/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
 * Copyright (C) 2014 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.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;

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

import org.junit.Test;

public class StockholmFileTest
{

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

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

  @Test
  public void rfamFileIO() throws Exception
  {
    testFileIOwithFormat(new File(RfamFile), "STH");
  }

  /**
   * 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
   */
  public static void testFileIOwithFormat(File f, String ioformat)
  {
    System.out.println("Reading file: " + f);
    String ff = f.getPath();
    try
    {
      AppletFormatAdapter rf = new AppletFormatAdapter();

      Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
              new IdentifyFile().Identify(ff, AppletFormatAdapter.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).setDatasetSequence(al.getSequenceAt(i));
      }
      String outputfile = rf.formatSequences(ioformat, al, true);
      System.out.println("Output file in '"+ioformat+"':\n"+outputfile+"\n<<EOF\n");
      // test for consistency in io
      Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
              AppletFormatAdapter.PASTE, ioformat);
      assertNotNull("Couldn't parse reimported alignment data.", al_input);

      String identifyoutput = new IdentifyFile().Identify(outputfile,
              AppletFormatAdapter.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);
    } 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
   */
  public static void testAlignmentEquivalence(AlignmentI al,
          AlignmentI al_input)
  {
    assertNotNull("Original alignment was null", al);
    assertNotNull("Generated alignment was null", al_input);

    assertTrue(
            "Alignment dimension mismatch: originl contains "
                    + al.getHeight() + " and generated has "
                    + al_input.getHeight() + " sequences; original has "
                    + al.getWidth() + " and generated has "
                    + al_input.getWidth() + " columns.",
            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), aa_original_size = (aa_original == null ? 0
            : aa_original.length);
    Map<Integer,java.util.BitSet> orig_groups=new HashMap<Integer,java.util.BitSet>(),new_groups=new HashMap<Integer,java.util.BitSet>();

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

          assertTrue(
                  "Sequence Features were not equivalent",
                  (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();

            assertTrue("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++)
            {
              assertTrue("Different features",
                      sequenceFeatures_original[feat]
                              .equals(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];
                assertTrue("Different annotation elements",
                        equalss(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)
          {
            assertTrue("Annotations differed between sequences ("
                    + al.getSequenceAt(i).getName() + ") and ("
                    + al_input.getSequenceAt(i).getName() + ")", false);
          }
          break;
        }
      }
    }
  }

  /*
   * compare annotations
   */
  private static boolean equalss(AlignmentAnnotation annot_or,
          AlignmentAnnotation annot_new)
  {
    if (annot_or.annotations.length != annot_new.annotations.length)
    {
      System.err.println("Different lengths for annotation row elements: "+annot_or.annotations.length +"!="+ annot_new.annotations.length);
      return false;
    }
    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 (!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 == null || !an_or.description
                          .equals(an_new.description))))
        {
          System.err.println("Annotation Element Mismatch\nElement "+i+" in original: "+annot_or.annotations[i].toString()+"\nElement "+i+" in new: "+annot_new.annotations[i].toString());
          return false;
        }
      }
      else if (annot_or.annotations[i] == null
              && annot_new.annotations[i] == null)
      {
        continue;
      }
      else
      {
        System.err.println("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()));
        return false;
      }
    }
    return true;
  }
}