ProteoWizard
SpectrumList_SorterTest.cpp
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1 //
2 // $Id: SpectrumList_SorterTest.cpp 4129 2012-11-20 00:05:37Z chambm $
3 //
4 //
5 // Original author: Matt Chambers <matt.chambers <a.t> vanderbilt.edu>
6 //
7 // Copyright 2008 Spielberg Family Center for Applied Proteomics
8 // Cedars-Sinai Medical Center, Los Angeles, California 90048
9 //
10 // Licensed under the Apache License, Version 2.0 (the "License");
11 // you may not use this file except in compliance with the License.
12 // You may obtain a copy of the License at
13 //
14 // http://www.apache.org/licenses/LICENSE-2.0
15 //
16 // Unless required by applicable law or agreed to in writing, software
17 // distributed under the License is distributed on an "AS IS" BASIS,
18 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19 // See the License for the specific language governing permissions and
20 // limitations under the License.
21 //
22 
23 
24 #include "SpectrumList_Sorter.hpp"
25 #include "pwiz/utility/misc/unit.hpp"
26 #include "pwiz/utility/misc/Std.hpp"
27 #include <cstring>
28 #include "pwiz/data/msdata/examples.hpp"
29 #include "pwiz/data/msdata/TextWriter.hpp"
30 #include "boost/logic/tribool.hpp"
31 
32 
33 using namespace pwiz::util;
34 using namespace pwiz::cv;
35 using namespace pwiz::msdata;
36 using namespace pwiz::analysis;
37 using boost::logic::tribool;
38 
39 ostream* os_ = 0;
40 
41 
42 struct DefaultArrayLengthSorter : public SpectrumList_Sorter::Predicate
43 {
44  virtual tribool less(const SpectrumIdentity& lhs,
45  const SpectrumIdentity& rhs) const
46  {
47  return boost::logic::indeterminate;
48  }
49 
50  virtual tribool less(const Spectrum& lhs,
51  const Spectrum& rhs) const
52  {
53  if (lhs.id.empty())
54  return boost::logic::indeterminate;
55  return lhs.defaultArrayLength < rhs.defaultArrayLength;
56  }
57 };
58 
59 struct MSLevelSorter : public SpectrumList_Sorter::Predicate
60 {
61  virtual tribool less(const SpectrumIdentity& lhs,
62  const SpectrumIdentity& rhs) const
63  {
64  return boost::logic::indeterminate;
65  }
66 
67  virtual tribool less(const Spectrum& lhs,
68  const Spectrum& rhs) const
69  {
70  CVParam lhsMSLevel = lhs.cvParam(MS_ms_level);
71  CVParam rhsMSLevel = rhs.cvParam(MS_ms_level);
72  if (lhsMSLevel.empty() || rhsMSLevel.empty())
73  return boost::logic::indeterminate;
74  return lhsMSLevel.valueAs<int>() < rhsMSLevel.valueAs<int>();
75  }
76 };
77 
78 
79 void test()
80 {
81  MSData msd;
82  examples::initializeTiny(msd);
83 
84  SpectrumListPtr originalList = msd.run.spectrumListPtr;
85 
86  SpectrumListPtr defaultArrayLengthSortedList(
87  new SpectrumList_Sorter(originalList, DefaultArrayLengthSorter()));
88 
89  SpectrumListPtr msLevelUnstableSortedList(
90  new SpectrumList_Sorter(originalList, MSLevelSorter()));
91 
92  SpectrumListPtr msLevelStableSortedList(
93  new SpectrumList_Sorter(originalList, MSLevelSorter(), true));
94 
95  SpectrumListPtr sillySortedList(
96  new SpectrumList_Sorter(msLevelStableSortedList, DefaultArrayLengthSorter()));
97 
98  if (os_)
99  {
100  *os_ << "Original spectrum list (" << originalList->size() << "):\n";
101  TextWriter write(*os_);
102  write(*originalList);
103  *os_ << endl;
104  }
105 
106  if (os_)
107  {
108  *os_ << "Default array length sorted spectrum list (" << defaultArrayLengthSortedList->size() << "):\n";
109  TextWriter write(*os_);
110  write(*defaultArrayLengthSortedList);
111  *os_ << endl;
112  }
113 
114  if (os_)
115  {
116  *os_ << "MS level unstable sorted spectrum list (" << msLevelUnstableSortedList->size() << "):\n";
117  TextWriter write(*os_);
118  write(*msLevelUnstableSortedList);
119  *os_ << endl;
120  }
121 
122  if (os_)
123  {
124  *os_ << "MS level stable sorted spectrum list (" << msLevelStableSortedList->size() << "):\n";
125  TextWriter write(*os_);
126  write(*msLevelStableSortedList);
127  *os_ << endl;
128  }
129 
130  if (os_)
131  {
132  *os_ << "Silly (nested) sorted spectrum list (" << sillySortedList->size() << "):\n";
133  TextWriter write(*os_);
134  write(*sillySortedList);
135  *os_ << endl;
136  }
137 
138  unit_assert_operator_equal(originalList->size(), defaultArrayLengthSortedList->size());
139  unit_assert_operator_equal(originalList->size(), msLevelUnstableSortedList->size());
140  unit_assert_operator_equal(originalList->size(), msLevelStableSortedList->size());
141  unit_assert_operator_equal(originalList->size(), sillySortedList->size());
142 
143  SpectrumPtr s;
144 
145  // assert that the original list is unmodified
146  unit_assert_operator_equal("scan=19", originalList->spectrumIdentity(0).id);
147  unit_assert_operator_equal(0, originalList->spectrumIdentity(0).index);
148  unit_assert_operator_equal("scan=20", originalList->spectrumIdentity(1).id);
149  unit_assert_operator_equal(1, originalList->spectrumIdentity(1).index);
150  unit_assert_operator_equal("scan=21", originalList->spectrumIdentity(2).id);
151  unit_assert_operator_equal(2, originalList->spectrumIdentity(2).index);
152  unit_assert_operator_equal("scan=22", originalList->spectrumIdentity(3).id);
153  unit_assert_operator_equal(3, originalList->spectrumIdentity(3).index);
154  s = originalList->spectrum(0);
155  unit_assert_operator_equal("scan=19", s->id);
156  unit_assert_operator_equal(0, s->index);
157 
158  // validate the default array length sorted list (ascending order, scan=19 and scan=22 are interchangeable)
159  unit_assert_operator_equal("scan=21", defaultArrayLengthSortedList->spectrumIdentity(0).id);
160  unit_assert_operator_equal(0, defaultArrayLengthSortedList->spectrumIdentity(0).index);
161  unit_assert_operator_equal("scan=20", defaultArrayLengthSortedList->spectrumIdentity(1).id);
162  unit_assert_operator_equal(1, defaultArrayLengthSortedList->spectrumIdentity(1).index);
163  unit_assert_operator_equal(2, defaultArrayLengthSortedList->spectrumIdentity(2).index);
164  unit_assert_operator_equal(3, defaultArrayLengthSortedList->spectrumIdentity(3).index);
165  s = defaultArrayLengthSortedList->spectrum(0);
166  unit_assert_operator_equal("scan=21", s->id);
167  unit_assert_operator_equal(0, s->index);
168  s = defaultArrayLengthSortedList->spectrum(1);
169  unit_assert_operator_equal("scan=20", s->id);
170  unit_assert_operator_equal(1, s->index);
171  s = defaultArrayLengthSortedList->spectrum(2);
172  unit_assert_operator_equal(2, s->index);
173  s = defaultArrayLengthSortedList->spectrum(3);
174  unit_assert_operator_equal(3, s->index);
175  for (size_t i=1, end=defaultArrayLengthSortedList->size(); i < end; ++i)
176  unit_assert(defaultArrayLengthSortedList->spectrum(i)->defaultArrayLength >=
177  defaultArrayLengthSortedList->spectrum(i-1)->defaultArrayLength);
178 
179  // validate the MS level unstable sorted list (scan=19, scan=21, and scan=22 are interchangeable)
180  unit_assert_operator_equal(0, msLevelUnstableSortedList->spectrumIdentity(0).index);
181  unit_assert_operator_equal(1, msLevelUnstableSortedList->spectrumIdentity(1).index);
182  unit_assert_operator_equal(2, msLevelUnstableSortedList->spectrumIdentity(2).index);
183  unit_assert_operator_equal("scan=20", msLevelUnstableSortedList->spectrumIdentity(3).id);
184  unit_assert_operator_equal(3, msLevelUnstableSortedList->spectrumIdentity(3).index);
185  s = msLevelUnstableSortedList->spectrum(0);
186  unit_assert_operator_equal(0, s->index);
187  s = msLevelUnstableSortedList->spectrum(1);
188  unit_assert_operator_equal(1, s->index);
189  s = msLevelUnstableSortedList->spectrum(2);
190  unit_assert_operator_equal(2, s->index);
191  s = msLevelUnstableSortedList->spectrum(3);
192  unit_assert_operator_equal("scan=20", s->id);
193  unit_assert_operator_equal(3, s->index);
194 
195  // validate the MS level stable sorted list (scan=19, scan=21, and scan=22 should stay in order)
196  unit_assert_operator_equal("scan=19", msLevelStableSortedList->spectrumIdentity(0).id);
197  unit_assert_operator_equal(0, msLevelStableSortedList->spectrumIdentity(0).index);
198  unit_assert_operator_equal("scan=21", msLevelStableSortedList->spectrumIdentity(1).id);
199  unit_assert_operator_equal(1, msLevelStableSortedList->spectrumIdentity(1).index);
200  unit_assert_operator_equal("sample=1 period=1 cycle=23 experiment=1", msLevelStableSortedList->spectrumIdentity(2).id);
201  unit_assert_operator_equal(2, msLevelStableSortedList->spectrumIdentity(2).index);
202  unit_assert_operator_equal("scan=20", msLevelStableSortedList->spectrumIdentity(3).id);
203  unit_assert_operator_equal(3, msLevelStableSortedList->spectrumIdentity(3).index);
204  s = msLevelStableSortedList->spectrum(0);
205  unit_assert_operator_equal("scan=19", s->id);
206  unit_assert_operator_equal(0, s->index);
207  s = msLevelStableSortedList->spectrum(1);
208  unit_assert_operator_equal("scan=21", s->id);
209  unit_assert_operator_equal(1, s->index);
210  s = msLevelStableSortedList->spectrum(2);
211  unit_assert_operator_equal("sample=1 period=1 cycle=23 experiment=1", s->id);
212  unit_assert_operator_equal(2, s->index);
213  s = msLevelStableSortedList->spectrum(3);
214  unit_assert_operator_equal("scan=20", s->id);
215  unit_assert_operator_equal(3, s->index);
216 
217  // validate the silly (nested) sorted list
218  unit_assert_operator_equal("scan=21", sillySortedList->spectrumIdentity(0).id);
219  unit_assert_operator_equal(0, sillySortedList->spectrumIdentity(0).index);
220  unit_assert_operator_equal("scan=20", sillySortedList->spectrumIdentity(1).id);
221  unit_assert_operator_equal(1, sillySortedList->spectrumIdentity(1).index);
222  unit_assert_operator_equal(2, sillySortedList->spectrumIdentity(2).index);
223  unit_assert_operator_equal(3, sillySortedList->spectrumIdentity(3).index);
224  s = sillySortedList->spectrum(0);
225  unit_assert_operator_equal("scan=21", s->id);
226  unit_assert_operator_equal(0, s->index);
227  s = sillySortedList->spectrum(1);
228  unit_assert_operator_equal("scan=20", s->id);
229  unit_assert_operator_equal(1, s->index);
230  s = sillySortedList->spectrum(2);
231  unit_assert_operator_equal(2, s->index);
232  s = sillySortedList->spectrum(3);
233  unit_assert_operator_equal(3, s->index);
234  for (size_t i=1, end=sillySortedList->size(); i < end; ++i)
235  unit_assert(sillySortedList->spectrum(i)->defaultArrayLength >=
236  sillySortedList->spectrum(i-1)->defaultArrayLength);
237 }
238 
239 
240 int main(int argc, char* argv[])
241 {
242  TEST_PROLOG(argc, argv)
243 
244  try
245  {
246  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
247  test();
248  }
249  catch (exception& e)
250  {
251  TEST_FAILED(e.what())
252  }
253  catch (...)
254  {
255  TEST_FAILED("Caught unknown exception.")
256  }
257 
258  TEST_EPILOG
259 }
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