package jalview.ws;

import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Vector;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;

/**
 * prototype of abstract sequence retrieval interface
 * 
 */
public class SequenceFetcher extends ASequenceFetcher
{
  /**
   * Thread safe construction of database proxies TODO: extend to a configurable
   * database plugin mechanism where classes are instantiated by reflection and
   * queried for their DbRefSource and version association.
   * 
   */
  public SequenceFetcher()
  {
    FETCHABLEDBS = new Hashtable();
    FETCHABLEDBS.put(DBRefSource.EMBL,
            new jalview.ws.dbsources.EmblSource());
    FETCHABLEDBS.put(DBRefSource.EMBLCDS,
            new jalview.ws.dbsources.EmblCdsSouce());
    FETCHABLEDBS.put(DBRefSource.UNIPROT,
            new jalview.ws.dbsources.Uniprot());
    FETCHABLEDBS.put(DBRefSource.UP_NAME,
            new jalview.ws.dbsources.Uniprot());
    FETCHABLEDBS.put(DBRefSource.PDB, new jalview.ws.dbsources.Pdb());
    FETCHABLEDBS.put(DBRefSource.PFAM, new jalview.ws.dbsources.Pfam());
  };

  public static void main(String[] argv)
  {
    AlignmentI ds = null;
    Vector noProds = new Vector();
    if (argv != null && argv.length > 0)
    {
      System.out
              .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");
    }
    SequenceFetcher sfetcher = new SequenceFetcher();
    Enumeration e = sfetcher.FETCHABLEDBS.keys();
    while (e.hasMoreElements())
    {
      String db = (String) e.nextElement();
      // skip me
      if (db.equals(DBRefSource.PDB))
        continue;
      DbSourceProxy sp = sfetcher.getSourceProxy(db);
      System.out
              .println("" + db + ": retrieving test:" + sp.getTestQuery());
      AlignmentI al = null;
      try
      {
        al = sp.getSequenceRecords(sp.getTestQuery());
        if (al != null && al.getHeight() > 0)
        {
          boolean dna = sp.getDbSourceProperties().containsKey(
                  DBRefSource.DNACODINGSEQDB)
                  || sp.getDbSourceProperties().containsKey(
                          DBRefSource.DNASEQDB)
                  || sp.getDbSourceProperties().containsKey(
                          DBRefSource.CODINGSEQDB);
          // try and find products
          String types[] = jalview.analysis.CrossRef.findSequenceXrefTypes(
                  dna, al.getSequencesArray());
          if (types != null)
          {
            System.out.println("Xref Types for: "+(dna ? "dna" : "prot"));
            for (int t = 0; t < types.length; t++)
            {
              System.out.println("Type: " + types[t]);
              SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al
                      .getSequencesArray(), dna, types[t]).getSequencesArray();
              System.out.println("Found "
                      + ((prod == null) ? "no" : "" + prod.length)
                      + " products");
              if (prod!=null)
              {
                for (int p=0; p<prod.length; p++)
                {
                  System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));
                }
              }
            }
          } else {
            noProds.addElement((dna ? new Object[] { al, al } : new Object[] { al }) ); 
          }

        }
      } catch (Exception ex)
      {
        System.out.println("ERROR:Failed to retrieve test query.");
        ex.printStackTrace(System.out);
      }
      if (al == null)
      {
        System.out.println("ERROR:No alignment retrieved.");
        StringBuffer raw = sp.getRawRecords();
        if (raw != null)
          System.out.println(raw.toString());
        else
          System.out.println("ERROR:No Raw results.");
      }
      else
      {
        System.out.println("Retrieved " + al.getHeight() + " sequences.");
        for (int s = 0; s < al.getHeight(); s++)
        {
          SequenceI sq = al.getSequenceAt(s);
          while (sq.getDatasetSequence() != null)
          {
            sq = sq.getDatasetSequence();

          }
          if (ds == null)
          {
            ds = new Alignment(new SequenceI[]
            { sq });

          }
          else
          {
            ds.addSequence(sq);
          }
        }
      }
      System.out.flush();
      System.err.flush();

    }
    if (noProds.size()>0)
    {
      Enumeration ts = noProds.elements();
      while (ts.hasMoreElements())
        
      {
        Object[] typeSq = (Object[]) ts.nextElement();
        boolean dna = (typeSq.length>1);
        AlignmentI al = (AlignmentI) typeSq[0];
        System.out.println("Trying getProducts for "+al.getSequenceAt(0).getDisplayId(true));
        System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));
        // have a bash at finding the products amongst all the retrieved sequences.
        SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al
              .getSequencesArray(), dna, null, ds).getSequencesArray(); // note should test rather than throw away codon mapping (if present)
        System.out.println("Found "
                + ((prod == null) ? "no" : "" + prod.length)
                + " products");
        if (prod!=null)
        {
          for (int p=0; p<prod.length; p++)
          {
            System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));
          }
        }
      }

    }
  }
}