+/*
+ * 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.datamodel;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.util.Arrays;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*/
public class MappingTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* trite test of the intersectVisContigs method for a simple DNA -> Protein
* exon map and a range of visContigs
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testIntersectVisContigs()
{
- MapList fk = new MapList(new int[]
- { 1, 6, 8, 13, 15, 23 }, new int[]
- { 1, 7 }, 3, 1);
+ MapList fk = new MapList(new int[] { 1, 6, 8, 13, 15, 23 }, new int[] {
+ 1, 7 }, 3, 1);
Mapping m = new Mapping(fk);
- Mapping m_1 = m.intersectVisContigs(new int[]
- { fk.getFromLowest(), fk.getFromHighest() });
- Mapping m_2 = m.intersectVisContigs(new int[]
- { 1, 7, 11, 20 });
+ Mapping m_1 = m.intersectVisContigs(new int[] { fk.getFromLowest(),
+ fk.getFromHighest() });
+ Mapping m_2 = m.intersectVisContigs(new int[] { 1, 7, 11, 20 });
// assertions from output values 'as is', not checked for correctness
- String result = Arrays.deepToString(m_1.map.getFromRanges()
- .toArray());
+ String result = Arrays.deepToString(m_1.map.getFromRanges().toArray());
System.out.println(result);
assertEquals("[[1, 6], [8, 13], [15, 23]]", result);
assertEquals("[[1, 6], [11, 13], [15, 20]]", result);
}
+ @Test(groups = { "Functional" })
+ public void testToString()
+ {
+ /*
+ * with no sequence
+ */
+ MapList fk = new MapList(new int[] { 1, 6, 8, 13 }, new int[] { 4, 7 },
+ 3, 1);
+ Mapping m = new Mapping(fk);
+ assertEquals("[ [1, 6] [8, 13] ] 3:1 to [ [4, 7] ] ", m.toString());
+
+ /*
+ * with a sequence
+ */
+ SequenceI seq = new Sequence("Seq1", "");
+ m = new Mapping(seq, fk);
+ assertEquals("[ [1, 6] [8, 13] ] 3:1 to [ [4, 7] ] Seq1", m.toString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testCopyConstructor()
+ {
+ MapList ml = new MapList(new int[] { 1, 6, 8, 13 }, new int[] { 4, 7 },
+ 3, 1);
+ SequenceI seq = new Sequence("seq1", "agtacg");
+ Mapping m = new Mapping(seq, ml);
+ m.setMappedFromId("abc");
+ Mapping copy = new Mapping(m);
+ assertEquals("abc", copy.getMappedFromId());
+ assertEquals(ml, copy.getMap());
+ assertSame(seq, copy.getTo());
+ }
}