/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
 * 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.*;
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.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/src/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().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);
    
  }
}