@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
}
PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
String content = ContactMatrix.contactToFloatString(dummyMat);
- Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
- float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
- assertEquals(vals[3][4],paevals[3][4]);
+ Assert.assertTrue(content.contains("\t1.")); // at least one element must be
+ // 1
+ float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
+ sq.getLength(), sq.getLength());
+ assertEquals(vals[3][4], paevals[3][4]);
dummyMat.makeGroups(0.5f, false);
+ Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
al.addAnnotation(paeCm);
File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
}
}
- Assert.assertEquals(dummyMat.hasGroups(), restoredMat.hasGroups());
- Assert.assertEquals(dummyMat.getGroups(), restoredMat.getGroups());
- Assert.assertEquals(dummyMat.hasTree(), restoredMat.hasTree());
- Assert.assertEquals(dummyMat.getNewick(), restoredMat.getNewick());
-
-
+ Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
+ Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
+ Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
+ Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
}
}