package jalview.io;

import static org.junit.Assert.*;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;

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.");
  }
}