package jalview.io.vamsas;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
import uk.ac.vamsas.objects.core.DataSet;
import uk.ac.vamsas.objects.core.Sequence;

/**
 * synchronize a vamsas dataset sequence with a jalview dataset sequence.
 * This class deals with all sequence features and database references associated with
 * the jalview sequence.
 * @author JimP
 *
 */
public class Datasetsequence extends DatastoreItem
{
  String dict;
  private DataSet dataset;
  // private AlignmentI jvdset;

  public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
          SequenceI sq, String dict, DataSet dataset)
  {
    super(vamsasAppDatastore, sq, uk.ac.vamsas.objects.core.Sequence.class);
    this.dataset = dataset;
    // this.jvdset = jvdset;
    this.dict = dict;
    doSync();
  }

  public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
          Sequence vdseq)
  {
    super(vamsasAppDatastore, vdseq, SequenceI.class);
    doJvUpdate();
  }

  public void addFromDocument()
  {
    Sequence vseq = (Sequence) vobj;
    SequenceI dsseq = new jalview.datamodel.Sequence(vseq.getName(), 
            vseq.getSequence(),
            (int) vseq.getStart(), (int) vseq.getEnd());
    dsseq.setDescription(vseq.getDescription());
    bindjvvobj(dsseq, vseq);
    dsseq.setVamsasId(vseq.getVorbaId().getId());
    jvobj = dsseq;
    modified=true;
  }
  public void updateFromDoc()
  {
    Sequence sq = (Sequence) vobj;
    SequenceI sequence = (SequenceI) jvobj;
    if (!sequence.getSequenceAsString().equals(sq.getSequence()))
    {
      log.warn("Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
    } else {
      // verify and update principal attributes.
      if (sequence.getDescription() != null
              && (sequence.getDescription() == null || !sequence
                      .getDescription().equals(sq.getDescription())))
      {
        sequence.setDescription(sq.getDescription());
        modified = true;
      }
      if (sequence.getSequence() == null
              || !sequence.getSequenceAsString().equals(
                      sq.getSequence()))
      {
        if (sequence.getStart() != sq.getStart()
                || sequence.getEnd() != sq.getEnd())
        {
          // update modified sequence.
          sequence.setSequence(sq.getSequence());
          sequence.setStart((int)sq.getStart());
          sequence.setEnd((int)sq.getEnd());
          modified = true;
        }
      }
      if (!sequence.getName().equals(sq.getName()))
      {
        sequence.setName(sq.getName());
        modified = true;
      }
    }    
  }


  public void addToDocument()
  {
    SequenceI sq = (SequenceI) jvobj;
    Sequence sequence = new Sequence();
    bindjvvobj(sq, sequence);
    sq.setVamsasId(sequence.getVorbaId().getId());
    sequence.setSequence(sq.getSequenceAsString());
    sequence.setDictionary(dict);
    sequence.setName(sq.getName());
    sequence.setStart(sq.getStart());
    sequence.setEnd(sq.getEnd());
    sequence.setDescription(sq.getDescription());
    dataset.addSequence(sequence);
    vobj = sequence;
    // add or update any new features/references on dataset sequence
    if (sq.getSequenceFeatures() != null)
    {
      int sfSize = sq.getSequenceFeatures().length;

      for (int sf = 0; sf < sfSize; sf++)
      {
        new jalview.io.vamsas.Sequencefeature(datastore, (jalview.datamodel.SequenceFeature) sq
                .getSequenceFeatures()[sf], dataset, (Sequence) vobj);
      }
    }
    if (sq.getDatasetSequence() == null && sq.getDBRef() != null)
    {
      // only sync database references for dataset sequences
      DBRefEntry[] entries = sq.getDBRef();
      jalview.datamodel.DBRefEntry dbentry;
      for (int db = 0; db < entries.length; db++)
      {
        Rangetype dbr = new jalview.io.vamsas.Dbref(datastore,
                dbentry = entries[db], sq, (Sequence) vobj, dataset);
      }

    }
    
  }

  public void conflict()
  {
    log.warn("Conflict in dataset sequence update to document. Overwriting document");
    // TODO: could try to import from document data to jalview first. and then
    updateToDoc();
  }
  boolean modified = false;
  public void updateToDoc()
  {
    SequenceI sq = (SequenceI) jvobj;
    Sequence sequence = (Sequence) vobj;
    // verify and update principal attributes.
    if (sequence.getDescription() != null
            && (sequence.getDescription() == null || !sequence
                    .getDescription().equals(sq.getDescription())))
    {
      sequence.setDescription(sq.getDescription());
      modified = true;
    }
    if (sequence.getSequence() == null
            || !sequence.getSequence().equals(
                    sq.getSequenceAsString()))
    {
      if (sequence.getStart() != sq.getStart()
              || sequence.getEnd() != sq.getEnd())
      {
        // update modified sequence.
        sequence.setSequence(sq.getSequenceAsString());
        sequence.setStart(sq.getStart());
        sequence.setEnd(sq.getEnd());
        modified = true;
      }
    }
    if (!dict.equals(sequence.getDictionary()))
    {
      sequence.setDictionary(dict);
      modified = true;
    }
    if (!sequence.getName().equals(sq.getName()))
    {
      sequence.setName(sq.getName());
      modified = true;
    }
  }

  /**
   * (probably could just do vobj.isModified(), but..)
   * @return true if document's dataset sequence was modified
   */
  public boolean getModified()
  {
    return modified;
  }

}