/*
 * 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.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;

import java.io.File;

import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;

public class Jalview2xmlTests
{

  /**
   * @throws java.lang.Exception
   */
  @BeforeClass
  public static void setUpBeforeClass() throws Exception
  {
    jalview.bin.Jalview.main(new String[]
    { "-props", "test/jalview/io/testProps.jvprops" });
  }

  /**
   * @throws java.lang.Exception
   */
  @AfterClass
  public static void tearDownAfterClass() throws Exception
  {
    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);

  }

  public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
  {
    int numdsann = 0;
    for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
    {
      if (sq.getAnnotation() != null)
      {
        for (AlignmentAnnotation dssa : sq.getAnnotation())
        {
          if (dssa.isValidStruc())
          {
            numdsann++;
          }
        }
      }
    }
    return numdsann;
  }

  @Test
  public void testRNAStructureRecovery() throws Exception
  {
    String inFile = "examples/RF00031_folded.stk";
    String tfile = File.createTempFile("JalviewTest", ".jvp")
            .getAbsolutePath();
    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
            inFile, FormatAdapter.FILE);
    assertTrue("Didn't read input file " + inFile, af != null);
    int olddsann = countDsAnn(af.getViewport());
    assertTrue("Didn't find any dataset annotations", olddsann > 0);
    af.rnahelicesColour_actionPerformed(null);
    assertTrue(
            "Couldn't apply RNA helices colourscheme",
            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
    assertTrue("Failed to store as a project.",
            af.saveAlignment(tfile, "Jalview"));
    af.closeMenuItem_actionPerformed(true);
    af = null;
    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
            FormatAdapter.FILE);
    assertTrue("Failed to import new project", af != null);
    int newdsann = countDsAnn(af.getViewport());
    assertTrue(
            "Differing numbers of dataset sequence annotation\nOriginally "
                    + olddsann + " and now " + newdsann,
            olddsann == newdsann);
    System.out
            .println("Read in same number of annotations as originally present ("
                    + olddsann + ")");
    assertTrue(
            "RNA helices colourscheme was not applied on import.",
            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
  }

  @Test
  public void testTCoffeeScores() throws Exception
  {
    String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
    String tfile = File.createTempFile("JalviewTest", ".jvp")
            .getAbsolutePath();
    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
            inFile, FormatAdapter.FILE);
    assertTrue("Didn't read input file " + inFile, af != null);
    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
    assertTrue(
            "Didn't set T-coffee colourscheme",
            af.getViewport().getGlobalColourScheme().getClass()
                    .equals(jalview.schemes.TCoffeeColourScheme.class));
    assertTrue(
            "Recognise T-Coffee score from string",
            jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
                    .getAlignment(),
                    jalview.schemes.ColourSchemeProperty.getColourName(af
                            .getViewport().getGlobalColourScheme())) != null);

    assertTrue("Failed to store as a project.",
            af.saveAlignment(tfile, "Jalview"));
    af.closeMenuItem_actionPerformed(true);
    af = null;
    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
            FormatAdapter.FILE);
    assertTrue("Failed to import new project", af != null);
    assertTrue(
            "Didn't set T-coffee colourscheme for imported project.",
            af.getViewport().getGlobalColourScheme().getClass()
                    .equals(jalview.schemes.TCoffeeColourScheme.class));
    System.out
            .println("T-Coffee score shading successfully recovered from project.");
  }

  @Test
  public void testColourByAnnotScores() throws Exception
  {
    String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
    String tfile = File.createTempFile("JalviewTest", ".jvp")
            .getAbsolutePath();
    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
            inFile, FormatAdapter.FILE);
    assertTrue("Didn't read input file " + inFile, af != null);
    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
    AlignmentAnnotation[] aa = af.getViewport().getAlignment()
            .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
    assertTrue(
            "Didn't find any IUPred annotation to use to shade alignment.",
            aa != null && aa.length > 0);
    AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(
            aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
    AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(
            aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
    cs.setSeqAssociated(true);
    gcs.setSeqAssociated(true);
    af.changeColour(cs);
    SequenceGroup sg = new SequenceGroup();
    sg.setStartRes(57);
    sg.setEndRes(92);
    sg.cs = gcs;
    af.getViewport().getAlignment().addGroup(sg);
    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
    af.alignPanel.alignmentChanged();
    assertTrue("Failed to store as a project.",
            af.saveAlignment(tfile, "Jalview"));
    af.closeMenuItem_actionPerformed(true);
    af = null;
    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
            FormatAdapter.FILE);
    assertTrue("Failed to import new project", af != null);

    // check for group and alignment colourschemes

    ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
    ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
            .get(0).cs;
    assertTrue("Didn't recover global colourscheme", _rcs != null);
    assertTrue("Didn't recover annotation colour global scheme",
            _rcs instanceof AnnotationColourGradient);
    AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
    assertTrue("Annotation colourscheme wasn't sequence associated",
            __rcs.isSeqAssociated());

    boolean diffseqcols = false, diffgseqcols = false;
    SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
    for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
            && (!diffseqcols || !diffgseqcols); p++)
    {
      if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
              .findColour(sqs[5].getCharAt(p), p, sqs[5]))
      {
        diffseqcols = true;
      }
    }
    assertTrue("Got Different sequence colours", diffseqcols);
    System.out
            .println("Per sequence colourscheme (Background) successfully applied and recovered.");

    assertTrue("Didn't recover group colourscheme", _rgcs != null);
    assertTrue("Didn't recover annotation colour group colourscheme",
            _rgcs instanceof AnnotationColourGradient);
    __rcs = (AnnotationColourGradient) _rgcs;
    assertTrue("Group Annotation colourscheme wasn't sequence associated",
            __rcs.isSeqAssociated());

    for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
            && (!diffseqcols || !diffgseqcols); p++)
    {
      if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
              .findColour(sqs[2].getCharAt(p), p, sqs[2]))
      {
        diffgseqcols = true;
      }
    }
    assertTrue("Got Different group sequence colours", diffgseqcols);
    System.out
            .println("Per sequence (Group) colourscheme successfully applied and recovered.");
  }

  @Test
  public void gatherViewsHere() throws Exception
  {
    int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
            .getAlignFrames().length;
    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
    assertTrue("Didn't read in the example file correctly.", af != null);
    assertTrue("Didn't gather the views in the example file.",
            Desktop.getAlignFrames().length == 1 + origCount);

  }

  @Test
  public void viewRefPdbAnnotation() throws Exception
  {
    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
    assertTrue("Didn't read in the example file correctly.", af != null);
    AlignmentViewPanel sps = null;
    for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
    {
      if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
      {
        sps = ap;
        break;
      }
    }
    assertTrue("Couldn't find the structure view", sps != null);
    SequenceI sq = sps.getAlignment().findName("1A70|");
    AlignmentAnnotation refan = null;
    for (AlignmentAnnotation ra:sps.getAlignment().getAlignmentAnnotation())
    {
      if (ra.graph != 0)
      {
        refan = ra;
        break;
      }
    }
    assertTrue("Annotation secondary structure not found.",refan!=null);
    assertTrue("Couldn't find 1a70 null chain", sq != null);
    // compare the manually added temperature factor annotation
    // to the track automatically transferred from the pdb structure on load
    for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
    {
      AlignmentAnnotation alaa;
      sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
      alaa.adjustForAlignment();
      if (ala.graph == refan.graph)
      {
        for (int p = 0; p < ala.annotations.length; p++)
        {
          sq.findPosition(p);
          try {
            assertTrue(
                    "Mismatch at alignment position " + p,
                  (alaa.annotations[p] == null && refan.annotations[p] == null)
                            || alaa.annotations[p].value == refan.annotations[p].value);
          }
          catch (NullPointerException q)
          {
            fail("Mismatch of alignment annotations at position " + p
                    + " Ref seq ann: " + refan.annotations[p]
                    + " alignment " + alaa.annotations[p]);
          }
          }
      }
    }
    
  }

  @Test
  public void testCopyViewSettings() throws Exception
  {
    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
    Assert.assertTrue("Didn't read in the example file correctly.", af != null);
    AlignmentViewPanel sps = null, groups = null;
    for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
    {
      if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
      {
        sps = ap;
      }
      if (ap.getViewName().contains("MAFFT"))
      {
        groups = ap;
      }
    }
    assertTrue("Couldn't find the structure view", sps != null);
    assertTrue("Couldn't find the MAFFT view", groups != null);

    ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
    ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
    Assert.assertFalse(structureStyle.sameStyle(groupStyle));

    groups.getAlignViewport().setViewStyle(structureStyle);
    Assert.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
            .getViewStyle()));
    Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
            .getViewStyle()));

  }
}