import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.fail;
-import static org.testng.AssertJUnit.assertNull;
import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.Set;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceFeature;
public class EmblFlatFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.initLogger();
+ }
+
/**
* A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
* one of them reverse strand
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1579);
- assertEquals(ranges.get(0)[1], 2934);
+ assertEquals(ranges.get(0)[1], 2931);
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 451);
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 2928);
- assertEquals(ranges.get(0)[1], 3992);
+ assertEquals(ranges.get(0)[1], 3989);
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 354);
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 4054);
- assertEquals(ranges.get(0)[1], 4848);
+ assertEquals(ranges.get(0)[1], 4845);
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 264);
assertEquals(ranges.get(0)[0], 7022);
assertEquals(ranges.get(0)[1], 7502);
assertEquals(ranges.get(1)[0], 1);
- assertEquals(ranges.get(1)[1], 437);
+ assertEquals(ranges.get(1)[1], 434);
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 305);
// complement(488..1480)
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1480);
- assertEquals(ranges.get(0)[1], 488);
+ assertEquals(ranges.get(0)[1], 491);
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 330);
{
int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
+ int[] exons_nostop = new int[] { 11, 15, 21, 25, 31, 35 }; // 15 bp
// exact length match:
assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
- // match if we assume exons include stop codon not in protein:
- assertSame(exons, EmblFlatFile.adjustForProteinLength(5, exons));
+ // trimmed if we assume exons include stop codon not in protein:
+ assertEquals(Arrays.toString(exons_nostop), Arrays.toString(EmblFlatFile.adjustForProteinLength(5, exons)));
// truncate last exon by 6bp
int[] truncated = EmblFlatFile.adjustForProteinLength(4, exons);