/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+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;
/**
*/
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.
*/
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, '-');
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, '-');
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);
+ new int[]
+ { 1, 3 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
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, '-');
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);
+ 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, '-');