ProteoWizard
Functions | Variables
ProteinListCacheTest.cpp File Reference
#include "ProteinListCache.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "Serializer_FASTA.hpp"

Go to the source code of this file.

Functions

ostream & std::operator<< (ostream &os, const ProteinListCache::CacheType &cache)
 
void testModeOff ()
 
void testModeMetaDataOnly ()
 
void testModeMetaDataAndSequence ()
 
void test ()
 
int main (int argc, char *argv[])
 

Variables

ostream * os_ = 0
 

Function Documentation

§ operator<<()

ostream& std::operator<< ( ostream &  os,
const ProteinListCache::CacheType cache 
)

Definition at line 38 of file ProteinListCacheTest.cpp.

References pwiz::util::mru_list< Item, KeyExtractor >::begin(), and pwiz::util::mru_list< Item, KeyExtractor >::end().

39 {
40  os << "Protein cache indices (from MRU to LRU):";
41  for (ProteinListCache::CacheType::const_iterator itr = cache.begin(); itr != cache.end(); ++itr)
42  os << " " << itr->second->index;
43  return os;
44 }
iterator begin()
Definition: mru_list.hpp:99

§ testModeOff()

void testModeOff ( )

Definition at line 49 of file ProteinListCacheTest.cpp.

References pwiz::proteome::ProteinListCache::cache(), pwiz::util::mru_list< Item, KeyExtractor >::empty(), os_, pwiz::proteome::ProteinListCache::protein(), ProteinListCacheMode_Off, pwiz::proteome::ProteomeData::proteinListPtr, pwiz::proteome::Serializer_FASTA::read(), unit_assert, unit_assert_operator_equal, and pwiz::proteome::Serializer_FASTA::write().

Referenced by test().

50 {
51  // initialize list
52  ProteomeData pd;
53  shared_ptr<ProteinListSimple> sl(new ProteinListSimple);
54  sl->proteins.push_back(ProteinPtr(new Protein("P1", 0, "0", "ABC")));
55  sl->proteins.push_back(ProteinPtr(new Protein("P2", 1, "1", "DEF")));
56  sl->proteins.push_back(ProteinPtr(new Protein("P3", 2, "2", "GHI")));
57  sl->proteins.push_back(ProteinPtr(new Protein("P4", 3, "3", "JKL")));
58  pd.proteinListPtr = sl;
59 
60  // ProteinListSimple returns the same shared_ptrs regardless of caching;
61  // serializing to FASTA and back will produce different shared_ptrs
62  boost::shared_ptr<stringstream> ss(new stringstream);
63  Serializer_FASTA serializer;
64  serializer.write(*ss, pd, 0);
65  serializer.read(ss, pd);
66 
67  // access a series of proteins and make sure the cache behaves appropriately:
68  // in off mode, the cache should always be empty
69 
70  ProteinPtr s;
71 
73  const ProteinListCache::CacheType& cache = slc.cache();
74 
75  unit_assert(cache.empty());
76 
77  s = slc.protein(0, false);
78  s = slc.protein(1, true);
79  unit_assert_operator_equal("1", s->description);
80  unit_assert_operator_equal("DEF", s->sequence());
81  s = slc.protein(2, false);
82  s = slc.protein(3, true);
83 
84  if (os_) *os_ << cache << endl;
85  unit_assert(cache.empty());
86 }
void write(std::ostream &os, const ProteomeData &pd, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry) const
write ProteomeData object to ostream as FASTA
adds a level of flexible MRU caching to a ProteinList processor chain
ostream * os_
ProteinListCacheMode_Off
#define unit_assert_operator_equal(expected, actual)
Definition: unit.hpp:92
void read(boost::shared_ptr< std::istream > is, ProteomeData &pd) const
read in ProteomeData object from a FASTA istream
bool empty() const
Definition: mru_list.hpp:91
boost::shared_ptr< Protein > ProteinPtr
#define unit_assert(x)
Definition: unit.hpp:85
ProteomeData <-> FASTA stream serialization.

§ testModeMetaDataOnly()

void testModeMetaDataOnly ( )

Definition at line 89 of file ProteinListCacheTest.cpp.

References pwiz::proteome::ProteinListCache::cache(), pwiz::util::mru_list< Item, KeyExtractor >::empty(), pwiz::util::mru_list< Item, KeyExtractor >::lru(), pwiz::util::mru_list< Item, KeyExtractor >::max_size(), pwiz::util::mru_list< Item, KeyExtractor >::mru(), os_, pwiz::proteome::ProteinListCache::protein(), ProteinListCacheMode_MetaDataOnly, pwiz::proteome::ProteomeData::proteinListPtr, pwiz::proteome::Serializer_FASTA::read(), pwiz::util::mru_list< Item, KeyExtractor >::size(), unit_assert, unit_assert_operator_equal, and pwiz::proteome::Serializer_FASTA::write().

Referenced by test().

90 {
91  // initialize list
92  ProteomeData pd;
93  shared_ptr<ProteinListSimple> sl(new ProteinListSimple);
94  sl->proteins.push_back(ProteinPtr(new Protein("P1", 0, "0", "ABC")));
95  sl->proteins.push_back(ProteinPtr(new Protein("P2", 1, "1", "DEF")));
96  sl->proteins.push_back(ProteinPtr(new Protein("P3", 2, "2", "GHI")));
97  sl->proteins.push_back(ProteinPtr(new Protein("P4", 3, "3", "JKL")));
98  pd.proteinListPtr = sl;
99 
100  // ProteinListSimple returns the same shared_ptrs regardless of caching;
101  // serializing to FASTA and back will produce different shared_ptrs
102  boost::shared_ptr<stringstream> ss(new stringstream);
103  Serializer_FASTA serializer;
104  serializer.write(*ss, pd, 0);
105  serializer.read(ss, pd);
106 
107  // access a series of proteins and make sure the cache behaves appropriately:
108  // in metadata-only mode, entries in the cache should:
109  // - always have metadata
110  // - never have sequences
111 
112  ProteinPtr s;
113 
115  const ProteinListCache::CacheType& cache = slc.cache();
116 
117  unit_assert(cache.empty());
119 
120  s = slc.protein(0, false);
121 
122  // pointers should be equal
123  unit_assert_operator_equal(slc.protein(0, false), s);
124 
125  if (os_) *os_ << cache << endl;
126  unit_assert(!cache.empty());
127  unit_assert_operator_equal(1, cache.size());
128  unit_assert_operator_equal(0, cache.mru().second->index);
129  unit_assert_operator_equal("0", cache.mru().second->description);
130  unit_assert_operator_equal("", cache.mru().second->sequence());
131 
132  // with-sequence access should return the sequence, but only cache the metadata
133  s = slc.protein(1, true);
134  unit_assert_operator_equal("DEF", s->sequence());
135 
136  if (os_) *os_ << cache << endl;
137  unit_assert_operator_equal(2, cache.size());
138  unit_assert_operator_equal(1, cache.mru().second->index);
139  unit_assert_operator_equal("", cache.mru().second->sequence());
140  unit_assert_operator_equal(0, cache.lru().second->index);
141 
142  s = slc.protein(2, false);
143 
144  // pointers should be equal
145  unit_assert_operator_equal(slc.protein(2, false), s);
146 
147  if (os_) *os_ << cache << endl;
148  unit_assert_operator_equal(2, cache.size());
149  unit_assert_operator_equal(2, cache.mru().second->index);
150  unit_assert_operator_equal("", cache.mru().second->sequence());
151  unit_assert_operator_equal(1, cache.lru().second->index);
152 
153  s = slc.protein(3, true);
154  unit_assert_operator_equal("JKL", s->sequence());
155 
156  if (os_) *os_ << cache << endl;
157  unit_assert_operator_equal(2, cache.size());
158  unit_assert_operator_equal(3, cache.mru().second->index);
159  unit_assert_operator_equal("", cache.mru().second->sequence());
160  unit_assert_operator_equal(2, cache.lru().second->index);
161 
162  s = slc.protein(2, true);
163  unit_assert_operator_equal("GHI", s->sequence());
164 
165  if (os_) *os_ << cache << endl;
166  unit_assert_operator_equal(2, cache.size());
167  unit_assert_operator_equal(2, cache.mru().second->index);
168  unit_assert_operator_equal("", cache.mru().second->sequence());
169  unit_assert_operator_equal(3, cache.lru().second->index);
170 }
void write(std::ostream &os, const ProteomeData &pd, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry) const
write ProteomeData object to ostream as FASTA
adds a level of flexible MRU caching to a ProteinList processor chain
ostream * os_
const item_type & lru() const
Definition: mru_list.hpp:97
#define unit_assert_operator_equal(expected, actual)
Definition: unit.hpp:92
std::size_t max_size() const
Definition: mru_list.hpp:93
void read(boost::shared_ptr< std::istream > is, ProteomeData &pd) const
read in ProteomeData object from a FASTA istream
std::size_t size() const
Definition: mru_list.hpp:92
ProteinListCacheMode_MetaDataOnly
bool empty() const
Definition: mru_list.hpp:91
const item_type & mru() const
Definition: mru_list.hpp:96
boost::shared_ptr< Protein > ProteinPtr
#define unit_assert(x)
Definition: unit.hpp:85
ProteomeData <-> FASTA stream serialization.

§ testModeMetaDataAndSequence()

void testModeMetaDataAndSequence ( )

Definition at line 173 of file ProteinListCacheTest.cpp.

References pwiz::proteome::ProteinListCache::cache(), pwiz::util::mru_list< Item, KeyExtractor >::empty(), pwiz::util::mru_list< Item, KeyExtractor >::lru(), pwiz::util::mru_list< Item, KeyExtractor >::max_size(), pwiz::util::mru_list< Item, KeyExtractor >::mru(), os_, pwiz::proteome::ProteinListCache::protein(), pwiz::proteome::ProteomeData::proteinListPtr, pwiz::proteome::Serializer_FASTA::read(), pwiz::util::mru_list< Item, KeyExtractor >::size(), unit_assert, unit_assert_operator_equal, and pwiz::proteome::Serializer_FASTA::write().

Referenced by test().

174 {
175  // initialize list
176  ProteomeData pd;
177  shared_ptr<ProteinListSimple> sl(new ProteinListSimple);
178  sl->proteins.push_back(ProteinPtr(new Protein("P1", 0, "0", "ABC")));
179  sl->proteins.push_back(ProteinPtr(new Protein("P2", 1, "1", "DEF")));
180  sl->proteins.push_back(ProteinPtr(new Protein("P3", 2, "2", "GHI")));
181  sl->proteins.push_back(ProteinPtr(new Protein("P4", 3, "3", "JKL")));
182  pd.proteinListPtr = sl;
183 
184  // ProteinListSimple returns the same shared_ptrs regardless of caching;
185  // serializing to FASTA and back will produce different shared_ptrs
186  boost::shared_ptr<stringstream> ss(new stringstream);
187  Serializer_FASTA serializer;
188  serializer.write(*ss, pd, 0);
189  serializer.read(ss, pd);
190 
191  // access a series of proteins and make sure the cache behaves appropriately:
192  // in metadata-and-sequence mode, entries in the cache should:
193  // - always have metadata
194  // - always have sequences
195 
196  ProteinPtr s;
197 
198  ProteinListCache slc(pd.proteinListPtr, ProteinListCacheMode_MetaDataAndSequence, 2);
199  const ProteinListCache::CacheType& cache = slc.cache();
200 
201  unit_assert(cache.empty());
203 
204  // metadata-only access should not affect the cache
205  s = slc.protein(0, false);
206 
207  if (os_) *os_ << cache << endl;
208  unit_assert(cache.empty());
209  unit_assert_operator_equal(0, cache.size());
210 
211  s = slc.protein(1, true);
212 
213  // pointers should be equal
214  unit_assert_operator_equal(slc.protein(1, true), s);
215 
216  if (os_) *os_ << cache << endl;
217  unit_assert_operator_equal(1, cache.size());
218  unit_assert_operator_equal(1, cache.mru().second->index);
219  unit_assert_operator_equal("1", cache.mru().second->description);
220  unit_assert_operator_equal("DEF", cache.mru().second->sequence());
221 
222  // metadata-only access should not affect the cache
223  s = slc.protein(2, false);
224 
225  if (os_) *os_ << cache << endl;
226  unit_assert_operator_equal(1, cache.size());
227  unit_assert_operator_equal(1, cache.mru().second->index);
228  unit_assert_operator_equal("DEF", cache.mru().second->sequence());
229 
230  s = slc.protein(3, true);
231 
232  // pointers should be equal
233  unit_assert_operator_equal(slc.protein(3, true), s);
234 
235  if (os_) *os_ << cache << endl;
236  unit_assert_operator_equal(2, cache.size());
237  unit_assert_operator_equal(3, cache.mru().second->index);
238  unit_assert_operator_equal("JKL", cache.mru().second->sequence());
239  unit_assert_operator_equal(1, cache.lru().second->index);
240 
241  s = slc.protein(2, true);
242 
243  if (os_) *os_ << cache << endl;
244  unit_assert_operator_equal(2, cache.size());
245  unit_assert_operator_equal(2, cache.mru().second->index);
246  unit_assert_operator_equal("GHI", cache.mru().second->sequence());
247  unit_assert_operator_equal(3, cache.lru().second->index);
248 }
void write(std::ostream &os, const ProteomeData &pd, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry) const
write ProteomeData object to ostream as FASTA
adds a level of flexible MRU caching to a ProteinList processor chain
ostream * os_
const item_type & lru() const
Definition: mru_list.hpp:97
#define unit_assert_operator_equal(expected, actual)
Definition: unit.hpp:92
std::size_t max_size() const
Definition: mru_list.hpp:93
void read(boost::shared_ptr< std::istream > is, ProteomeData &pd) const
read in ProteomeData object from a FASTA istream
std::size_t size() const
Definition: mru_list.hpp:92
bool empty() const
Definition: mru_list.hpp:91
const item_type & mru() const
Definition: mru_list.hpp:96
boost::shared_ptr< Protein > ProteinPtr
#define unit_assert(x)
Definition: unit.hpp:85
ProteomeData <-> FASTA stream serialization.

§ test()

void test ( )

Definition at line 251 of file ProteinListCacheTest.cpp.

References testModeMetaDataAndSequence(), testModeMetaDataOnly(), and testModeOff().

Referenced by main().

252 {
253  testModeOff();
256 }
void testModeMetaDataAndSequence()
void testModeMetaDataOnly()
void testModeOff()

§ main()

int main ( int  argc,
char *  argv[] 
)

Definition at line 259 of file ProteinListCacheTest.cpp.

References os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG.

260 {
261  TEST_PROLOG(argc, argv)
262 
263  try
264  {
265  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
266  test();
267  }
268  catch (exception& e)
269  {
270  TEST_FAILED(e.what())
271  }
272  catch (...)
273  {
274  TEST_FAILED("Caught unknown exception.")
275  }
276 
278 }
void test()
#define TEST_EPILOG
Definition: unit.hpp:182
ostream * os_
#define TEST_FAILED(x)
Definition: unit.hpp:176
#define TEST_PROLOG(argc, argv)
Definition: unit.hpp:174

Variable Documentation

§ os_

ostream* os_ = 0