source: trunk/test/Suite.h @ 3538

Last change on this file since 3538 was 3538, checked in by Peter, 6 years ago

convenience classes for archetypes of data iterators

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1#ifndef _theplu_yat_test_suite_
2#define _theplu_yat_test_suite_
3
4// $Id: Suite.h 3538 2016-12-22 07:21:12Z peter $
5
6/*
7  Copyright (C) 2008 Jari Häkkinen, Peter Johansson
8  Copyright (C) 2009, 2010, 2011, 2013, 2014, 2015 Peter Johansson
9
10  This file is part of the yat library, http://dev.thep.lu.se/yat
11
12  The yat library is free software; you can redistribute it and/or
13  modify it under the terms of the GNU General Public License as
14  published by the Free Software Foundation; either version 3 of the
15  License, or (at your option) any later version.
16
17  The yat library is distributed in the hope that it will be useful,
18  but WITHOUT ANY WARRANTY; without even the implied warranty of
19  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20  General Public License for more details.
21
22  You should have received a copy of the GNU General Public License
23  along with yat. If not, see <http://www.gnu.org/licenses/>.
24*/
25
26// ensure that config.h always is included first
27#ifndef YAT_VERSION
28#error header 'config.h' not included
29#endif
30
31#include <yat/utility/config_public.h>
32
33#define YAT_TEST_PROLOGUE "\n=== " << __func__ << " ===\n"
34
35// used to tell automake that test should be skipped
36#define EXIT_SKIP 77
37
38// SKIP_BAM_TEST is defined if we should skip bam tests
39#if !defined (YAT_HAVE_LIBBAM) || !defined (HAVE_SAMTOOLS_EXECUTABLE)
40#define SKIP_BAM_TEST
41#endif
42
43#include <yat/utility/VectorMutable.h>
44#include <yat/utility/WeightedIteratorArchetype.h>
45#include <yat/classifier/Target.h>
46
47#include <boost/concept_archetype.hpp>
48#include <boost/concept_check.hpp>
49#include <boost/iterator/iterator_categories.hpp>
50#include <boost/iterator/iterator_concepts.hpp>
51
52#include <iosfwd>
53#include <sstream>
54#include <vector>
55
56namespace theplu {
57namespace yat {
58namespace test {
59
60  /**
61     \internal utility class for tests
62   */
63  class Suite
64  {
65  public:
66    Suite(int argc, char* argv[], bool require_bam=false);
67
68    /**
69     */
70    ~Suite(void);
71
72    /**
73       set ok to 'b && ok'
74
75       \return b
76    */
77    bool add(bool b);
78
79    /**
80       \return In verbose mode std::cerr, else a ofstream to "/dev/null".
81    */
82    std::ostream& err(void) const;
83
84    /**
85       \return true if \f$ |a-b| <= N * \epsilon * min(|a|,|b|) \f$
86       where \f$ \epsilon \f$ is std::numeric_limits<double>().epsilon()
87    */
88    bool equal(double a, double b, unsigned long int N=1);
89
90    /**
91       \return true if |\a a - \a b| <= \a margin
92    */
93    bool equal_fix(double a, double b, double margin=0);
94
95    /**
96       \return true if \f$ |a-b| <= N * sqrt(\epsilon) * min(|a|,|b|) \f$
97       where \f$ \epsilon \f$ is std::numeric_limits<double>().epsilon()
98    */
99    bool equal_sqrt(double a, double b, unsigned long int N=1);
100
101    /**
102       apply equal on ranges [first1, last1) and [first2, ...)
103    */
104    template<typename Iterator1, typename Iterator2>
105    bool equal_range(Iterator1 first1, Iterator1 last1, Iterator2 first2,
106                     unsigned int N=1);
107
108    /**
109       apply equal_fix on ranges [first1, last1) and [first2, ...)
110    */
111    template<typename Iterator1, typename Iterator2>
112    bool equal_range_fix(Iterator1 first1, Iterator1 last1, Iterator2 first2,
113                         double margin);
114
115    /**
116      \return true if test is ok
117    */
118    bool ok(void) const;
119
120    /**
121       \return In verbose mode std::cout, else a ofstream to "/dev/null".
122    */
123    std::ostream& out(void) const;
124
125    /**
126       In verbose mode a final message is sent to std::cout.
127
128       If ok() is true: "Test is ok." otherwise
129       "Test failed."
130
131       \return 0 if ok.
132     */
133    int return_value(void) const;
134
135    template<typename TrivialIterator>
136    void test_trivial_iterator(const TrivialIterator&);
137
138    template<typename InputIterator>
139    void test_input_iterator(InputIterator&);
140
141    template<typename OutputIterator>
142    void test_output_iterator(OutputIterator&);
143
144    template<typename ForwardIterator>
145    void test_forward_iterator(ForwardIterator);
146
147    template<typename BidirectionalIterator>
148    void test_bidirectional_iterator(BidirectionalIterator);
149
150    template<typename RandomAccessIterator>
151    void test_random_access_iterator(RandomAccessIterator);
152
153    template<typename Container2D>
154    void test_concept_container2d(const Container2D&);
155
156    template<typename MutableContainer2D>
157    void test_concept_mutable_container2d(MutableContainer2D&);
158
159    /**
160       Function writes to a stream using operator<<, creates a new
161       object using stream constructor, and the new object is written
162       to another stream, and function check if the two outputs are
163       equal.
164    */
165    template<class T>
166    bool test_stream(const T&) const;
167
168    /**
169       This function is similar to add(bool) and could be used to
170       detect/count known issues. When the issue is fixed, one can
171       replace the call to xadd(bool) with a call to add(bool).
172
173       If \a b is false a counter is incremented, which is used to in
174       return_value() to generate some printout on how many known
175       issues were detected.
176
177       If \a b is true, ok_ is set to false, becasue the known issue
178       is no longer an issue and one should replace the call with a
179       call to add(bool).
180     */
181    bool xadd(bool b);
182
183  private:
184    unsigned int known_issues_;
185    bool ok_;
186  };
187
188  /**
189     \return absolute path to test src dir
190  */
191  std::string abs_srcdir(void);
192
193  /**
194     \return absolute path to file
195     \param local_path path relative to srcdir
196   */
197  std::string filename(const std::string& local_path);
198
199  /*
200    class to test (at compile time) that a function (or class) works
201    with a Container2D. Do not run any test using this class because
202    the class is not really functional at run time.
203
204    \see boost/concept_archetype.hpp
205   */
206  template<typename T>
207  class container2d_archetype
208  {
209  public:
210    typedef T value_type;
211    typedef const T& const_reference;
212    typedef const T* const_iterator;
213    typedef const_iterator const_column_iterator;
214    typedef const_iterator const_row_iterator;
215    const_iterator begin(void) const { return &element_; }
216    const_column_iterator begin_column(size_t) const { return &element_; }
217    const_iterator begin_row(size_t) const { return &element_; }
218    const_iterator end(void) const { return NULL; }
219    const_column_iterator end_column(size_t) const { return NULL; }
220    const_iterator end_row(size_t) const { return NULL; }
221    size_t columns(void) const { return 0; }
222    size_t rows(void) const { return 0; }
223    const_reference operator()(size_t row, size_t column) const
224    { return element_; }
225
226  protected:
227    T element_;
228  };
229
230  /*
231    class to test (at compile time) that a function (or class) works
232    with a MutableContainer2D. Do not run any test using this class because
233    the class is not really functional at run time.
234
235    \see boost/concept_archetype.hpp
236   */
237  template<typename T>
238  class mutable_container2d_archetype : public container2d_archetype<T>
239  {
240  public:
241    typedef T& reference;
242    typedef T* iterator;
243    typedef iterator column_iterator;
244    typedef iterator row_iterator;
245    iterator begin(void) { return &this->element_; }
246    column_iterator begin_column(size_t) { return &this->element_; }
247    iterator begin_row(size_t) { return &this->element_; }
248    iterator end(void) { return NULL; }
249    column_iterator end_column(size_t) { return NULL; }
250    iterator end_row(size_t) { return NULL; }
251    reference operator()(size_t row, size_t column)
252    { return this->element_; }
253  };
254
255  /*
256    class to test (at compile time) that a function (or class) works
257    with a Distance. Do not run any test using this class because
258    the class is not really functional at run time.
259
260    \see boost/concept_archetype.hpp
261   */
262  class distance_archetype
263  {
264  public:
265    /// class must be constructible somehow, but we don't wanna assume
266    /// void constructor or any other common constructor so we use the
267    /// signature to allow construction without assuming too much.
268    distance_archetype(const boost::detail::dummy_constructor&) {};
269    distance_archetype(const distance_archetype&) {};
270    template<typename T1, typename T2>
271    double operator()(T1 first1, T1 last1, T2 first2) const { return 0.0; }
272  private:
273    distance_archetype(void);
274    distance_archetype& operator=(const distance_archetype&);
275  };
276
277  /*
278    class to test (at compile time) that a function (or class) works
279    with a NeighborWeighting. Do not run any test using this class because
280    the class is not really functional at run time.
281
282    \see boost/concept_archetype.hpp
283   */
284  class neighbor_weighting_archetype
285  {
286  public:
287    neighbor_weighting_archetype(void) {}
288    void operator()(const utility::VectorBase& distance,
289                    const std::vector<size_t>& k_sorted,
290                    const classifier::Target& target,
291                    utility::VectorMutable& prediction) const {}
292    neighbor_weighting_archetype& operator=(const neighbor_weighting_archetype&)
293    { return *this; }
294  private:
295    neighbor_weighting_archetype(const neighbor_weighting_archetype&) {};
296  };
297
298
299  // compilation tests on iterators
300
301  template<typename Iterator>
302  void test_readable_iterator(Iterator iterator)
303  {
304    BOOST_CONCEPT_ASSERT((boost_concepts::ReadableIterator<Iterator>));
305  }
306
307
308  template<typename Iterator>
309  void test_writable_iterator(Iterator iterator)
310  {
311    BOOST_CONCEPT_ASSERT((boost_concepts::WritableIterator<Iterator>));
312  }
313
314
315  template<typename Iterator>
316  void test_swappable_iterator(Iterator iterator)
317  {
318    BOOST_CONCEPT_ASSERT((boost_concepts::SwappableIterator<Iterator>));
319  }
320
321  template<typename Iterator>
322  void test_lvalue_iterator(Iterator iterator)
323  {
324    BOOST_CONCEPT_ASSERT((boost_concepts::LvalueIterator<Iterator>));
325  }
326
327  template<typename Iterator>
328  void test_incrementable_iterator(Iterator iterator)
329  {
330    BOOST_CONCEPT_ASSERT((boost_concepts::IncrementableIterator<Iterator>));
331  }
332
333  template<typename Iterator>
334  void test_single_pass_iterator(Iterator iterator)
335  {
336    BOOST_CONCEPT_ASSERT((boost_concepts::SinglePassIterator<Iterator>));
337  }
338
339
340  template<typename Iterator>
341  void test_forward_traversal_iterator(Iterator iterator)
342  {
343    BOOST_CONCEPT_ASSERT((boost_concepts::ForwardTraversal<Iterator>));
344  }
345
346
347  template<typename Iterator>
348  void test_bidirectional_traversal_iterator(Iterator iterator)
349  {
350    BOOST_CONCEPT_ASSERT((boost_concepts::BidirectionalTraversal<Iterator>));
351  }
352
353
354  template<typename Iterator>
355  void test_random_access_traversal_iterator(Iterator iterator)
356  {
357    BOOST_CONCEPT_ASSERT((boost_concepts::RandomAccessTraversal<Iterator>));
358  }
359
360
361  // This function pulls out the iterator_category and checks that the
362  // iterator has implemented what is promised in the category.
363  //
364  // Likewise it pulls out the boost::iterator_traversal type and
365  // checks that the traversal is implemented as promised.
366  //
367  // Iterator is a model of input iterator (output iterator makes no
368  // sense as a const iterator)
369  template<typename Iterator>
370  void test_const_iterator(Iterator iterator);
371
372
373  // Similar to test_const_iterator but function also works for
374  // output_iterator and it tests that the iterator is mutable.
375  template<typename Iterator>
376  void test_mutable_iterator(Iterator iterator);
377
378  // functions used by test_const_iterator and test_mutable_iterator
379  namespace detail {
380
381    template<typename Iterator>
382    void test_iterator_traversal(Iterator iterator,
383                                 boost::incrementable_traversal_tag tag)
384    {
385      test_incrementable_iterator(iterator);
386    }
387
388
389    template<typename Iterator>
390    void test_iterator_traversal(Iterator iterator,
391                                 boost::single_pass_traversal_tag tag)
392    {
393      test_single_pass_iterator(iterator);
394    }
395
396
397    template<typename Iterator>
398    void test_iterator_traversal(Iterator iterator,
399                                 boost::forward_traversal_tag tag)
400    {
401      test_forward_traversal_iterator(iterator);
402    }
403
404
405    template<typename Iterator>
406    void test_iterator_traversal(Iterator iterator,
407                                 boost::bidirectional_traversal_tag tag)
408    {
409      test_bidirectional_traversal_iterator(iterator);
410    }
411
412
413    template<typename Iterator>
414    void test_iterator_traversal(Iterator iterator,
415                                 boost::random_access_traversal_tag tag)
416    {
417      test_random_access_traversal_iterator(iterator);
418    }
419
420
421    template<typename Iterator>
422    void test_iterator(Iterator iterator, std::forward_iterator_tag tag)
423    {
424      test_lvalue_iterator(iterator);
425      test_iterator(iterator);
426    }
427
428
429    template<typename Iterator>
430    void test_iterator(Iterator iterator, std::bidirectional_iterator_tag tag)
431    {
432      test_lvalue_iterator(iterator);
433      test_iterator(iterator);
434    }
435
436
437    template<typename Iterator>
438    void test_iterator(Iterator iterator, std::random_access_iterator_tag tag)
439    {
440      test_lvalue_iterator(iterator);
441      test_iterator(iterator);
442    }
443
444
445    // testing forward iterator (or bidirectional or random access)
446    template<typename Iterator>
447    void test_iterator(Iterator iterator)
448    {
449      typename boost::iterator_category<Iterator>::type tag;
450      test_iterator(iterator, tag);
451      typename boost::iterator_traversal<Iterator>::type trav_tag;
452      test_iterator_traversal(iterator, trav_tag);
453    }
454
455
456    template<typename Iterator>
457    void test_mutable_iterator(Iterator iterator, std::output_iterator_tag tag)
458    {
459      test_incrementable_iterator(iterator);
460    }
461
462
463    template<typename Iterator>
464    void test_mutable_iterator(Iterator iterator, std::input_iterator_tag tag)
465    {
466      test_single_pass_iterator(iterator);
467    }
468
469
470    template<typename Iterator>
471    void test_mutable_iterator(Iterator iterator, std::forward_iterator_tag tag)
472    {
473      test_lvalue_iterator(iterator);
474      test_iterator(iterator);
475    }
476
477
478    template<typename Iterator>
479    void test_const_iterator(Iterator iterator, std::input_iterator_tag tag)
480    {
481      test_single_pass_iterator(iterator);
482      test_readable_iterator(iterator);
483    }
484
485
486    template<typename Iterator>
487    void test_const_iterator(Iterator iterator, std::forward_iterator_tag tag)
488    {
489      test_lvalue_iterator(iterator);
490      test_iterator(iterator);
491    }
492
493
494  } // end of namespace detail
495
496
497  // template implementations
498
499  template<typename Iterator1, typename Iterator2>
500  bool Suite::equal_range(Iterator1 first1, Iterator1 last1, Iterator2 first2,
501                          unsigned int N)
502  {
503    while (first1!=last1){
504      if (!this->equal(*first1, *first2, N) )  {
505        return false;
506      }
507      ++first1;
508      ++first2;
509    }
510    return true;
511  }
512
513
514  template<typename Iterator1, typename Iterator2>
515  bool Suite::equal_range_fix(Iterator1 first1, Iterator1 last1, 
516                              Iterator2 first2, double margin)
517  {
518    while (first1!=last1){
519      if (!this->equal_fix(*first1, *first2, margin) )   {
520        return false;
521      }
522      ++first1;
523      ++first2;
524    }
525    return true;
526  }
527
528
529  // return true if we can write to a write-protected file
530  bool run_as_root(void);
531
532  // function that can be used to avoid warning: '-Wunused-but-set-variable'
533  template<typename T>
534  void avoid_compiler_warning(T) {}
535
536  template<class T>
537  bool Suite::test_stream(const T& t) const
538  {
539    this->err() << "Checking that output stream is valid as an input stream\n";
540    std::stringstream ss;
541    this->err() << "writing to output\n";
542    ss << t;
543    this->err() << "creating a new object from output\n";
544    T t2(ss);
545    std::stringstream ss2;
546    this->err() << "writing to output\n";
547    ss2 << t2;
548    bool ok = ss2.str()==ss.str();
549    if (!ok) {
550      this->err() << "ERROR: first object gave following output:\n"
551                  << ss.str() << "\n"
552                  << "ERROR: and second object gave following output:\n"
553                  << ss2.str() << "\n";
554    }
555    return ok;
556  }
557
558  template<typename TrivialIterator>
559  void Suite::test_trivial_iterator(const TrivialIterator& iter)
560  {
561    err() << "  testing Trivial features" << std::endl;
562    typename std::iterator_traits<TrivialIterator>::value_type tmp = *iter;
563    add(tmp==*iter);
564    TrivialIterator default_constructed;
565    avoid_compiler_warning(default_constructed);
566  }
567
568  template<typename InputIterator>
569  void Suite::test_input_iterator(InputIterator& iter)
570  {
571    BOOST_CONCEPT_ASSERT((boost::InputIterator<InputIterator>));
572    test_trivial_iterator(iter);
573    err() << "  testing Input features" << std::endl;
574    // just to check compilation
575    if (false) {
576      ++iter;
577      iter++;
578    }
579  }
580
581  template<typename OutputIterator>
582  void Suite::test_output_iterator(OutputIterator& iter)
583  {
584    err() << "  testing Output features" << std::endl;
585    // OutputIterator should be default constructible and assignable
586    OutputIterator oi;
587    oi = iter;
588    ++oi;
589  }
590
591  template<typename ForwardIterator>
592  void Suite::test_forward_iterator(ForwardIterator iter)
593  {
594    BOOST_CONCEPT_ASSERT((boost::ForwardIterator<ForwardIterator>));
595    test_output_iterator(iter);
596    test_input_iterator(iter);
597    err() << "  testing Forward features" << std::endl;
598
599    typename std::iterator_traits<ForwardIterator>::value_type tmp = *iter;
600    // testing multiple traversing is possible and does not change the data
601    ForwardIterator iter1 = iter;
602    ++iter1;
603    add(iter!=iter1);
604    ForwardIterator iter2 = iter;
605    ++iter2;
606    add(tmp==*iter);
607  }
608
609  template<typename BidirectionalIterator>
610  void Suite::test_bidirectional_iterator(BidirectionalIterator iter)
611  {
612    BOOST_CONCEPT_ASSERT((boost::BidirectionalIterator<BidirectionalIterator>));
613    test_forward_iterator(iter);
614    bool ok_cached = ok();
615    err() << "  testing Bidirectional features" << std::endl;
616    const BidirectionalIterator i = iter;
617    BidirectionalIterator tmp = iter++;
618    if (!add(tmp==i)) {
619      err() << "iter++ does not return iter\n";
620    }
621    if (!add(++tmp==iter)) {
622      err() << "++iter failed\n";
623    }
624    if (!add(--tmp==i)) {
625      err() << "--iter failed\n";
626    }
627    tmp = iter--;
628    if (!add(--tmp==iter))
629      err() << "iter-- failed" << std::endl;
630    if (ok_cached && !ok())
631      err() << "failed" << std::endl;
632  }
633
634  template<typename RandomAccessIterator>
635  void Suite::test_random_access_iterator(RandomAccessIterator iter)
636  {
637    BOOST_CONCEPT_ASSERT((boost::RandomAccessIterator<RandomAccessIterator>));
638    test_bidirectional_iterator(iter);
639    err() << "  testing RandomAccess features" << std::endl;
640    bool ok_cached = ok();
641    RandomAccessIterator iter2 = iter;
642    iter2 += 1;
643    iter2 -= 1;
644    RandomAccessIterator& iter3 = (iter2 += 1);
645    RandomAccessIterator& iter4 = (iter3 -= 1);
646    if (!add(iter2 == iter4))
647      err() << "operator-(int) failed" << std::endl;
648    add(++iter2 == iter3);
649
650    RandomAccessIterator iter5 = iter + 0;
651    RandomAccessIterator iter6 = 0 + iter;
652    add(iter6 == iter5);
653
654    RandomAccessIterator iter7 = iter - 0;
655    add(iter7 == iter);
656    add(iter7 - iter == 0);
657    add(! (iter7<iter));
658
659    typename RandomAccessIterator::value_type tmp = iter[0];
660    typename RandomAccessIterator::value_type tmp2 = *iter;
661    tmp = tmp; // avoid compiler warning
662    if (!add(tmp == tmp2))
663      err() << "operator[] failed" << std::endl;
664    if (!add(iter[0] == *iter))
665      err() << "operator[] failed" << std::endl;
666    if (ok_cached && !ok())
667      err() << "failed" << std::endl;
668  }
669
670  template<typename Container2D>
671  void Suite::test_concept_container2d(const Container2D& c)
672  {
673    typedef typename Container2D::value_type value_type;
674    typedef typename Container2D::const_reference const_reference;
675    typedef typename Container2D::const_iterator const_iterator;
676    typedef typename Container2D::const_column_iterator const_column_iterator;
677    typedef typename Container2D::const_row_iterator const_row_iterator;
678    const_iterator ci = c.begin();
679    const_column_iterator cci = c.begin_column(0);
680    const_row_iterator cri = c.begin_row(0);
681    ci = c.end();
682    cci = c.end_column(0);
683    cri = c.end_row(0);
684    size_t cols = c.columns();
685    size_t rows = c.rows();
686    // just to avoid compiler warning
687    avoid_compiler_warning(cols);
688    avoid_compiler_warning(rows);
689    const_reference x = c(0,0);
690    value_type y;
691    y = x;
692    avoid_compiler_warning(y);
693  }
694
695  template<typename MutableContainer2D>
696  void Suite::test_concept_mutable_container2d(MutableContainer2D& mc)
697  {
698    test_concept_container2d(mc);
699    typedef typename MutableContainer2D::reference reference;
700    typedef typename MutableContainer2D::iterator iterator;
701    typedef typename MutableContainer2D::column_iterator column_iterator;
702    typedef typename MutableContainer2D::row_iterator row_iterator;
703    iterator i = mc.begin();
704    column_iterator ci = mc.begin_column(0);
705    row_iterator ri = mc.begin_row(0);
706    *i = *ci;
707    *ci = *i;
708    *ri = *i;
709    i = mc.end();
710    ci = mc.end_column(0);
711    ri = mc.end_row(0);
712    reference x = mc(0,0);
713    x = *mc.begin();
714  }
715
716
717  template<typename Iterator>
718  void test_const_iterator(Iterator iterator)
719  {
720    typename boost::iterator_category<Iterator>::type tag;
721    detail::test_const_iterator(iterator, tag);
722  }
723
724
725  template<typename Iterator>
726  void test_mutable_iterator(Iterator iterator)
727  {
728    typename boost::iterator_category<Iterator>::type tag;
729    detail::test_mutable_iterator(iterator, tag);
730    test_writable_iterator(iterator);
731  }
732
733
734  // For convenience four classes that are typical data iterators for
735  // combinations of const/mutable and weighted/unweighted. Traversal
736  // is eccpected to be one of:
737  // boost::incrementable_traversal_tag
738  // boost::single_pass_traversal_tag
739  // boost::forward_traversal_tag
740  // boost::bidirectional_traversal_tag
741  // boost::random_access_traversal_tag
742  template<typename Traversal>
743  class UnweightedConstDataIterator
744    : public boost::iterator_archetype<
745    double,
746    boost::iterator_archetypes::readable_iterator_t,
747    Traversal
748    >
749  {};
750
751
752  template<typename Traversal>
753  class UnweightedDataIterator
754    : public boost::iterator_archetype<
755    double,
756    boost::iterator_archetypes::readable_writable_iterator_t,
757    Traversal
758    >
759  {};
760
761  template<typename Traversal>
762  class WeightedConstDataIterator
763    : public utility::WeightedIteratorArchetype<
764    boost::iterator_archetypes::readable_iterator_t,
765    Traversal>
766  {};
767
768  template<typename Traversal>
769  class WeightedDataIterator
770    : public utility::WeightedIteratorArchetype<
771    boost::iterator_archetypes::readable_writable_iterator_t,
772    Traversal>
773  {};
774
775
776}}}
777
778#endif
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