
- public void testGetResidueBoxColour_zappo()
+ SequenceI seq1;
+
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
{
- SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
- AlignmentI al = new Alignment(new SequenceI[]
- { seq });
- final AlignViewport av = new AlignViewport(al);
- SequenceRenderer sr = new SequenceRenderer(av);
- av.setGlobalColourScheme(new ZappoColourScheme());
+ Jalview.main(
+ new String[]
+ { "-nonews", "-props", "test/jalview/testProps.jvprops" });
+ }
- // @see ResidueProperties.zappo
- assertEquals(Color.pink, sr.getResidueColour(seq, 0, null)); // M
- assertEquals(Color.green, sr.getResidueColour(seq, 2, null)); // T
- assertEquals(Color.magenta, sr.getResidueColour(seq, 5, null)); // G
- assertEquals(Color.orange, sr.getResidueColour(seq, 12, null)); // F
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ seq1 = new Sequence("Seq1", "ABCEEEABCABC");
+ SequenceI seq2 = new Sequence("Seq2", "ABCABCABCABC");
+ SequenceI seq3 = new Sequence("Seq3", "ABCABCABCABC");
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
+ al = new Alignment(seqs);
+ al.setDataset(null);
+ av = new AlignViewport(al);
}
- // TODO more tests for getResidueBoxColour covering groups, feature rendering,
- // gaps, overview...
+ @Test(groups = "Functional")
+ public void testGetResidueColour_WithGroup()
+ {
+ SequenceRenderer sr = new SequenceRenderer(av);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(seq1, false);
+ sg.setStartRes(3);
+ sg.setEndRes(5);
+
+ ResidueShaderI rs = new ResidueShader();
+ rs.setColourScheme(new ZappoColourScheme());
+ sg.setGroupColourScheme(rs);
+
+ av.getAlignment().addGroup(sg);
+
+ // outside group residues are white
+ assertEquals(Color.white, sr.getResidueColour(seq1, 1, null));
+
+ // within group use Zappo scheme - E = red
+ assertEquals(Color.red, sr.getResidueColour(seq1, 3, null));
+ }
}