protected AlignmentI loadAlignment(final String data, String format)
throws IOException
{
- Alignment a = new FormatAdapter().readFile(data,
+ AlignmentI a = new FormatAdapter().readFile(data,
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
/**
* Test method that returns annotations that match on calcId.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testFindAnnotation_byCalcId()
{
Iterable<AlignmentAnnotation> anns = al
assertFalse(iter.hasNext());
}
- @Test
+ @Test(groups ={ "Functional" })
public void testDeleteAllAnnotations_includingAutocalculated()
{
AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
}
- @Test
+ @Test(groups ={ "Functional" })
public void testDeleteAllAnnotations_excludingAutocalculated()
{
AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignAs_dnaAsDna() throws IOException
{
// aligned cDNA:
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignAs_proteinAsCdna() throws IOException
{
// see also AlignmentUtilsTests
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignAs_cdnaAsProtein() throws IOException
{
/*
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
{
/*