-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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;
/**
*/
public class TestHtsContigDb
{
- @Test
- public final void testHTSReferenceSequence() throws Exception
+ @Test(groups = "Functional")
+ 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
- Assert.assertTrue(remmadb.isValid());
+ SequenceI sq = db.getSequenceProxy("Deminut");
+ assertNotNull(sq);
+ assertEquals(sq.getLength(), 606);
- SequenceI sq = remmadb.getSequenceProxy("Deminut");
- Assert.assertNotNull(sq);
- Assert.assertNotEquals(0, sq.getLength());
+ /*
+ * read a sequence earlier in the file
+ */
+ sq = db.getSequenceProxy("PPL_06716");
+ assertNotNull(sq);
+ assertEquals(sq.getLength(), 602);
+
+ // 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
+ * <ul>
+ * <li>opening an unindexed fasta file</li>
+ * <li>creating a .fai index</li>
+ * <li>opening the fasta file, now using the index</li>
+ * <li>error on creating index if overwrite not allowed</li>
+ * </ul>
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testCreateFastaSequenceIndex() throws IOException
+ {
+ File fasta = new File("test/jalview/ext/htsjdk/pgmB.fasta");
+
+ /*
+ * create .fai with no overwrite fails if it exists
+ */
+ try
+ {
+ HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false);
+ fail("Expected exception");
+ } catch (IOException e)
+ {
+ // we expect an IO Exception because the pgmB.fasta.fai exists, since it
+ // was checked it in.
+ }
+
+ /*
+ * create a copy of the .fasta (as a temp file)
+ */
+ File copyFasta = File.createTempFile("copyFasta", ".fasta");
+ copyFasta.deleteOnExit();
+ assertTrue(copyFasta.exists());
+ Files.copy(fasta.toPath(), copyFasta.toPath(),
+ StandardCopyOption.REPLACE_EXISTING);
+
+ /*
+ * open the Fasta file - not indexed, as no .fai file yet exists
+ */
+ HtsContigDb db = new HtsContigDb("ADB", copyFasta);
+ assertTrue(db.isValid());
+ assertFalse(db.isIndexed());
+ db.close();
+
+ /*
+ * create the .fai index, re-open the .fasta file - now indexed
+ */
+ HtsContigDb.createFastaSequenceIndex(copyFasta.toPath(), true);
+ db = new HtsContigDb("ADB", copyFasta);
+ assertTrue(db.isValid());
+ assertTrue(db.isIndexed());
+ db.close();
+ }
+
+ /**
+ * A convenience 'test' that may be run to create a .fai file for any given
+ * fasta file
+ *
+ * @throws IOException
+ */
+ @Test(enabled = false)
+ public void testCreateIndex() throws IOException
+ {
+
+ File fasta = new File("test/jalview/io/vcf/contigs.fasta");
+ HtsContigDb.createFastaSequenceIndex(fasta.toPath(), true);
+ }
}