package jalview.io.vamsas;

import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import uk.ac.vamsas.objects.core.DbRef;
import uk.ac.vamsas.objects.core.Map;
import uk.ac.vamsas.objects.core.Sequence;
import jalview.io.VamsasAppDatastore;

public class Dbref extends Rangetype
{
  jalview.datamodel.SequenceI sq = null;
  uk.ac.vamsas.objects.core.Sequence sequence = null;
  DbRef dbref = null;
  DBRefEntry dbentry=null;
  public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry, jalview.datamodel.SequenceI sq2, uk.ac.vamsas.objects.core.Sequence sequence2)
  {
    super(datastore);
    dbref = (DbRef) getjv2vObj(dbentry);
    sq = sq2;
    sequence = sequence2;
    this.dbentry = dbentry;
    if (dbref==null)
    {
      add();
    } else {
      if (dbref.isUpdated())
      {
        conflict();
      } else {
        update();
      }
        
    }
    
  }

  public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq, SequenceI dsseq)
  {
    super(datastore);
    dbref = ref;
    sequence = vdseq;
    sq = dsseq;
    dbentry = (jalview.datamodel.DBRefEntry) getvObj2jv(dbref);
    if (dbentry == null)
    {
      addFromDocument();
    } else {
      if (dbref.isUpdated())
      {
        update();
      }
    }
  }

  private void update()
  {
    // TODO: verify and update dbrefs in vamsas document
    // there will be trouble when a dataset sequence is modified to
    // contain more residues than were originally referenced - we must
    // then make a number of dataset sequence entries - this info is already stored 
    jalview.bin.Cache.log.debug("TODO verify update of dataset sequence database references.");
  }

  private void conflict()
  {
    jalview.bin.Cache.log.debug("Conflict in dbentry update for "+dbref.getAccessionId()+dbref.getSource()+" "+dbref.getVorbaId());
    // TODO Auto-generated method stub
    
  }
  private void addFromDocument()
  {
    // add new dbref
    sq.addDBRef(dbentry = new jalview.datamodel.DBRefEntry
            (
                    dbref.getSource().toString(),
                 dbref.getVersion().toString(),
                 dbref.getAccessionId().toString()));
    if (dbref.getMapCount()>0)
    {
      // TODO: Jalview ignores all the other maps
      if (dbref.getMapCount()>1)
      {
        jalview.bin.Cache.log.debug("Ignoring additional mappings on DbRef: "+dbentry.getSource()+":"+dbentry.getAccessionId());
      }
      jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(parsemapType(dbref.getMap(0)));
      dbentry.setMap(mp);
    }
    // TODO: jalview ignores links and properties because it doesn't know what to do with them.
    
    bindjvvobj(dbentry, dbref);
  }
  private void add()
  {
    DbRef dbref = new DbRef();
    bindjvvobj(dbentry, dbref);
    dbref.setAccessionId(dbentry.getAccessionId());
    dbref.setSource(dbentry.getSource());
    dbref.setVersion(dbentry.getVersion());
    if (dbentry.getMap()!=null)
    {
      jalview.datamodel.Mapping mp = dbentry.getMap();
      if (mp.getMap()!=null)
      {
        Map vMap = new Map();
        initMapType(vMap, mp.getMap(), true);
        dbref.addMap(vMap);
      } else {
        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "+dbentry.getSrcAccString());
      }
    }
    sequence.addDbRef(dbref);
  }

}