+/*
+ * 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.assertFalse;
-import org.testng.annotations.Test;
-import org.testng.Assert;
+
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.util.Iterator;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
/**
* Unit tests for Mapping$AlignedCodonIterator
*
*/
public class AlignedCodonIteratorTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test normal case for iterating over aligned codons.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testNext()
{
SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "-PQ-R-");
to.createDatasetSequence();
- MapList map = new MapList(new int[]
- { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[]
- { 1, 3 }, 3, 1);
+ MapList map = new MapList(
+ new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
+ new int[] { 1, 3 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
/**
* Test weird case where the mapping skips over a peptide.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testNext_unmappedPeptide()
{
SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "-PQ-TR-");
to.createDatasetSequence();
- MapList map = new MapList(new int[]
- { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[]
- { 1, 2, 4, 4 }, 3, 1);
+ MapList map = new MapList(
+ new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[] { 1,
+ 2, 4, 4 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
assertEquals("R", codon.product);
assertFalse(codons.hasNext());
}
-
+
/**
* Test for exception thrown for an incomplete codon.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testNext_incompleteCodon()
{
SequenceI from = new Sequence("Seq1", "-CgC-C-cCgTt");
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "-PQ-R-");
to.createDatasetSequence();
- MapList map = new MapList(new int[]
- { 1, 1, 3, 4, 6, 6, 8, 8 }, new int[]
- { 1, 3 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 8 },
+ new int[] { 1, 3 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
/**
* Test normal case for iterating over aligned codons.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testAnother()
{
SequenceI from = new Sequence("Seq1", "TGCCATTACCAG-");
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "CHYQ");
to.createDatasetSequence();
- MapList map = new MapList(new int[]
- { 1, 12 }, new int[]
- { 1, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
-
+
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
AlignedCodon codon = codons.next();
assertEquals("[0, 1, 2]", codon.toString());
assertEquals("Q", codon.product);
assertFalse(codons.hasNext());
}
+
+ /**
+ * Test for a case with sequence (and mappings) not starting at 1
+ */
+ @Test(groups = { "Functional" })
+ public void testNext_withOffset()
+ {
+ SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc", 7, 20);
+ from.createDatasetSequence();
+ SequenceI to = new Sequence("Seq1/10-12", "-PQ-R-");
+ to.createDatasetSequence();
+ MapList map = new MapList(new int[] { 7, 7, 9, 10, 12, 12, 14, 16, 18,
+ 19 }, new int[] { 10, 12 }, 3, 1);
+ Mapping m = new Mapping(to.getDatasetSequence(), map);
+
+ Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
+ AlignedCodon codon = codons.next();
+ assertEquals("[1, 3, 5]", codon.toString());
+ assertEquals("P", codon.product);
+ codon = codons.next();
+ assertEquals("[8, 10, 11]", codon.toString());
+ assertEquals("Q", codon.product);
+ codon = codons.next();
+ assertEquals("[13, 15, 17]", codon.toString());
+ assertEquals("R", codon.product);
+ assertFalse(codons.hasNext());
+ }
}