+/*
+ * 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.schemes;
import static org.testng.Assert.assertEquals;
">seq0\nKKKWWWQW\n";
// @formatter:on
- @Test
+ @Test(groups = "Functional")
public void testFindColour()
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(FASTA,
DataSourceType.PASTE);
AlignmentI al = af.getViewport().getAlignment();
- ColourSchemeI cs = new ClustalxColourScheme(al, null);
+ ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
/*
* column 1 is 70% A which is above Clustalx threshold of 60%
// 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);
+ }
+ @Test
+ public void testDocString()
+ {
+ /* verify we have some sort of useful output */
+ ClustalxColourScheme x = new ClustalxColourScheme();
+ String out = x.toRuleRep();
+ System.out.print(out);
+ }
}