/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.io;

import static org.testng.AssertJUnit.assertTrue;

import jalview.analysis.CrossRef;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;

import java.util.IdentityHashMap;
import java.util.List;

import org.testng.Assert;
import org.testng.annotations.Test;

@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{

  /**
   * test store and recovery of expanded views
   * 
   * @throws Exception
   */
  @Test(groups = { "Operational" }, enabled = true)
  public void testRetrieveAndShowCrossref() throws Exception
  {
    // for every set of db queries
    // retrieve db query
    // verify presence of expected xrefs
    // show xrefs - verify expected type of frame is shown for each xref
    // show xrefs again
    // - verify original -> xref -> xref(original) recovers frame containing at
    // least the first retrieved sequence
    // store
    // 1. whole project
    // 2. individual frames
    // 3. load each one back and verify
    // . aligned sequences (.toString() )
    // . xrefs (.toString() )
    // . codonframes
    //
    //
    for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
    {
      AlignFrame af = jalview.gui.SequenceFetcher.fetchAndShow(did[0],
              did[1]).get(0);
      assertTrue("Didn't read in the example file correctly.", af != null);
      boolean dna = af.getViewport().getAlignment().isNucleotide();
      AlignmentI retral = af.getViewport().getAlignment();
      AlignmentI dataset = retral.getDataset();
      SequenceI[] seqs = retral.getSequencesArray();
      List<String> ptypes = (seqs == null || seqs.length == 0) ? null
              : new CrossRef(seqs, dataset)
                      .findXrefSourcesForSequences(dna);
      /*
       * map between a view, and views generated after retrieving xrefs
       */
      IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>> viewxrefview = new IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>>();
      /*
       * map between a particular view and it's originating dbref path
       */
      IdentityHashMap<AlignmentViewPanel, String> viewsourcedb = new IdentityHashMap<AlignmentViewPanel, String>();

      String first = did[0] + " " + did[1];
      viewsourcedb.put(af.alignPanel, first);
      for (String db : ptypes)
      {
        // retrieve and show cross-refs in this thread
        CrossRefAction cra = new CrossRefAction(af, seqs, dna, db);
        cra.run();
        Assert.assertTrue(cra.getXrefViews().size() > 0,
                "No crossrefs retrieved for " + db);
        viewxrefview.put(af.alignPanel, cra.getXrefViews());

        for (AlignmentViewPanel avp : cra.getXrefViews())
        {

          SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
          String nextxref = first + " -> " + db;
          viewsourcedb.put(avp, nextxref);
          List<String> xrptypes = (seqs == null || seqs.length == 0) ? null
                  : new CrossRef(xrseqs, dataset)
                          .findXrefSourcesForSequences(avp
                                  .getAlignViewport().isNucleotide());
          for (String xrefdb : xrptypes)
          {
            AlignFrame nextaf = Desktop.getAlignFrameFor(avp
                    .getAlignViewport());
            cra = new CrossRefAction(nextaf, xrseqs, avp.getAlignViewport()
                    .isNucleotide(), xrefdb);
            cra.run();
            Assert.assertTrue(cra.getXrefViews().size() > 0,
                    "No crossrefs found for '" + nextxref + "' to "
                            + xrefdb + " via '" + nextaf.getTitle() + "'");
            // save views for analysis
            viewxrefview.put(avp, cra.getXrefViews());
            for (AlignmentViewPanel nextavp : cra.getXrefViews())
            {

              viewsourcedb.put(nextavp, nextxref + " -> " + xrefdb);
            }
          }
        }
      }
    }
    Thread.sleep(50000);
  }

}