+/*
+ * 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.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
import java.util.Collections;
import java.util.List;
+import org.testng.annotations.Test;
+
public class ResiduePropertiesTest
{
/**
* Test 'standard' codon translations (no ambiguity codes)
*/
- @Test
+ @Test(groups = { "Functional" })
public void testCodonTranslate()
{
// standard translation table order column 1/2/3/4
* Test a sample of codon translations involving ambiguity codes. Should
* return a protein value where the ambiguity does not affect the translation.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testCodonTranslate_ambiguityCodes()
{
// Y is C or T
assertNull(ResidueProperties.codonTranslate("WSK"));
}
- @Test
+ @Test(groups = { "Functional" })
public void testGetResidues_nucleotide()
{
/*
assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString());
}
- @Test
+ @Test(groups = { "Functional" })
public void testGetResidues_peptide()
{
/*
"[ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, XAA]",
residues.toString());
}
+
+ @Test(groups = { "Functional" })
+ public void testGetCanonicalAminoAcid()
+ {
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
+ assertEquals(null, ResidueProperties.getCanonicalAminoAcid(null));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetSingleCharacterCode()
+ {
+ assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
+ assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
+ assertEquals('0', ResidueProperties.getSingleCharacterCode(""));
+ assertEquals('Q', ResidueProperties.getSingleCharacterCode("GLN"));
+ assertEquals('Q', ResidueProperties.getSingleCharacterCode("Gln"));
+ assertEquals('Q', ResidueProperties.getSingleCharacterCode("gln"));
+ }
}