X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fext%2Fhtsjdk%2FTestHtsContigDb.java;h=69634a91163d2c99e70a542bed4903731a440ecd;hb=32a2c42a535d809dfcb48db1e8cc91bb03193f8e;hp=bdc14db3c8d0c5cb14bf42e80ec1b1c40a753090;hpb=956deeb079bf76f9a0e9dc076154ff4865743e63;p=jalview.git diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java index bdc14db..69634a9 100644 --- a/test/jalview/ext/htsjdk/TestHtsContigDb.java +++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java @@ -20,11 +20,19 @@ */ package jalview.ext.htsjdk; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertFalse; +import static org.testng.Assert.assertNotNull; +import static org.testng.Assert.assertTrue; +import static org.testng.Assert.fail; + import jalview.datamodel.SequenceI; import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.StandardCopyOption; -import org.testng.Assert; import org.testng.annotations.Test; /** @@ -34,16 +42,109 @@ import org.testng.annotations.Test; public class TestHtsContigDb { @Test(groups = "Functional") - public final void testHTSReferenceSequence() throws Exception + public final void testGetSequenceProxy() throws Exception { - HtsContigDb remmadb = new HtsContigDb("REEMADB", new File( - "test/jalview/ext/htsjdk/pgmb.fasta")); + String pathname = "test/jalview/ext/htsjdk/pgmB.fasta"; + HtsContigDb db = new HtsContigDb("ADB", new File(pathname)); + + assertTrue(db.isValid()); + assertTrue(db.isIndexed()); // htsjdk opens the .fai file + + SequenceI sq = db.getSequenceProxy("Deminut"); + assertNotNull(sq); + assertEquals(sq.getLength(), 606); - Assert.assertTrue(remmadb.isValid()); + /* + * read a sequence earlier in the file + */ + sq = db.getSequenceProxy("PPL_06716"); + assertNotNull(sq); + assertEquals(sq.getLength(), 602); - SequenceI sq = remmadb.getSequenceProxy("Deminut"); - Assert.assertNotNull(sq); - Assert.assertNotEquals(0, sq.getLength()); + // dict = db.getDictionary(f, truncate)) } + /** + * Trying to open a .fai file directly results in IllegalArgumentException - + * have to provide the unindexed file name instead + */ + @Test( + groups = "Functional", + expectedExceptions = java.lang.IllegalArgumentException.class) + public final void testGetSequenceProxy_indexed() + { + String pathname = "test/jalview/ext/htsjdk/pgmB.fasta.fai"; + new HtsContigDb("ADB", new File(pathname)); + fail("Expected exception opening .fai file"); + } + + /** + * Tests that exercise + *