test/jalview/ws/ebi/HmmerJSONProcessTest.java

   1 package jalview.ws.ebi;
   2
   3 import jalview.datamodel.AlignmentI;
   4 import jalview.io.FileParse;
   5 import jalview.io.FormatAdapter;
   6
   7 import java.io.File;
   8
   9 import org.json.simple.JSONObject;
  10 import org.json.simple.parser.JSONParser;
  11 import org.testng.Assert;
  12 import org.testng.annotations.Test;
  13
  14 public class HmmerJSONProcessTest {
  15   public static File alignmentFragFile = new File(
  16           "examples/testdata/hmmer3/alignment_frag.fa.gz");
  17
  18   private AlignmentI getSearchResultFragmentAlignment() throws Exception
  19   {
  20     AlignmentI alf = new FormatAdapter().readFile(
  21             alignmentFragFile.getAbsolutePath(), FormatAdapter.FILE,
  22             "FASTA");
  23
  24     return alf;
  25   }
  26
  27   public static File alignmentResultFile = new File(
  28           "examples/testdata/hmmer3/alignment_res.fa.gz");
  29
  30   private AlignmentI getSearchResultAlignment() throws Exception
  31   {
  32     AlignmentI alf = new FormatAdapter().readFile(
  33             alignmentResultFile.getAbsolutePath(), FormatAdapter.FILE,
  34             "FASTA");
  35
  36     return alf;
  37   }
  38
  39   public static String hitTestFile = "examples/testdata/hmmer3/hit_fragment.json.gz",
  40           hmmerResultFile = "examples/testdata/hmmer3/hmmeresult.json.gz";
  41
  42
  43   @Test(groups = { "Functional" })
  44   public void parseHitTest() throws Exception
  45   {
  46
  47     Assert.assertTrue(new File(hitTestFile).exists(),
  48             "Can't find test data.\n"
  49             + hitTestFile);
  50     JSONParser jp = new JSONParser();
  51     // read JSON in same way - via fileparse
  52     Object hitfragment = jp.parse(new FileParse(hitTestFile,
  53             FormatAdapter.FILE).getReader());
  54     Assert.assertTrue((hitfragment instanceof JSONObject),
  55             "Didn't find a JSON object map in " + hitTestFile);
  56     AlignmentI searchResult = getSearchResultFragmentAlignment();
  57
  58     Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
  59             "Didn't read search result alignment from " + alignmentFragFile);
  60
  61     HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
  62     hjsp.addHit((JSONObject) hitfragment, 1);
  63     // check that
  64     // scores, posterior probabilities and stuff exist.
  65   }
  66
  67   @Test(groups = { "Functional" })
  68   public void parseJsonResultTest() throws Exception
  69   {
  70
  71     Assert.assertTrue(new File(hmmerResultFile).exists(),
  72             "Can't find test data.\n" + hmmerResultFile);
  73
  74     AlignmentI searchResult = getSearchResultAlignment();
  75
  76     Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
  77             "Didn't read search result alignment from " + alignmentFragFile);
  78
  79     HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
  80     hjsp.parseFrom(new FileParse(hmmerResultFile, FormatAdapter.FILE));
  81     // check that
  82     // scores, posterior probabilities and stuff exist.
  83   }
  84   // Groovy test
  85   // def al = Jalview.getAlignFrames()[0].getViewport().getAlignment()
  86   // new jalview.ws.ebi.HmmerJSONProcessor(al).parseFrom(new
  87   // jalview.io.FileParse("examples/testdata/hmmer3/hmmeresult.json.gz","File"))
  88
  89 }