package jalview.ws.ebi;

import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;

import java.io.File;

import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.testng.Assert;
import org.testng.annotations.Test;

public class HmmerJSONProcessTest {
  public static File alignmentFragFile = new File(
          "examples/testdata/hmmer3/alignment_frag.fa.gz");

  private AlignmentI getSearchResultFragmentAlignment() throws Exception
  {
    AlignmentI alf = new FormatAdapter().readFile(
            alignmentFragFile.getAbsolutePath(), DataSourceType.FILE,
            FileFormat.Fasta);

    return alf;
  }

  public static File alignmentResultFile = new File(
          "examples/testdata/hmmer3/alignment_res.fa.gz");

  private AlignmentI getSearchResultAlignment() throws Exception
  {
    AlignmentI alf = new FormatAdapter().readFile(
            alignmentResultFile.getAbsolutePath(), DataSourceType.FILE,
            FileFormat.Fasta);

    return alf;
  }

  public static String hitTestFile = "examples/testdata/hmmer3/hit_fragment.json.gz",
          hmmerResultFile = "examples/testdata/hmmer3/hmmeresult.json.gz";


  @Test(groups = { "Functional" })
  public void parseHitTest() throws Exception
  {

    Assert.assertTrue(new File(hitTestFile).exists(),
            "Can't find test data.\n"
            + hitTestFile);
    JSONParser jp = new JSONParser();
    // read JSON in same way - via fileparse
    Object hitfragment = jp.parse(new FileParse(hitTestFile,
            DataSourceType.FILE).getReader());
    Assert.assertTrue((hitfragment instanceof JSONObject),
            "Didn't find a JSON object map in " + hitTestFile);
    AlignmentI searchResult = getSearchResultFragmentAlignment();

    Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
            "Didn't read search result alignment from " + alignmentFragFile);

    HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
    hjsp.addHit((JSONObject) hitfragment, 1);
    // check that
    // scores, posterior probabilities and stuff exist.
  }

  @Test(groups = { "Functional" })
  public void parseJsonResultTest() throws Exception
  {

    Assert.assertTrue(new File(hmmerResultFile).exists(),
            "Can't find test data.\n" + hmmerResultFile);

    AlignmentI searchResult = getSearchResultAlignment();

    Assert.assertTrue(searchResult != null && searchResult.getHeight() > 0,
            "Didn't read search result alignment from " + alignmentFragFile);

    HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
    hjsp.parseFrom(new FileParse(hmmerResultFile, DataSourceType.FILE));
    AlignmentAnnotation[] aa = searchResult.getSequenceAt(5)
            .getAnnotation();
    Assert.assertNotNull(aa);
    Assert.assertEquals(aa.length, 3,
            "didn't get expected set of annotation.\n");
    // DPTSERWFHGHLSGKEAEKLLTeKGKHGSFLVRESQSHPGDFVLSVRTgddkgesndgKSKVTHVMIR-CQELKYDVGGGERFDSLTDLVEHYKKNPmvet
    // LGTVLQLKQP
    // 5789*****************9799***********************999998888888********.99**************************9999
    // 899999*999
    // AlignmentAnnotation
    // 101 == 8
    String seq = "tLGT";
    SequenceI s5 = searchResult.getSequenceAt(5);
    Assert.assertEquals(
            s5.getSubSequence(s5.findIndex(225), s5.findIndex(229))
                    .getSequenceAsString(),
            seq);
    int pos = s5.findIndex(226);
    for (AlignmentAnnotation an : aa)
    {
      if (an.label.startsWith("Posterior"))
      {
        Assert.assertEquals(an.annotations[pos].value, 8f);

      }
    }
    ;
    // check that
    // scores, posterior probabilities and stuff exist.
  }
  // Groovy test
  // def al = Jalview.getAlignFrames()[0].getViewport().getAlignment()
  // def jproc = new jalview.ws.ebi.HmmerJSONProcessor(al)
  // jproc.parseFrom(new
  // jalview.io.FileParse("examples/testdata/hmmer3/hmmeresult.json.gz","File"))
  // jproc.updateView(Jalview.getAlignFrames()[0].getViewport())

}