test/jalview/ws/ebi/HmmerJSONProcessTest.java

   1 package jalview.ws.ebi;
   2
   3 import jalview.datamodel.AlignmentAnnotation;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.io.FileParse;
   7 import jalview.io.FormatAdapter;
   8
   9 import java.io.File;
  10
  11 import org.json.simple.JSONObject;
  12 import org.json.simple.parser.JSONParser;
  13 import org.testng.Assert;
  14 import org.testng.annotations.Test;
  15
  16 public class HmmerJSONProcessTest {
  17   public static File alignmentFragFile = new File(
  18           "examples/testdata/hmmer3/alignment_frag.fa.gz");
  19
  20   private AlignmentI getSearchResultFragmentAlignment() throws Exception
  21   {
  22     AlignmentI alf = new FormatAdapter().readFile(
  23             alignmentFragFile.getAbsolutePath(), FormatAdapter.FILE,
  24             "FASTA");
  25
  26     return alf;
  27   }
  28
  29   public static File alignmentResultFile = new File(
  30           "examples/testdata/hmmer3/alignment_res.fa.gz");
  31
  32   private AlignmentI getSearchResultAlignment() throws Exception
  33   {
  34     AlignmentI alf = new FormatAdapter().readFile(
  35             alignmentResultFile.getAbsolutePath(), FormatAdapter.FILE,
  36             "FASTA");
  37
  38     return alf;
  39   }
  40
  41   public static String hitTestFile = "examples/testdata/hmmer3/hit_fragment.json.gz",
  42           hmmerResultFile = "examples/testdata/hmmer3/hmmeresult.json.gz";
  43
  44
  45   @Test(groups = { "Functional" })
  46   public void parseHitTest() throws Exception
  47   {
  48
  49     Assert.assertTrue(new File(hitTestFile).exists(),
  50             "Can't find test data.\n"
  51             + hitTestFile);
  52     JSONParser jp = new JSONParser();
  53     // read JSON in same way - via fileparse
  54     Object hitfragment = jp.parse(new FileParse(hitTestFile,
  55             FormatAdapter.FILE).getReader());
  56     Assert.assertTrue((hitfragment instanceof JSONObject),
  57             "Didn't find a JSON object map in " + hitTestFile);
  58     AlignmentI searchResult = getSearchResultFragmentAlignment();
  59
  60     Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
  61             "Didn't read search result alignment from " + alignmentFragFile);
  62
  63     HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
  64     hjsp.addHit((JSONObject) hitfragment, 1);
  65     // check that
  66     // scores, posterior probabilities and stuff exist.
  67   }
  68
  69   @Test(groups = { "Functional" })
  70   public void parseJsonResultTest() throws Exception
  71   {
  72
  73     Assert.assertTrue(new File(hmmerResultFile).exists(),
  74             "Can't find test data.\n" + hmmerResultFile);
  75
  76     AlignmentI searchResult = getSearchResultAlignment();
  77
  78     Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
  79             "Didn't read search result alignment from " + alignmentFragFile);
  80
  81     HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
  82     hjsp.parseFrom(new FileParse(hmmerResultFile, FormatAdapter.FILE));
  83     AlignmentAnnotation[] aa = searchResult.getSequenceAt(5)
  84             .getAnnotation();
  85     Assert.assertNotNull(aa);
  86     Assert.assertEquals(aa.length, 3,
  87             "didn't get expected set of annotation.\n");
  88     // DPTSERWFHGHLSGKEAEKLLTeKGKHGSFLVRESQSHPGDFVLSVRTgddkgesndgKSKVTHVMIR-CQELKYDVGGGERFDSLTDLVEHYKKNPmvet
  89     // LGTVLQLKQP
  90     // 5789*****************9799***********************999998888888********.99**************************9999
  91     // 899999*999
  92     // AlignmentAnnotation
  93     // 101 == 8
  94     String seq = "tLGT";
  95     SequenceI s5 = searchResult.getSequenceAt(5);
  96     Assert.assertEquals(
  97             s5.getSubSequence(s5.findIndex(225), s5.findIndex(229))
  98                     .getSequenceAsString(),
  99             seq);
 100     int pos = s5.findIndex(226);
 101     for (AlignmentAnnotation an : aa)
 102     {
 103       if (an.label.startsWith("Posterior"))
 104       {
 105         Assert.assertEquals(an.annotations[pos].value, 8f);
 106
 107       }
 108     }
 109     ;
 110     // check that
 111     // scores, posterior probabilities and stuff exist.
 112   }
 113   // Groovy test
 114   // def al = Jalview.getAlignFrames()[0].getViewport().getAlignment()
 115   // def jproc = new jalview.ws.ebi.HmmerJSONProcessor(al)
 116   // jproc.parseFrom(new
 117   // jalview.io.FileParse("examples/testdata/hmmer3/hmmeresult.json.gz","File"))
 118   // jproc.updateView(Jalview.getAlignFrames()[0].getViewport())
 119
 120 }