+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class ClustalxColourSchemeTest
+{
+ // @formatter:off
+ private static final String FASTA =
+ ">seq1\nAAANNNRQ\n" +
+ ">seq2\nAAANNNRQ\n" +
+ ">seq3\nAAANNNRQ\n" +
+ ">seq4\nAAANNNRQ\n" +
+ ">seq5\nAAANYYKQ\n" +
+ ">seq6\nAAANYYKQ\n" +
+ ">seq7\nAVKWYYKQ\n" +
+ ">seq8\nKKKWYYQQ\n" +
+ ">seq9\nKKKWWYQQ\n" +
+ ">seq0\nKKKWWWQW\n";
+ // @formatter:on
+
+ @Test(groups = "Functional")
+ public void testFindColour()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(FASTA,
+ DataSourceType.PASTE);
+ AlignmentI al = af.getViewport().getAlignment();
+ ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
+
+ /*
+ * column 1 is 70% A which is above Clustalx threshold of 60%
+ */
+ Color clustalBlue = new Color(0.5f, 0.7f, 0.9f);
+ assertEquals(cs.findColour('A', 0, al.getSequenceAt(0)), clustalBlue);
+
+ /*
+ * column 2 is 70% A or V which is above Clustalx threshold for group
+ */
+ assertEquals(cs.findColour('A', 0, al.getSequenceAt(1)), clustalBlue);
+
+ /*
+ * column 3 is 60% A which is not above Clustalx threshold
+ * the Ks in the other rows are not in the same Clustalx group
+ */
+ assertEquals(cs.findColour('A', 2, al.getSequenceAt(1)), Color.white);
+
+ /*
+ * column 4 is 60% N which is above Clustalx threshold of 50%
+ */
+ Color clustalGreen = new Color(0.1f, 0.8f, 0.1f);
+ assertEquals(cs.findColour('N', 3, al.getSequenceAt(1)), clustalGreen);
+
+ /*
+ * column 5 is 40% N and 40% Y which fails to pass the threshold of
+ * 50% N or 85% either
+ */
+ assertEquals(cs.findColour('N', 4, al.getSequenceAt(1)), Color.white);
+
+ /*
+ * column 6 is 40% N and 50% Y which fails to pass the threshold of
+ * 85% for either
+ */
+ assertEquals(cs.findColour('N', 5, al.getSequenceAt(1)), Color.white);
+
+ /*
+ * column 7 is 40% R and 30% K which combine to make > 60%
+ */
+ Color clustalRed = new Color(0.9f, 0.2f, 0.1f);
+ assertEquals(cs.findColour('R', 6, al.getSequenceAt(1)), clustalRed);
+ assertEquals(cs.findColour('K', 6, al.getSequenceAt(7)), clustalRed);
+
+ /*
+ * column 8 is >85% Q which qualifies K and R to be red
+ */
+ assertEquals(cs.findColour('R', 7, al.getSequenceAt(1)), clustalRed);
+ assertEquals(cs.findColour('K', 7, al.getSequenceAt(1)), clustalRed);
+
+ // TODO more test cases; check if help documentation matches implementation
+ }
+
+ // @formatter:on
+
+ /**
+ * Test for colour calculation when the consensus percentage ignores gapped
+ * sequences
+ */
+ @Test(groups = "Functional")
+ public void testFindColour_ignoreGaps()
+ {
+ /*
+ * CCC
+ * CCC
+ * -CC
+ * first column is 66% C (blue) including gaps
+ * or 100% C ignoring gaps
+ */
+ String fasta = ">seq1\nCCC\n>seq2\nccc\n>seq3\n-CC\n";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
+ DataSourceType.PASTE);
+ AlignmentI al = af.getViewport().getAlignment();
+ ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
+
+ /*
+ * column 1 is 66% C which is above Clustalx threshold of 60%
+ */
+ Color clustalBlue = ClustalxColourScheme.ClustalColour.BLUE.colour;
+ assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
+
+ /*
+ * set directly to ignore gaps
+ */
+ cs.setIncludeGaps(false);
+ Color clustalPink = ClustalxColourScheme.ClustalColour.PINK.colour;
+ assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
+
+ /*
+ * set ignore gaps on the viewport...
+ */
+ cs.setIncludeGaps(true);
+ assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalBlue);
+ af.getViewport().setIgnoreGapsConsensus(true, af.alignPanel);
+ // next test fails: colour scheme does not read ignore gaps flag from
+ // viewport
+ // assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
+ }
+}