Package net.sourceforge.align.filter

Examples of net.sourceforge.align.filter.Filter.apply()

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   */
  @Test
  public void testEmpty() {
    Filter filter = new FractionSelector(0.8f);
    List<Alignment> alignmentList = new ArrayList<Alignment>();
    alignmentList = filter.apply(alignmentList);
    assertEquals(0, alignmentList.size());
  }
 
  /**
   * Test if a selecting from a list containing one element returns empty
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    List<Alignment> filteredAlignmentList;
    Alignment alignment = new Alignment();
    alignment.setScore(1.0f);
    alignmentList.add(alignment);
    filter = new FractionSelector(0.4999f);
    filteredAlignmentList = filter.apply(alignmentList);
    assertEquals(0, filteredAlignmentList.size());
    filter = new FractionSelector(0.5f);
    filteredAlignmentList = filter.apply(alignmentList);
    assertEquals(1, filteredAlignmentList.size());
  }
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    alignmentList.add(alignment);
    filter = new FractionSelector(0.4999f);
    filteredAlignmentList = filter.apply(alignmentList);
    assertEquals(0, filteredAlignmentList.size());
    filter = new FractionSelector(0.5f);
    filteredAlignmentList = filter.apply(alignmentList);
    assertEquals(1, filteredAlignmentList.size());
  }
 
  /**
   * Test if the list contains elements with identical score,
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  @Test
  public void testIdentical() {
    Filter filter = new FractionSelector(0.79f);
    List<Alignment> alignmentList = createAlignmentList(
        new float[]{2.0f, 2.0f, 2.0f, 2.0f, 2.0f});
    alignmentList = filter.apply(alignmentList);
    assertEquals(5, alignmentList.size());
  }

  /**
   * Tests if fraction selector selects correct number of elements.
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  @Test
  public void testDifferent() {
    Filter filter = new FractionSelector(0.79f);
    List<Alignment> alignmentList = createAlignmentList(
        new float[]{1.0f, 4.0f, 2.0f, 5.0f, 2.0f});
    alignmentList = filter.apply(alignmentList);
    assertEquals(4, alignmentList.size());
  } 
 
  /**
   * Helper function to create mock alignment list containing elements
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    rightAlignmentList.add(new Alignment(new String[]{"a"}, new String[]{"1"}));
    rightAlignmentList.add(new Alignment(new String[]{"b"}, new String[]{"2"}));
    rightAlignmentList.add(new Alignment(new String[]{"c"}, new String[]{"3"}));

    Filter filter = new DifferenceSelector(rightAlignmentList);
    List<Alignment> resultAlignmentList = filter.apply(leftAlignmentList);

    assertEquals(1, resultAlignmentList.size());
    assertEquals(leftAlignmentList.get(1), resultAlignmentList.get(0));

  }
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  @Test
  public void compare() {
    List<Alignment> alignmentList = createAlignmentList(
        SOURCE_ARRAY, TARGET_ARRAY);
    Filter filter = new OneToOneSelector();
    List<Alignment> resultAlignmentList = filter.apply(alignmentList);
    assertAlignmentListEquals(
        filterSegmentArray(SOURCE_ARRAY, RESULT_INDEXES),
        filterSegmentArray(TARGET_ARRAY, RESULT_INDEXES),
        resultAlignmentList);
  }
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    rightAlignmentList.add(new Alignment(new String[]{"a"}, new String[]{"1"}));
    rightAlignmentList.add(new Alignment(new String[]{"b"}, new String[]{"2"}));
    rightAlignmentList.add(new Alignment(new String[]{"c"}, new String[]{"3"}));

    Filter filter = new IntersectionSelector(rightAlignmentList);
    List<Alignment> resultAlignmentList = filter.apply(leftAlignmentList);

    assertEquals(2, resultAlignmentList.size());
    assertEquals(rightAlignmentList.get(0), resultAlignmentList.get(0));
    assertEquals(rightAlignmentList.get(2), resultAlignmentList.get(1));
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    AlignAlgorithm algorithm =
      new AdaptiveBandAlgorithm(algorithmFactory, calculator);
   
    Filter filter = new Aligner(algorithm);
   
    return filter.apply(alignmentList);

  }

}
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    filter = FilterDecorators.decorate(filter);

    Parser parser = new AlParser(getIn());
    Formatter formatter = new AlFormatter(getOut());
    List<Alignment> alignmentList = parser.parse();
    alignmentList = filter.apply(alignmentList);
    formatter.format(alignmentList);
  }

}
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