@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);
sq = db.getSequenceProxy("PPL_06716");
assertNotNull(sq);
assertEquals(sq.getLength(), 602);
-
+
// dict = db.getDictionary(f, truncate))
}
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");
}
@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)
{
+ System.out.println(
+ "Caught IOException in testCreateFastaSequenceIndex");
+ e.printStackTrace();
// expected
}