/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */

package org.biojava.bio.seq;

import java.util.Iterator;

import junit.framework.TestCase;

import org.biojava.bio.Annotation;
import org.biojava.bio.seq.impl.SimpleSequence;
import org.biojava.bio.symbol.Location;
import org.biojava.bio.symbol.RangeLocation;
import org.biojava.bio.symbol.SymbolList;

/**
 * Tests for SimpleAssembly.  By dependancy, this also
 * tests ProjectedFeatureHolder and SimpleAssembly.
 *
 * @author Thomas Down
 * @since 1.2
 */

public class SimpleAssemblyTest extends TestCase {
  protected Sequence fragment1;
  protected Sequence fragment2;
  protected Sequence assembly;

  public SimpleAssemblyTest(String name) {
    super(name);
  }

  protected void setUp() throws Exception {
    fragment1 = new SimpleSequence(DNATools.createDNA("aacgta"),
                                   "fragment1",
                                   "fragment1",
                                   Annotation.EMPTY_ANNOTATION);
    fragment2 = new SimpleSequence(DNATools.createDNA("ttgatgc"),
                                   "fragment2",
                                   "fragment2",
                                   Annotation.EMPTY_ANNOTATION);

    StrandedFeature.Template sft = new StrandedFeature.Template();
    sft.type = "project_test";
    sft.source = "test";
    sft.annotation = Annotation.EMPTY_ANNOTATION;
    sft.strand = StrandedFeature.NEGATIVE;
    sft.location = new RangeLocation(1, 3);
    fragment2.createFeature(sft);

    assembly = new SimpleAssembly(12, "test", "test");
    ComponentFeature.Template templ = new ComponentFeature.Template();
    templ.type = "component";
    templ.source = "test";
    templ.annotation = Annotation.EMPTY_ANNOTATION;

    templ.strand = StrandedFeature.POSITIVE;
    templ.location = new RangeLocation(1, 4);
    templ.componentSequence = fragment1;
    templ.componentLocation = new RangeLocation(2, 5);
    assembly.createFeature(templ);

    templ.strand = StrandedFeature.NEGATIVE;
    templ.location = new RangeLocation(6, 12);
    templ.componentSequence = fragment2;
    templ.componentLocation = new RangeLocation(1, fragment2.length());
    assembly.createFeature(templ);
  }

  public void testAssembledSymbols()
          throws Exception {
    assertTrue(compareSymbolList(assembly,
                                 DNATools.createDNA("acgtngcatcaa")));
    assertTrue(compareSymbolList(assembly.subList(1, 4),
                                 DNATools.createDNA("acgt")));
    assertTrue(compareSymbolList(assembly.subList(1, 5),
                                 DNATools.createDNA("acgtn")));
    assertTrue(compareSymbolList(assembly.subList(5, 5),
                                 DNATools.createDNA("n")));
    assertTrue(compareSymbolList(assembly.subList(11, 12),
                                 DNATools.createDNA("aa")));
  }

  public void testProjectedFeatures()
          throws Exception {
    FeatureHolder f = assembly.filter(new FeatureFilter.ByType("project_test"), true);
    assertEquals(f.countFeatures(), 1);
    Feature pf = (Feature) f.features().next();
    Location pfl = pf.getLocation();
    assertEquals(pfl.getMin(), 10);
    assertEquals(pfl.getMax(), 12);
  }

  private boolean compareSymbolList(SymbolList sl1, SymbolList sl2) {
    if (sl1.length() != sl2.length()) {
      return false;
    }

    Iterator si1 = sl1.iterator();
    Iterator si2 = sl2.iterator();
    while (si1.hasNext()) {
      if (!(si1.next() == si2.next())) {
        return false;
      }
    }

    return true;
  }
}