package jalview.analysis;

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;
import java.util.Map;

import org.junit.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;

import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FastaFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.util.Platform;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;

public class AverageDistanceEngineTest
{

    @BeforeClass(alwaysRun = true)
    public void setUpJvOptionPane()
    {
      JvOptionPane.setInteractiveMode(false);
      JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
    }

    @BeforeMethod(alwaysRun = true)
    public void loadProperties()
    {
      Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
    }
    @Test
    public void testUPGMAEngine() throws Exception
    {
      AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded("examples/test_fab41.result/sample.a3m",DataSourceType.FILE);
      AlignmentI seqs = af.getViewport().getAlignment();
      SequenceI target = seqs.getSequenceAt(0);
      File testPAE = new File("examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
      List<Object> pae_obj = (List<Object>) Platform.parseJSON(new FileInputStream(testPAE));
      if (pae_obj == null)
      {
        Assert.fail("JSON PAE file did not parse properly.");
      }
      ContactMatrixI matrix = new PAEContactMatrix(target,
              (Map<String, Object>) pae_obj.get(0));
      AlignmentAnnotation aa = target.addContactList(matrix);
      long start = System.currentTimeMillis();
      AverageDistanceEngine clusterer = new AverageDistanceEngine(af.getViewport(), null, matrix);
      System.out.println("built a tree in "+(System.currentTimeMillis()-start)*0.001+" seconds.");
      StringBuffer sb = new StringBuffer(); 
      System.out.println("Newick string\n"+      new jalview.io.NewickFile(clusterer.getTopNode(),true,true).print());
      
    }

}