+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeMethod(alwaysRun = true)
+ public void loadProperties()
+ {
+ Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testUPGMAEngine() throws Exception
+ {
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ "examples/test_fab41.result/sample.a3m", DataSourceType.FILE);
+ AlignmentI seqs = af.getViewport().getAlignment();
+ SequenceI target = seqs.getSequenceAt(0);
+ File testPAE = new File(
+ "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
+ List<Object> pae_obj = (List<Object>) Platform
+ .parseJSON(new FileInputStream(testPAE));
+ if (pae_obj == null)