package jalview.ws.jabaws;

import static org.junit.Assert.*;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Vector;

import jalview.api.AlignCalcManagerI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.io.AnnotationFile;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.AADisorderClient;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.RNAalifoldClient;
import jalview.ws.jws2.jabaws2.Jws2Instance;

import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;

public class RNAStructExportImport 
{
  public static String testseqs = "examples/unfolded_RF00031.aln";

  public static Jws2Discoverer disc;

  public static Jws2Instance rnaalifoldws;

  jalview.ws.jws2.RNAalifoldClient alifoldClient;

  public static jalview.gui.AlignFrame af = null;

  @BeforeClass
  public static void setUpBeforeClass() throws Exception
  {
  	
  	
    jalview.bin.Cache.initLogger();
    disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
    
    for (Jws2Instance svc : disc.getServices())
    {
    	
    	System.out.println("Service type: " + svc.serviceType);
    	
      if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
      {
        rnaalifoldws = svc;
      }
    }
    
    System.out.println("State of rnaalifoldws: " + rnaalifoldws);
    
    if (rnaalifoldws == null) System.exit(0);
    
    jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
    
    // Following this method a long way we find some (probably important!)
    //  code that I have just commented out!
    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
    
    assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
    
  }

  @AfterClass
  public static void tearDownAfterClass() throws Exception
  {
    if (af != null)
    {
      af.setVisible(false);
      af.dispose();
    }
  }

  /**
   * test for patches to JAL-1294
   */
  @Test
  public void testRNAStructExport()
  {
    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
    
    
    System.out.println("START FOLDING");
    af.getViewport().getCalcManager().startWorker(alifoldClient);
    
    
    do
    {
      try
      {
        Thread.sleep(50);
      } catch (InterruptedException x)
      {
      }
      ;
    } while (af.getViewport().getCalcManager().isWorking());
    
    System.out.println("END FOLDING");
    
    // ALL FOR TESTING
    AlignCalcManagerI test = af.getViewport().getCalcManager();
    RNAalifoldClient testWorker = ((RNAalifoldClient)test.getRegisteredWorkersOfClass(RNAalifoldClient.class).get(0));
    testWorker.updateResultAnnotation(true);
    System.out.println("Annotation from RNAalifoldclient");
    for (Annotation ann : testWorker.ourAnnots.get(0).annotations) {
    	System.out.print(ann.toString()+"|");
    }
    System.out.println();
    
    
    // Why are the AlignViewport.alignment and the RNAalifoldClient alignment
    //  Annotations different
    AlignmentI orig_alig = af.getViewport().getAlignment();
    
    System.out.println("orig_alig has class: " + orig_alig.getClass());
    
    // some time before here but after the RNAalifoldClient Update method
    //  the alignment annotation is replaced....
    
    System.out.println("orig_alig annotation:\n");
    for (AlignmentAnnotation an : orig_alig.getAlignmentAnnotation()) {
    	for (Annotation ann : an.annotations) {
    		System.out.print(ann.toString()+"|");
    	}
    	System.out.println();
    }
    
    
    testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);

  }

  public static void testAnnotationFileIO(String testname, AlignmentI al)
  {
    try
    {
      String aligfileout = new FormatAdapter().formatSequences("CLUSTAL",
              al.getSequencesArray());
      
      // test
//      System.out.println("aligfileout:\n" + aligfileout);
      
      String anfileout = new AnnotationFile().printAnnotations(
              al.getAlignmentAnnotation(), al.getGroups(),
              al.getProperties());
      assertTrue(
              "Test "
                      + testname
                      + "\nAlignment annotation file was not regenerated. Null string",
              anfileout != null);
      assertTrue(
              "Test "
                      + testname
                      + "\nAlignment annotation file was not regenerated. Empty string",
              anfileout.length() > "JALVIEW_ANNOTATION".length());

      System.out.println("Output annotation file:\n" + anfileout
              + "\n<<EOF\n");

      AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
              FormatAdapter.PASTE, "CLUSTAL");
      assertTrue(
              "Test "
                      + testname
                      + "\nregenerated annotation file did not annotate alignment.",
              new AnnotationFile().readAnnotationFile(al_new, anfileout,
                      FormatAdapter.PASTE));

      // test for consistency in io
      StockholmFileTest.testAlignmentEquivalence(al, al_new);
      return;
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    fail("Test "
            + testname
            + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
  }

}