package jalview.structure;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;

import org.junit.Test;

import MCview.PDBfile;

public class Mapping
{

  @Test
  public void testPDBentryMapping() throws Exception
  {
    Sequence sq = new Sequence(
            "1GAQ A subseq 126 to 219",
            "EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
    Sequence sq1 = new Sequence(sq);
    String inFile;
    StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
    // Associate the 1GAQ pdb file with the subsequence 'imported' from another
    // source
    PDBfile pde = ssm.setMapping(true, new SequenceI[]
    { sq }, new String[]
    { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
    assertTrue("PDB File couldn't be found", pde != null);
    StructureMapping[] mp = ssm.getMapping(inFile);
    assertTrue("No mappings made.", mp != null && mp.length > 0);
    int nsecStr = 0, nsTemp = 0;
    // test for presence of transferred annotation on sequence
    for (AlignmentAnnotation alan : sq.getAnnotation())
    {
      if (alan.hasIcons)
      {
        nsecStr++;
      }
      if (alan.graph == alan.LINE_GRAPH)
      {
        nsTemp++;
      }
    }
    assertEquals(
            "Only one secondary structure should be transferred to associated sequence.",
            1, nsecStr);
    assertEquals(
            "Only two line graphs should be transferred to associated sequence.",
            2, nsTemp);
    // Now test the transfer function and compare annotated positions
    for (StructureMapping origMap:mp)
    {
      if (origMap.getSequence()==sq)
      {
        assertEquals("Mapping was incomplete.", sq.getLength() - 1,
                (origMap.getPDBResNum(sq.getEnd()) - origMap
                        .getPDBResNum(sq.getStart())));
        // sanity check - if this fails, mapping from first position in sequence
        // we want to transfer to is not where we expect
        assertEquals(1, origMap.getSeqPos(126));
        SequenceI firstChain = pde.getSeqs().get(0);
        // Compare the annotated positions on the PDB chain sequence with the
        // annotation on the associated sequence
        for (AlignmentAnnotation alan : firstChain.getAnnotation())
        {
          AlignmentAnnotation transfer = origMap.transfer(alan);
          System.out.println("pdb:" + firstChain.getSequenceAsString());
          System.out.println("ann:" + alan.toString());
          System.out.println("pdb:" + sq.getSequenceAsString());
          System.out.println("ann:" + transfer.toString());

          for (int p = 0, pSize = firstChain.getLength() - 1; p < pSize; p++)
          {
            // walk along the pdb chain's jalview sequence
            int rseqpos;
            int fpos = origMap.getSeqPos(rseqpos = firstChain
                    .findPosition(p));
            // only look at positions where there is a corresponding position in
            // mapping
            if (fpos < 1)
            {
              continue;
            }
            // p is index into PDB residue entries
            // rseqpos is pdb sequence position for position p
            // fpos is sequence position for associated position for rseqpos
            int tanpos = sq.findIndex(fpos);
            if (transfer.annotations.length <= tanpos)
            {
              // gone beyond mapping to the sequence
              break;
            }
            Annotation a = transfer.annotations[sq.findIndex(fpos)], b = alan.annotations[p];
            assertEquals("Non-equivalent annotation element at " + p + "("
                    + rseqpos + ")"
                            + " expected at " + fpos + " (alIndex "
                            + sq.findIndex(fpos) + ")",
                    a == null ? a : a.toString(),
                    b == null ? b : b.toString());
            System.out.print("(" + a + "|" + b + ")");
          }

        }
      }
    }
  }

}