X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fhtsjdk%2FTestHtsContigDb.java;h=28c5cf0ddaf1fe0ca052b08b819129ea1580e336;hb=d8720fc191cba996c440171ef8e07462ef9f7035;hp=350b599117067649d9c4e4cdb57aebac3f64d781;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java index 350b599..28c5cf0 100644 --- a/test/jalview/ext/htsjdk/TestHtsContigDb.java +++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java @@ -20,13 +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 jalview.gui.JvOptionPane; 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.BeforeClass; import org.testng.annotations.Test; /** @@ -35,25 +41,108 @@ import org.testng.annotations.Test; */ public class TestHtsContigDb { + @Test(groups = "Functional") + public final void testGetSequenceProxy() throws Exception + { + 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); + + /* + * read a sequence earlier in the file + */ + sq = db.getSequenceProxy("PPL_06716"); + assertNotNull(sq); + assertEquals(sq.getLength(), 602); + + // dict = db.getDictionary(f, truncate)) + } - @BeforeClass(alwaysRun = true) - public void setUpJvOptionPane() + /** + * 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() { - JvOptionPane.setInteractiveMode(false); - JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + String pathname = "test/jalview/ext/htsjdk/pgmb.fasta.fai"; + new HtsContigDb("ADB", new File(pathname)); + fail("Expected exception opening .fai file"); } + /** + * Tests that exercise + *