package jalview.ext.paradise;

import static org.junit.Assert.assertTrue;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.ext.paradise.Annotate3D;
import jalview.io.FastaFile;
import jalview.io.FormatAdapter;

import java.io.BufferedReader;
import java.io.File;
import java.io.Reader;
import java.util.Iterator;

import org.junit.Assert;
import org.junit.Test;

import MCview.PDBfile;

import compbio.util.FileUtil;

public class TestAnnotate3D
{

  @Test
  public void testIdVsContent() throws Exception
  {
    Iterator<Reader> ids = Annotate3D
            .getRNAMLForPDBId("2GIS");
    assertTrue("Didn't retrieve 2GIS by id.", ids != null);
    Iterator<Reader> files = Annotate3D
            .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
                    "examples/2GIS.pdb")));
    assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
    int i=0;
    while (ids.hasNext() && files.hasNext())
    {
      BufferedReader file=new BufferedReader(files.next()), id=new BufferedReader(ids.next());
    String iline, fline;
    do
    {
      iline = id.readLine();
      fline = file.readLine();
      if (iline != null)
        System.out.println(iline);
      if (fline != null)
        System.out.println(fline);
      // next assert fails for latest RNAview - because the XMLID entries change between file and ID based RNAML generation.
      assertTrue("Results differ for ID and file upload based retrieval (chain entry "+(++i)+")",
              ((iline == fline && iline == null) || (iline != null
                      && fline != null && iline.equals(fline))));

    } while (iline != null);
    }
  }

  /**
   * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
   * Annotate3d vs those extracted by Jalview from the originl PDB file
   * 
   * @throws Exception
   */
  @Test
  public void testPDBfileVsRNAML() throws Exception
  {
    PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
    Assert.assertTrue(pdbf.isValid());
    StringBuffer sb = new StringBuffer();
    // Comment - should add new FileParse constructor like new FileParse(Reader
    // ..). for direct reading
    Iterator<Reader> readers = Annotate3D
            .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
                    "examples/2GIS.pdb")));
    int r=0;
    while (readers.hasNext())
    {
      System.out.println("Testing RNAML input number "+(++r));
      BufferedReader br = new BufferedReader(readers.next());
      String line;
      while ((line = br.readLine()) != null)
      {
        sb.append(line + "\n");
      }
      assertTrue("No data returned by Annotate3D", sb.length() > 0);
      AlignmentI al = new FormatAdapter().readFile(sb.toString(),
              FormatAdapter.PASTE, "RNAML");

      assertTrue("No alignment returned.", al != null);
      assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
      for (SequenceI sq : al.getSequences())
      {
        {
          SequenceI struseq = null;
          String sq_ = new String(sq.getSequence()).toLowerCase();
          for (SequenceI _struseq : pdbf.getSeqsAsArray())
          {
            if (new String(_struseq.getSequence()).toLowerCase()
                    .equals(sq_))
            {
              struseq = _struseq;
              break;
            }
          }
          if (struseq == null)
          {
            Assert.fail("Couldn't find this sequence in original input:\n"
                    + new FastaFile().print(new SequenceI[]
                    { sq }) + "\n\nOriginal input:\n"
                    + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");
          }
        }
      }
    }
  }
}