/*
 * 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.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;

import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;

import java.io.File;
import java.util.BitSet;
import java.util.HashMap;
import java.util.Map;

import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;

public class StockholmFileTest
{

  @BeforeClass(alwaysRun = true)
  public void setUpJvOptionPane()
  {
    JvOptionPane.setInteractiveMode(false);
    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  }

  static String PfamFile = "examples/PF00111_seed.stk",
          RfamFile = "examples/RF00031_folded.stk";

  @Test(groups = { "Functional" })
  public void pfamFileIO() throws Exception
  {
    testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0,
            false);
  }

  @Test(groups = { "Functional" })
  public void pfamFileDataExtraction() throws Exception
  {
    AppletFormatAdapter af = new AppletFormatAdapter();
    AlignmentI al = af.readFile(PfamFile, DataSourceType.FILE,
            new IdentifyFile().identify(PfamFile, DataSourceType.FILE));
    int numpdb = 0;
    for (SequenceI sq : al.getSequences())
    {
      if (sq.getAllPDBEntries() != null)
      {
        numpdb += sq.getAllPDBEntries().size();
      }
    }
    assertTrue(
            "PF00111 seed alignment has at least 1 PDB file, but the reader found none.",
            numpdb > 0);
  }

  @Test(groups = { "Functional" })
  public void rfamFileIO() throws Exception
  {
    testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
            false);
  }

  /**
   * test alignment data in given file can be imported, exported and reimported
   * with no dataloss
   * 
   * @param f
   *          - source datafile (IdentifyFile.identify() should work with it)
   * @param ioformat
   *          - label for IO class used to write and read back in the data from
   *          f
   * @param ignoreRowVisibility
   */

  public static void testFileIOwithFormat(File f, FileFormatI ioformat,
          int naliannot, int nminseqann, boolean ignoreRowVisibility)
  {
    System.out.println("Reading file: " + f);
    String ff = f.getPath();
    try
    {
      AppletFormatAdapter rf = new AppletFormatAdapter();

      AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
              new IdentifyFile().identify(ff, DataSourceType.FILE));

      assertNotNull("Couldn't read supplied alignment data.", al);

      // make sure dataset is initialised ? not sure about this
      for (int i = 0; i < al.getSequencesArray().length; ++i)
      {
        al.getSequenceAt(i).createDatasetSequence();
      }
      String outputfile = rf.formatSequences(ioformat, al, true);
      System.out.println("Output file in '" + ioformat + "':\n"
              + outputfile + "\n<<EOF\n");
      // test for consistency in io
      AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
              DataSourceType.PASTE, ioformat);
      assertNotNull("Couldn't parse reimported alignment data.", al_input);

      FileFormatI identifyoutput = new IdentifyFile().identify(outputfile,
              DataSourceType.PASTE);
      assertNotNull("Identify routine failed for outputformat " + ioformat,
              identifyoutput);
      assertTrue(
              "Identify routine could not recognise output generated by '"
                      + ioformat + "' writer",
              ioformat.equals(identifyoutput));
      testAlignmentEquivalence(al, al_input, false);
      int numaliannot = 0, numsqswithali = 0;
      for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
      {
        if (ala.sequenceRef == null)
        {
          numaliannot++;
        }
        else
        {
          numsqswithali++;
        }
      }
      if (naliannot > -1)
      {
        assertEquals("Number of alignment annotations", naliannot,
                numaliannot);
      }

      assertTrue(
              "Number of sequence associated annotations wasn't at least "
                      + nminseqann, numsqswithali >= nminseqann);

    } catch (Exception e)
    {
      e.printStackTrace();
      assertTrue("Couln't format the alignment for output file.", false);
    }
  }

  /**
   * assert alignment equivalence
   * 
   * @param al
   *          'original'
   * @param al_input
   *          'secondary' or generated alignment from some datapreserving
   *          transformation
   * @param ignoreFeatures
   *          when true, differences in sequence feature annotation are ignored
   */
  public static void testAlignmentEquivalence(AlignmentI al,
          AlignmentI al_input, boolean ignoreFeatures)
  {
  }

  /**
   * assert alignment equivalence
   * 
   * @param al
   *          'original'
   * @param al_input
   *          'secondary' or generated alignment from some datapreserving
   *          transformation
   * @param ignoreFeatures
   *          when true, differences in sequence feature annotation are ignored
   * 
   * @param ignoreRowVisibility
   *          when true, do not fail if there are differences in the visibility
   *          of annotation rows
   */
  public static void testAlignmentEquivalence(AlignmentI al,
          AlignmentI al_input, boolean ignoreFeatures,
          boolean ignoreRowVisibility)
  {
    assertNotNull("Original alignment was null", al);
    assertNotNull("Generated alignment was null", al_input);

    assertTrue("Alignment dimension mismatch: original: " + al.getHeight()
            + "x" + al.getWidth() + ", generated: " + al_input.getHeight()
            + "x" + al_input.getWidth(),
            al.getHeight() == al_input.getHeight()
                    && al.getWidth() == al_input.getWidth());

    // check Alignment annotation
    AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
    AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();

    // note - at moment we do not distinguish between alignment without any
    // annotation rows and alignment with no annotation row vector
    // we might want to revise this in future
    int aa_new_size = (aa_new == null ? 0 : aa_new.length);
    int aa_original_size = (aa_original == null ? 0 : aa_original.length);
    Map<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
    Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();

    if (aa_new != null && aa_original != null)
    {
      for (int i = 0; i < aa_original.length; i++)
      {
        if (aa_new.length > i)
        {
          assertEqualSecondaryStructure(
                  "Different alignment annotation at position " + i,
                  aa_original[i], aa_new[i]);
          // compare graphGroup or graph properties - needed to verify JAL-1299
          assertEquals("Graph type not identical.", aa_original[i].graph,
                  aa_new[i].graph);
          if (!ignoreRowVisibility)
          {
            assertEquals("Visibility not identical.",
                    aa_original[i].visible,
                  aa_new[i].visible);
          }
          assertEquals("Threshold line not identical.",
                  aa_original[i].threshold, aa_new[i].threshold);
          // graphGroup may differ, but pattern should be the same
          Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2);
          Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2);
          BitSet orig_g = orig_groups.get(o_ggrp);
          BitSet new_g = new_groups.get(n_ggrp);
          if (orig_g == null)
          {
            orig_groups.put(o_ggrp, orig_g = new BitSet());
          }
          if (new_g == null)
          {
            new_groups.put(n_ggrp, new_g = new BitSet());
          }
          assertEquals("Graph Group pattern differs at annotation " + i,
                  orig_g, new_g);
          orig_g.set(i);
          new_g.set(i);
        }
        else
        {
          System.err.println("No matching annotation row for "
                  + aa_original[i].toString());
        }
      }
    }
    assertEquals(
            "Generated and imported alignment have different annotation sets",
            aa_original_size, aa_new_size);

    // check sequences, annotation and features
    SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
    seq_original = al.getSequencesArray();
    SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
    seq_new = al_input.getSequencesArray();
    SequenceFeature[] sequenceFeatures_original, sequenceFeatures_new;
    AlignmentAnnotation annot_original, annot_new;
    //
    for (int i = 0; i < al.getSequencesArray().length; i++)
    {
      String name = seq_original[i].getName();
      int start = seq_original[i].getStart();
      int end = seq_original[i].getEnd();
      System.out.println("Check sequence: " + name + "/" + start + "-"
              + end);

      // search equal sequence
      for (int in = 0; in < al_input.getSequencesArray().length; in++)
      {
        if (name.equals(seq_new[in].getName())
                && start == seq_new[in].getStart()
                && end == seq_new[in].getEnd())
        {
          String ss_original = seq_original[i].getSequenceAsString();
          String ss_new = seq_new[in].getSequenceAsString();
          assertEquals("The sequences " + name + "/" + start + "-" + end
                  + " are not equal", ss_original, ss_new);

          assertTrue(
                  "Sequence Features were not equivalent"
                          + (ignoreFeatures ? " ignoring." : ""),
                  ignoreFeatures
                          || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
                                  .getSequenceFeatures() == null)
                          || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
                                  .getSequenceFeatures() != null));
          // compare sequence features
          if (seq_original[i].getSequenceFeatures() != null
                  && seq_new[in].getSequenceFeatures() != null)
          {
            System.out.println("There are feature!!!");
            sequenceFeatures_original = new SequenceFeature[seq_original[i]
                    .getSequenceFeatures().length];
            sequenceFeatures_original = seq_original[i]
                    .getSequenceFeatures();
            sequenceFeatures_new = new SequenceFeature[seq_new[in]
                    .getSequenceFeatures().length];
            sequenceFeatures_new = seq_new[in].getSequenceFeatures();

            assertEquals("different number of features",
                    seq_original[i].getSequenceFeatures().length,
                    seq_new[in].getSequenceFeatures().length);

            for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
            {
              assertEquals("Different features",
                      sequenceFeatures_original[feat],
                      sequenceFeatures_new[feat]);
            }
          }
          // compare alignment annotation
          if (al.getSequenceAt(i).getAnnotation() != null
                  && al_input.getSequenceAt(in).getAnnotation() != null)
          {
            for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
            {
              if (al.getSequenceAt(i).getAnnotation()[j] != null
                      && al_input.getSequenceAt(in).getAnnotation()[j] != null)
              {
                annot_original = al.getSequenceAt(i).getAnnotation()[j];
                annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
                assertEqualSecondaryStructure(
                        "Different annotation elements", annot_original,
                        annot_new);
              }
            }
          }
          else if (al.getSequenceAt(i).getAnnotation() == null
                  && al_input.getSequenceAt(in).getAnnotation() == null)
          {
            System.out.println("No annotations");
          }
          else if (al.getSequenceAt(i).getAnnotation() != null
                  && al_input.getSequenceAt(in).getAnnotation() == null)
          {
            fail("Annotations differed between sequences ("
                    + al.getSequenceAt(i).getName() + ") and ("
                    + al_input.getSequenceAt(i).getName() + ")");
          }
          break;
        }
      }
    }
  }

  private static void assertEqualSecondaryStructure(String message,
          AlignmentAnnotation annot_or,
          AlignmentAnnotation annot_new)
  {
    // TODO: test to cover this assert behaves correctly for all allowed
    // variations of secondary structure annotation row equivalence
    if (annot_or.annotations.length != annot_new.annotations.length)
    {
      fail("Different lengths for annotation row elements: "
              + annot_or.annotations.length + "!="
              + annot_new.annotations.length);
    }
    boolean isRna = annot_or.isRNA();
    assertTrue("Expected " + (isRna ? " valid RNA " : " no RNA ")
            + " secondary structure in the row.",
            isRna == annot_new.isRNA());
    for (int i = 0; i < annot_or.annotations.length; i++)
    {
      Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
      if (an_or != null && an_new != null)
      {

        if (isRna)
        {
          if (an_or.secondaryStructure != an_new.secondaryStructure
                  || an_or.value != an_new.value)
          {
            fail("Different RNA secondary structure at column " + i
                    + " expected: [" + annot_or.annotations[i].toString()
                    + "] but got: [" + annot_new.annotations[i].toString()
                    + "]");
          }
        }
        else
        {
          // not RNA secondary structure, so expect all elements to match...
          if (!an_or.displayCharacter.trim().equals(
                  an_new.displayCharacter.trim())
                  || !("" + an_or.secondaryStructure).trim().equals(
                          ("" + an_new.secondaryStructure).trim())
                  || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
                          .trim().length() == 0)
                          || (an_new.description == null && an_or.description
                                  .trim().length() == 0) || an_or.description
                          .trim().equals(an_new.description.trim()))))
          {
            fail("Annotation Element Mismatch\nElement " + i
                    + " in original: " + annot_or.annotations[i].toString()
                    + "\nElement " + i + " in new: "
                    + annot_new.annotations[i].toString());
          }
        }
      }
      else if (annot_or.annotations[i] == null
              && annot_new.annotations[i] == null)
      {
        continue;
      }
      else
      {
        fail("Annotation Element Mismatch\nElement "
                + i
                + " in original: "
                + (annot_or.annotations[i] == null ? "is null"
                        : annot_or.annotations[i].toString())
                + "\nElement "
                + i
                + " in new: "
                + (annot_new.annotations[i] == null ? "is null"
                        : annot_new.annotations[i].toString()));
      }
    }
  }
}