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.DataSourceType;
   7 import jalview.io.FileFormat;
   8 import jalview.io.FileParse;
   9 import jalview.io.FormatAdapter;
  10
  11 import java.io.File;
  12
  13 import org.json.simple.JSONObject;
  14 import org.json.simple.parser.JSONParser;
  15 import org.testng.Assert;
  16 import org.testng.annotations.Test;
  17
  18 public class HmmerJSONProcessTest {
  19   public static File alignmentFragFile = new File(
  20           "examples/testdata/hmmer3/alignment_frag.fa.gz");
  21
  22   private AlignmentI getSearchResultFragmentAlignment() throws Exception
  23   {
  24     AlignmentI alf = new FormatAdapter().readFile(
  25             alignmentFragFile.getAbsolutePath(), DataSourceType.FILE,
  26             FileFormat.Fasta);
  27
  28     return alf;
  29   }
  30
  31   public static File alignmentResultFile = new File(
  32           "examples/testdata/hmmer3/alignment_res.fa.gz");
  33
  34   private AlignmentI getSearchResultAlignment() throws Exception
  35   {
  36     AlignmentI alf = new FormatAdapter().readFile(
  37             alignmentResultFile.getAbsolutePath(), DataSourceType.FILE,
  38             FileFormat.Fasta);
  39
  40     return alf;
  41   }
  42
  43   public static String hitTestFile = "examples/testdata/hmmer3/hit_fragment.json.gz",
  44           hmmerResultFile = "examples/testdata/hmmer3/hmmeresult.json.gz";
  45
  46
  47   @Test(groups = { "Functional" })
  48   public void parseHitTest() throws Exception
  49   {
  50
  51     Assert.assertTrue(new File(hitTestFile).exists(),
  52             "Can't find test data.\n"
  53             + hitTestFile);
  54     JSONParser jp = new JSONParser();
  55     // read JSON in same way - via fileparse
  56     Object hitfragment = jp.parse(new FileParse(hitTestFile,
  57             DataSourceType.FILE).getReader());
  58     Assert.assertTrue((hitfragment instanceof JSONObject),
  59             "Didn't find a JSON object map in " + hitTestFile);
  60     AlignmentI searchResult = getSearchResultFragmentAlignment();
  61
  62     Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
  63             "Didn't read search result alignment from " + alignmentFragFile);
  64
  65     HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
  66     hjsp.addHit((JSONObject) hitfragment, 1);
  67     // check that
  68     // scores, posterior probabilities and stuff exist.
  69   }
  70
  71   @Test(groups = { "Functional" })
  72   public void parseJsonResultTest() throws Exception
  73   {
  74
  75     Assert.assertTrue(new File(hmmerResultFile).exists(),
  76             "Can't find test data.\n" + hmmerResultFile);
  77
  78     AlignmentI searchResult = getSearchResultAlignment();
  79
  80     Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
  81             "Didn't read search result alignment from " + alignmentFragFile);
  82
  83     HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
  84     hjsp.parseFrom(new FileParse(hmmerResultFile, DataSourceType.FILE));
  85     AlignmentAnnotation[] aa = searchResult.getSequenceAt(5)
  86             .getAnnotation();
  87     Assert.assertNotNull(aa);
  88     Assert.assertEquals(aa.length, 3,
  89             "didn't get expected set of annotation.\n");
  90     // DPTSERWFHGHLSGKEAEKLLTeKGKHGSFLVRESQSHPGDFVLSVRTgddkgesndgKSKVTHVMIR-CQELKYDVGGGERFDSLTDLVEHYKKNPmvet
  91     // LGTVLQLKQP
  92     // 5789*****************9799***********************999998888888********.99**************************9999
  93     // 899999*999
  94     // AlignmentAnnotation
  95     // 101 == 8
  96     String seq = "tLGT";
  97     SequenceI s5 = searchResult.getSequenceAt(5);
  98     Assert.assertEquals(
  99             s5.getSubSequence(s5.findIndex(225), s5.findIndex(229))
 100                     .getSequenceAsString(),
 101             seq);
 102     int pos = s5.findIndex(226);
 103     for (AlignmentAnnotation an : aa)
 104     {
 105       if (an.label.startsWith("Posterior"))
 106       {
 107         Assert.assertEquals(an.annotations[pos].value, 8f);
 108
 109       }
 110     }
 111     ;
 112     // check that
 113     // scores, posterior probabilities and stuff exist.
 114   }
 115   // Groovy test
 116   // def al = Jalview.getAlignFrames()[0].getViewport().getAlignment()
 117   // def jproc = new jalview.ws.ebi.HmmerJSONProcessor(al)
 118   // jproc.parseFrom(new
 119   // jalview.io.FileParse("examples/testdata/hmmer3/hmmeresult.json.gz","File"))
 120   // jproc.updateView(Jalview.getAlignFrames()[0].getViewport())
 121
 122 }