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prefix.h
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27 
28 #pragma once
29 
30 #include <nvbio/strings/string_set.h>
31 
32 
33 namespace nvbio {
34 
37 
40 
43 typedef uint32 string_prefix_coord_type;
44 
47 typedef uint64 long_string_prefix_coord_type;
48 
51 typedef uint32_2 string_set_prefix_coord_type;
52 
55 typedef uint64_2 long_string_set_prefix_coord_type;
56 
59 
66 template <
67  typename StringType,
68  typename CoordType,
69  uint32 CoordDim>
70 struct PrefixCore {};
71 
77 template <
78  typename StringType,
79  typename CoordType>
80 struct PrefixCore<StringType,CoordType,1u>
81 {
82  typedef StringType string_type;
83  typedef CoordType coord_type;
84  typedef typename vector_traits<CoordType>::value_type index_type;
85 
86  typedef typename std::iterator_traits<string_type>::value_type symbol_type;
87  typedef typename std::iterator_traits<string_type>::value_type value_type;
88  typedef typename std::iterator_traits<string_type>::reference reference;
89 
90  typedef typename string_traits<StringType>::iterator iterator;
91  typedef typename string_traits<StringType>::const_iterator const_iterator;
92  typedef typename string_traits<StringType>::forward_iterator forward_iterator;
93 
96  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
97  PrefixCore() {}
98 
101  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
102  PrefixCore(
103  const string_type string,
104  const coord_type prefix) :
105  m_string( string ),
106  m_coords( prefix ) {}
107 
110  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
111  uint32 size() const { return m_coords; }
112 
115  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
116  uint32 length() const { return size(); }
117 
120  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
121  symbol_type operator[] (const uint32 i) const { return m_string[ i ]; }
122 
125  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
126  reference operator[] (const uint32 i) { return m_string[ i ]; }
127 
130  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
131  coord_type coords() const { return m_coords; }
132 
135  iterator begin() { return m_string.begin(); }
136 
139  iterator end() { return m_string.begin() + m_coords; }
140 
143  const_iterator begin() const { return m_string.begin(); }
144 
147  const_iterator end() const { return m_string.begin() + m_coords; }
148 
149  string_type m_string;
150  coord_type m_coords;
151 };
152 
158 template <
159  typename StringType,
160  typename CoordType>
161 struct PrefixCore<StringType,CoordType,2u>
162 {
163  typedef StringType string_type;
164  typedef CoordType coord_type;
165  typedef typename vector_traits<CoordType>::value_type index_type;
166 
167  typedef typename std::iterator_traits<string_type>::value_type symbol_type;
168  typedef typename std::iterator_traits<string_type>::value_type value_type;
169  typedef typename std::iterator_traits<string_type>::reference reference;
170 
171  typedef typename string_traits<StringType>::iterator iterator;
172  typedef typename string_traits<StringType>::const_iterator const_iterator;
173  typedef typename string_traits<StringType>::forward_iterator forward_iterator;
174 
177  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
178  PrefixCore() {}
179 
182  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
183  PrefixCore(
184  const string_type string,
185  const coord_type prefix) :
186  m_string( string ),
187  m_coords( prefix ) {}
188 
191  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
192  uint32 size() const { return m_coords.y; }
193 
196  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
197  uint32 length() const { return size(); }
198 
201  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
202  symbol_type operator[] (const uint32 i) const { return m_string[ i ]; }
203 
206  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
207  reference operator[] (const uint32 i) { return m_string[ i ]; }
208 
211  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
212  coord_type coords() const { return m_coords; }
213 
216  iterator begin() { return m_string.begin(); }
217 
220  iterator end() { return m_string.begin() + m_coords.y; }
221 
224  const_iterator begin() const { return m_string.begin(); }
225 
228  const_iterator end() const { return m_string.begin() + m_coords.y; }
229 
230  string_type m_string;
231  coord_type m_coords;
232 };
233 
235 
242 template <
243  typename StringType,
244  typename CoordType>
245 struct Prefix : PrefixCore< StringType, CoordType, vector_traits<CoordType>::DIM >
246 {
247  static const uint32 SYMBOL_SIZE = string_traits<StringType>::SYMBOL_SIZE;
248 
249  typedef PrefixCore< StringType, CoordType, vector_traits<CoordType>::DIM > core_type;
250  typedef StringType string_type;
251  typedef CoordType coord_type;
252 
253  typedef typename std::iterator_traits<string_type>::value_type symbol_type;
254  typedef typename std::iterator_traits<string_type>::value_type value_type;
255  typedef typename std::iterator_traits<string_type>::reference reference;
256 
257  typedef typename string_traits<StringType>::iterator iterator;
258  typedef typename string_traits<StringType>::const_iterator const_iterator;
259  typedef typename string_traits<StringType>::forward_iterator forward_iterator;
260 
263  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
264  Prefix() {}
265 
268  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
269  Prefix(
270  const string_type string,
271  const coord_type infix) : core_type( string, infix ) {}
272 };
273 
282 template <typename StringType, typename CoordType>
283 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
284 Prefix<StringType,CoordType> make_prefix(const StringType string, const CoordType coords)
285 {
286  return Prefix<StringType,CoordType>( string, coords );
287 }
288 
291 
298 template <
299  typename SequenceType,
300  typename PrefixIterator,
301  uint32 CoordDim>
302 struct PrefixSetCore {};
303 
309 template <
310  typename SequenceType,
311  typename PrefixIterator>
312 struct PrefixSetCore<SequenceType,PrefixIterator,1u>
313 {
314  typedef SequenceType sequence_type;
315  typedef PrefixIterator prefix_iterator;
316 
317  typedef typename std::iterator_traits<PrefixIterator>::value_type coord_type;
318  typedef Prefix<sequence_type, coord_type> string_type;
319 
322  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
323  PrefixSetCore() {}
324 
327  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
328  PrefixSetCore(
329  const uint32 size,
330  const sequence_type sequence,
331  const prefix_iterator prefixes) :
332  m_size( size ),
333  m_sequence( sequence ),
334  m_prefixes( prefixes ) {}
335 
338  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
339  uint32 size() const { return m_size; }
340 
343  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
344  string_type operator[] (const uint32 i) const
345  {
346  const coord_type coords = m_prefixes[i];
347  return string_type( m_sequence, coords );
348  }
349 
350  uint32 m_size;
351  sequence_type m_sequence;
352  prefix_iterator m_prefixes;
353 };
354 
360 template <
361  typename SequenceType,
362  typename PrefixIterator>
363 struct PrefixSetCore<SequenceType,PrefixIterator,2u>
364 {
365  typedef SequenceType sequence_type;
366  typedef PrefixIterator prefix_iterator;
367 
368  typedef typename sequence_type::string_type base_string_type;
369  typedef typename std::iterator_traits<PrefixIterator>::value_type coord_type;
370  typedef Prefix<base_string_type, coord_type> string_type;
371 
374  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
375  PrefixSetCore() {}
376 
379  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
380  PrefixSetCore(
381  const uint32 size,
382  const sequence_type sequence,
383  const prefix_iterator prefixes) :
384  m_size( size ),
385  m_sequence( sequence ),
386  m_prefixes( prefixes ) {}
387 
390  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
391  uint32 size() const { return m_size; }
392 
395  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
396  string_type operator[] (const uint32 i) const
397  {
398  const coord_type coords = m_prefixes[i];
399  return string_type( m_sequence[ coords.x ], coords );
400  }
401 
402  uint32 m_size;
403  sequence_type m_sequence;
404  prefix_iterator m_prefixes;
405 };
406 
408 
411 template <typename StringType, typename CoordType>
412 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
413 uint32 string_id(const PrefixCore<StringType,CoordType,2u>& prefix) { return prefix.m_coords.x; }
414 
417 template <typename StringType, typename CoordType, uint32 CoordDim>
418 NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
419 uint32 length(const PrefixCore<StringType,CoordType,CoordDim>& prefix) { return prefix.length(); }
420 
436 template <
437  typename SequenceType,
438  typename PrefixIterator>
439 struct PrefixSet : public PrefixSetCore<
440  SequenceType,
441  PrefixIterator,
442  vector_traits<typename std::iterator_traits<PrefixIterator>::value_type>::DIM>
443 {
444  typedef PrefixSetCore<
445  SequenceType,
446  PrefixIterator,
447  vector_traits<typename std::iterator_traits<PrefixIterator>::value_type>::DIM> base_type;
448 
449  typedef SequenceType sequence_type;
450  typedef PrefixIterator prefix_iterator;
451  typedef typename iterator_system<PrefixIterator>::type system_tag;
452 
453  typedef typename base_type::coord_type coord_type;
454  typedef typename base_type::string_type string_type;
455 
456  typedef StringSetIterator< PrefixSet<SequenceType,InfixIterator> > iterator;
457  typedef StringSetIterator< PrefixSet<SequenceType,InfixIterator> > const_iterator;
458 
461  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
462  PrefixSet() {}
463 
466  NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
467  PrefixSet(
468  const uint32 size,
469  const sequence_type sequence,
470  const prefix_iterator prefixes) :
471  base_type( size, sequence, prefixes ) {}
472 
475  const_iterator begin() const { return const_iterator(*this,0u); }
476 
479  const_iterator end() const { return const_iterator(*this,base_type::size()); }
480 
483  iterator begin() { return iterator(*this,0u); }
484 
487  iterator end() { return iterator(*this,base_type::size()); }
488 };
489 
492 
493 } // namespace nvbio
494 
495 //#include <nvbio/basic/prefix_inl.h>
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