Commit e8be187
committed
Added basic integration test to demonstrate the issue
1 parent 0570329 commit e8be187
1 file changed
Lines changed: 13 additions & 22 deletions
Lines changed: 13 additions & 22 deletions
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
@@ -22,41 +22,24 @@ | |||
| 22 | 22 | ||
| 23 | 23 | import org.biojava.nbio.core.exceptions.CompoundNotFoundException; | |
| 24 | 24 | import org.biojava.nbio.core.sequence.DNASequence; | |
| 25 | - import org.biojava.nbio.core.sequence.RNASequence; | ||
| 26 | 25 | import org.biojava.nbio.core.sequence.ProteinSequence; | |
| 27 | - import org.biojava.nbio.core.sequence.compound.AminoAcidCompound; | ||
| 28 | - import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet; | ||
| 29 | - import org.biojava.nbio.core.sequence.compound.DNACompoundSet; | ||
| 30 | - import org.biojava.nbio.core.sequence.compound.RNACompoundSet; | ||
| 31 | - import org.biojava.nbio.core.sequence.compound.NucleotideCompound; | ||
| 26 | + import org.biojava.nbio.core.sequence.RNASequence; | ||
| 27 | + import org.biojava.nbio.core.sequence.compound.*; | ||
| 32 | 28 | import org.biojava.nbio.core.sequence.features.FeatureInterface; | |
| 33 | 29 | import org.biojava.nbio.core.sequence.features.Qualifier; | |
| 34 | 30 | import org.biojava.nbio.core.sequence.template.AbstractSequence; | |
| 35 | - import org.junit.After; | ||
| 36 | - import org.junit.AfterClass; | ||
| 37 | - import org.junit.Assert; | ||
| 38 | - import org.junit.Before; | ||
| 39 | - import org.junit.BeforeClass; | ||
| 40 | - import org.junit.Test; | ||
| 31 | + import org.junit.*; | ||
| 41 | 32 | import org.slf4j.Logger; | |
| 42 | 33 | import org.slf4j.LoggerFactory; | |
| 43 | 34 | ||
| 44 | - import java.io.BufferedInputStream; | ||
| 45 | - import java.io.BufferedReader; | ||
| 46 | - import java.io.IOException; | ||
| 47 | - import java.io.InputStream; | ||
| 48 | - import java.io.InputStreamReader; | ||
| 35 | + import java.io.*; | ||
| 49 | 36 | import java.util.ArrayList; | |
| 50 | 37 | import java.util.LinkedHashMap; | |
| 51 | 38 | import java.util.List; | |
| 52 | 39 | import java.util.Map; | |
| 53 | 40 | ||
| 54 | 41 | import static org.hamcrest.CoreMatchers.is; | |
| 55 | - import static org.junit.Assert.assertEquals; | ||
| 56 | - import static org.junit.Assert.assertFalse; | ||
| 57 | - import static org.junit.Assert.assertNotNull; | ||
| 58 | - import static org.junit.Assert.assertThat; | ||
| 59 | - import static org.junit.Assert.assertTrue; | ||
| 42 | + import static org.junit.Assert.*; | ||
| 60 | 43 | ||
| 61 | 44 | /** | |
| 62 | 45 | * | |
@@ -350,6 +333,14 @@ public void testLegacyLocusCompatable() throws IOException, CompoundNotFoundExce | |||
| 350 | 333 | ||
| 351 | 334 | } | |
| 352 | 335 | ||
| 336 | + @Test | ||
| 337 | + public void readSequenceWithZeroSpanFeature() throws IOException, CompoundNotFoundException { | ||
| 338 | + logger.info("make or read genbank file error when feature spans zero point of circular sequence (issue #855)"); | ||
| 339 | + final DNASequence seq = readGenbankResource("/feature-spans-zero-point-circular-sequence.gb"); | ||
| 340 | + | ||
| 341 | + assertNotNull(seq); | ||
| 342 | + } | ||
| 343 | + | ||
| 353 | 344 | /** | |
| 354 | 345 | * Helper class to be able to verify the closed state of the input stream. | |
| 355 | 346 | */ | |
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