package jalview.io;

import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import jalview.datamodel.AlignmentI;

import java.io.File;

import org.junit.Test;

public class AnnotationFileIOTest
{

  static String TestFiles[][] = {{ "Test example annotation import/export","examples/uniref50.fa", "examples/testdata/example_annot_file.jva" }
          ,{"Test multiple combine annotation statements import/export","examples/uniref50.fa", "examples/testdata/test_combine_annot.jva"}
          ,{"Test multiple combine annotation statements with sequence_ref import/export","examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva"}};

  @Test
  public void exampleAnnotationFileIO() throws Exception
  {
    for (String[] testPair:TestFiles)
    {
      testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(testPair[2]));
    }
  }

  public static AlignmentI readAlignmentFile(File f)
  {
    System.out.println("Reading file: " + f);
    String ff = f.getPath();
    try
    {
      FormatAdapter rf = new FormatAdapter();

      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
              new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
      
      // 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).createDatasetSequence());
      }
      assertNotNull("Couldn't read supplied alignment data.", al);
      return al;
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    fail("Couln't read the alignment in file '"+f.toString()+"'");
    return null;
  }
  /**
   * 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 testAnnotationFileIO(String testname, File f, File annotFile)
  {
    System.out.println("Test: "+testname+"\nReading annotation file '"+annotFile+"' onto : " + f);
    String af = annotFile.getPath();
    try
    {
      AlignmentI al = readAlignmentFile(f);
      
      assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
      
      String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
      assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
      assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length());

      System.out.println("Output annotation file:\n"+anfileout+"\n<<EOF\n");
      
      AlignmentI al_new = readAlignmentFile(f);
      assertTrue("Test "+testname+"\nregenerated annotation file did not annotate alignment.",new AnnotationFile().readAnnotationFile(al_new, anfileout, FormatAdapter.PASTE));
      
      // test for consistency in io
      StockholmFileTest.testAlignmentEquivalence(al, al_new);
      return;
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
  }
}