/**
* Test predict using the hivpredmanager
*
* @throws Xws4jException
* @throws XmppException
* @throws InterruptedException
*/
@Test
public void testPredictString() throws Xws4jException, XmppException, InterruptedException {
String seq =
"AAAALWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF";
HIVPredOutputType res = hivdrc.predictPI(seq);
assertNotNull(res);
/*
<?xml version="1.0" encoding="ASCII"?><hivpred:HIVPredOutput xmlns:hivpred="http://www.hivdrc.org/hivpred" errorMessage="">
<hivpred:mutNotInDataset name="P1A"/>
<hivpred:mutOutsideModelBoundaries name="Q2A"/>
<hivpred:mutOutsideModelBoundaries name="I3A"/>
<hivpred:result name="amprenavir" result="-9.344846031197962"/>
<hivpred:result name="atazanavir" result="-8.081778845481008"/>
<hivpred:result name="indinavir" result="-8.306376101045098"/>
<hivpred:result name="lopinavir" result="-8.789871555954795"/>
<hivpred:result name="nelfinavir" result="-7.661361493579009"/>
<hivpred:result name="ritonavir" result="-8.108639981136413"/>
<hivpred:result name="saquinanvir" result="-8.702355550536716"/>
</hivpred:HIVPredOutput>
*/
assertEquals("", res.getErrorMessage());
assertEquals(1, res.getMutNotInDataset().size());
assertEquals("P1A", res.getMutNotInDataset().get(0).getName());
assertEquals(2, res.getMutOutsideModelBoundaries().size());
assertEquals("Q2A", res.getMutOutsideModelBoundaries().get(0).getName());
assertEquals("I3A", res.getMutOutsideModelBoundaries().get(1).getName());
assertEquals(7, res.getResult().size());
assertEquals("amprenavir", res.getResult().get(0).getName());
assertEquals(-9.344846031197962, res.getResult().get(0).getResult(), EPSILON);
assertEquals("atazanavir", res.getResult().get(1).getName());
assertEquals(-8.081778845481008, res.getResult().get(1).getResult(), EPSILON);
assertEquals("indinavir", res.getResult().get(2).getName());
assertEquals(-8.306376101045098, res.getResult().get(2).getResult(), EPSILON);
assertEquals("lopinavir", res.getResult().get(3).getName());
assertEquals(-8.789871555954795, res.getResult().get(3).getResult(), EPSILON);
assertEquals("nelfinavir", res.getResult().get(4).getName());
assertEquals(-7.661361493579009, res.getResult().get(4).getResult(), EPSILON);
assertEquals("ritonavir", res.getResult().get(5).getName());
assertEquals(-8.108639981136413, res.getResult().get(5).getResult(), EPSILON);
// assertEquals("saquinavir", res.getResult().get(6).getName());
// TODO: fix misspelling in sus7.jar class PredictionResult
// saquinanvir -> saquinavir
assertEquals(-8.702355550536716, res.getResult().get(6).getResult(), EPSILON);
System.out.println(res);
}
@Test
public void testPredictFileWithSingleLine()
throws Xws4jException, XmppException, InterruptedException, URISyntaxException,
MalformedURLException, IOException {
URI uri = getClass().getResource("/testFiles/single.seq").toURI();
URL url = FileLocator.toFileURL(uri.toURL());
String path = url.getFile();
System.out.println("Trying to predict file: " + path);
HIVPredOutputType res = hivdrc.predictPI(path);
assertNotNull(res);
// File contains same string as in testPredictString() method
assertEquals("", res.getErrorMessage());
assertEquals(1, res.getMutNotInDataset().size());
assertEquals("P1A", res.getMutNotInDataset().get(0).getName());
assertEquals(2, res.getMutOutsideModelBoundaries().size());
assertEquals("Q2A", res.getMutOutsideModelBoundaries().get(0).getName());
assertEquals("I3A", res.getMutOutsideModelBoundaries().get(1).getName());
assertEquals(7, res.getResult().size());
assertEquals("amprenavir", res.getResult().get(0).getName());
assertEquals(-9.344846031197962, res.getResult().get(0).getResult(), EPSILON);
assertEquals("atazanavir", res.getResult().get(1).getName());
assertEquals(-8.081778845481008, res.getResult().get(1).getResult(), EPSILON);
assertEquals("indinavir", res.getResult().get(2).getName());
assertEquals(-8.306376101045098, res.getResult().get(2).getResult(), EPSILON);
assertEquals("lopinavir", res.getResult().get(3).getName());
assertEquals(-8.789871555954795, res.getResult().get(3).getResult(), EPSILON);
assertEquals("nelfinavir", res.getResult().get(4).getName());
assertEquals(-7.661361493579009, res.getResult().get(4).getResult(), EPSILON);
assertEquals("ritonavir", res.getResult().get(5).getName());
assertEquals(-8.108639981136413, res.getResult().get(5).getResult(), EPSILON);
// assertEquals("saquinavir", res.getResult().get(6).getName());
// TODO: fix misspelling in sus7.jar class PredictionResult
// saquinanvir -> saquinavir
assertEquals(-8.702355550536716, res.getResult().get(6).getResult(), EPSILON);
System.out.println(res);
}