+/*
+ * 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.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+import jalview.datamodel.Sequence;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignSeqTest
{
- @Test(groups ={ "Functional" })
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Functional" })
public void testExtractGaps()
{
assertNull(AlignSeq.extractGaps(null, null));
assertNull(AlignSeq.extractGaps(null, "ACG"));
assertNull(AlignSeq.extractGaps("-. ", null));
- assertEquals(" AC-G.T", AlignSeq.extractGaps("", " AC-G.T"));
- assertEquals("AC-G.T", AlignSeq.extractGaps(" ", " AC-G.T"));
- assertEquals("ACG.T", AlignSeq.extractGaps(" -", " AC-G.T"));
- assertEquals("ACGT", AlignSeq.extractGaps(" -.", " AC-G.T ."));
- assertEquals(" ACG.T", AlignSeq.extractGaps("-", " AC-G.T"));
+ assertEquals(AlignSeq.extractGaps("", " AC-G.T"), " AC-G.T");
+ assertEquals(AlignSeq.extractGaps(" ", " AC-G.T"), "AC-G.T");
+ assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T");
+ assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT");
+ assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T");
+ assertEquals(AlignSeq.extractGaps("-. ", " -. .-"), "");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIndexEncode_nucleotide()
+ {
+ AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), new Sequence(
+ "s2", "ACGT"), AlignSeq.DNA);
+ int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
+ 7, 7, 8, 8, 9, 9, -1, -1, 10, -1 };
+ String s = "aAcCgGtTuUiIxXrRyYnN .-?";
+ assertArrayEquals(expected, as.indexEncode(s));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIndexEncode_peptide()
+ {
+ AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence(
+ "s2", "RQW"), AlignSeq.PEP);
+ int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 23,
+ -1, -1, -1 };
+ String s = "aArRnNzZxX *.-?";
+ assertArrayEquals(expected, as.indexEncode(s));
}
}