X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fhtsjdk%2FTestHtsContigDb.java;h=69634a91163d2c99e70a542bed4903731a440ecd;hb=0435cd1ec60c5f90521835a79fb6702220a12a55;hp=28c5cf0ddaf1fe0ca052b08b819129ea1580e336;hpb=296593216c47a835f462d1d74a40b41e4818f737;p=jalview.git diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java index 28c5cf0..69634a9 100644 --- a/test/jalview/ext/htsjdk/TestHtsContigDb.java +++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java @@ -44,12 +44,12 @@ public class TestHtsContigDb @Test(groups = "Functional") public final void testGetSequenceProxy() throws Exception { - String pathname = "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); @@ -60,7 +60,7 @@ public class TestHtsContigDb sq = db.getSequenceProxy("PPL_06716"); assertNotNull(sq); assertEquals(sq.getLength(), 602); - + // dict = db.getDictionary(f, truncate)) } @@ -73,7 +73,7 @@ public class TestHtsContigDb expectedExceptions = java.lang.IllegalArgumentException.class) public final void testGetSequenceProxy_indexed() { - String pathname = "test/jalview/ext/htsjdk/pgmb.fasta.fai"; + String pathname = "test/jalview/ext/htsjdk/pgmB.fasta.fai"; new HtsContigDb("ADB", new File(pathname)); fail("Expected exception opening .fai file"); } @@ -92,17 +92,19 @@ public class TestHtsContigDb @Test(groups = "Functional") public void testCreateFastaSequenceIndex() throws IOException { - File fasta = new File("test/jalview/ext/htsjdk/pgmb.fasta"); - + File fasta = new File("test/jalview/ext/htsjdk/pgmB.fasta"); + /* * create .fai with no overwrite fails if it exists */ - try { + try + { HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false); fail("Expected exception"); } catch (IOException e) { - // expected + // we expect an IO Exception because the pgmB.fasta.fai exists, since it + // was checked it in. } /*