libpappsomspp
Library for mass spectrometry
massspectrumpluscombiner.cpp
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1 /////////////////////// StdLib includes
2 #include <numeric>
3 #include <limits>
4 #include <vector>
5 #include <map>
6 #include <cmath>
7 #include <iostream>
8 #include <iomanip>
9 
10 
11 /////////////////////// Qt includes
12 #include <QDebug>
13 #include <QFile>
14 #include <QThread>
15 #if 0
16 // For debugging purposes.
17 #include <QFile>
18 #endif
19 
20 
21 /////////////////////// Local includes
23 #include "../../types.h"
24 #include "../../utils.h"
25 #include "../../pappsoexception.h"
26 #include "../../exception/exceptionoutofrange.h"
27 #include "../../exception/exceptionnotpossible.h"
28 
29 
30 namespace pappso
31 {
32 
33 
34 //! Construct an uninitialized instance.
36 {
37 }
38 
39 
41  : MassSpectrumCombiner(decimal_places)
42 {
43 }
44 
45 
47  const MassSpectrumPlusCombiner &other)
48  : MassSpectrumCombiner(other)
49 
50 {
51 }
52 
53 
56  : MassSpectrumCombiner(other)
57 
58 {
59 }
60 
61 
62 //! Destruct the instance.
64 {
65 }
66 
67 
70 {
71  if(this == &other)
72  return *this;
73 
75 
76  m_bins.assign(other.m_bins.begin(), other.m_bins.end());
77 
78  return *this;
79 }
80 
81 
82 // We get a trace as parameter that this combiner needs to combine to the
83 // map_trace we also get as parameter. This combiner is for a mass spectrum, and
84 // thus it needs to have been configured to hold a vector of m/z values that are
85 // bins into which DataPoints from trace are combined into map_trace. It is the
86 // bins that drive the the traversal of trace. For each bin, check if there is
87 // (or are, if bins are big) data points in the trace that fit in it.
88 
89 MapTrace &
90 MassSpectrumPlusCombiner::combine(MapTrace &map_trace, const Trace &trace) const
91 {
92  // qDebug();
93 
94  // If there is no single point in the trace we need to combine into the
95  // map_trace, then there is nothing to do.
96  if(!trace.size())
97  {
98  // qDebug() << "Thread:" << QThread::currentThreadId()
99  //<< "Returning right away because trace is empty.";
100  return map_trace;
101  }
102 
103  // We will need to only use these iterator variables if we do not want to
104  // loose consistency.
105 
106  using TraceIter = std::vector<DataPoint>::const_iterator;
107  TraceIter trace_iter_begin = trace.begin();
108  TraceIter trace_iter = trace_iter_begin;
109  TraceIter trace_iter_end = trace.end();
110 
111  // The destination map trace will be filled-in with the result of the
112  // combination.
113 
114  // Sanity check:
115  if(!m_bins.size())
116  throw(ExceptionNotPossible("The bin vector cannot be empty."));
117 
118  using BinIter = std::vector<pappso_double>::const_iterator;
119 
120  BinIter bin_iter = m_bins.begin();
121  BinIter bin_end_iter = m_bins.end();
122 
123  // qDebug() << "initial bins iter at a distance of:"
124  //<< std::distance(m_bins.begin(), bin_iter)
125  //<< "bins distance:" << std::distance(m_bins.begin(), m_bins.end())
126  //<< "bins size:" << m_bins.size() << "first bin:" << m_bins.front()
127  //<< "last bin:" << m_bins.back();
128 
129  // Iterate in the vector of bins and for each bin check if there are matching
130  // data points in the trace.
131 
132  pappso_double current_bin_mz = 0;
133 
134  pappso_double trace_x = 0;
135  pappso_double trace_y = 0;
136 
137  // Lower bound returns an iterator pointing to the first element in the
138  // range [first, last) that is not less than (i.e. greater or equal to)
139  // value, or last if no such element is found.
140 
141  auto bin_iter_for_mz = lower_bound(bin_iter, bin_end_iter, trace_iter->x);
142 
143  if(bin_iter_for_mz != bin_end_iter)
144  {
145  if(bin_iter_for_mz != m_bins.begin())
146  bin_iter = --bin_iter_for_mz;
147  }
148  else
149  throw(ExceptionNotPossible("The bin vector must match the mz value."));
150 
151  while(bin_iter != bin_end_iter)
152  {
153  current_bin_mz = *bin_iter;
154 
155  // std::cout << std::setprecision(10) << "current bin: " << current_bin_mz
156  //<< std::endl;
157 
158  // qDebug() << "Current bin:"
159  //<< QString("%1").arg(current_bin_mz, 0, 'f', 15)
160  //<< "at a distance of:"
161  //<< std::distance(m_bins.begin(), bin_iter);
162 
163  // For the current bin, we start by instantiating a new DataPoint. By
164  // essence, each bin will have at most one corresponding DataPoint.
165 
166  DataPoint new_data_point;
167 
168  // Do not set the y value to 0 so that we can actually test if the
169  // data point is valid later on (try not to push back y=0 data
170  // points).
171  new_data_point.x = current_bin_mz;
172 
173  // Now perform a loop over the data points in the mass spectrum.
174 
175  // qDebug() << "Start looping in the trace to check if its DataPoint.x "
176  //"value matches that of the current bin."
177  //<< "trace_iter:" << trace_iter->toString()
178  //<< "data point distance:"
179  //<< std::distance(trace_iter_begin, trace_iter);
180 
181  while(trace_iter != trace_iter_end)
182  {
183  // std::cout << std::setprecision(10)
184  //<< "trace data point being iterated into: " << trace_iter->x
185  //<< " - " << trace_iter->y << std::endl;
186 
187  bool trace_matched = false;
188 
189  // If trace is not to the end and the y value is not 0
190  // apply the shift, perform the rounding and check if the obtained
191  // x value is in the current bin, that is if it is less or equal
192  // to the current bin.
193 
194  // qDebug() << "Thread:" << QThread::currentThreadId();
195  // qDebug() << "trace_iter:" << trace_iter->toString()
196  //<< "data point distance:"
197  //<< std::distance(trace_iter_begin, trace_iter);
198 
199  // if(!Utils::almostEqual(trace_iter->y, 0.0, 10))
200 
201  trace_x = trace_iter->x;
202  trace_y = trace_iter->y;
203 
204  if(trace_y)
205  {
206 
207  // FIXME: unbelievable behaviour: when building in release mode
208  // this code, under i386 (but not x86_64), this code fails if the
209  // following cout statement is missing. There are a variety of
210  // variants that work, the common denominator being that trace_x
211  // has to be output along with a string.
212 
213  // std::cout << std::setprecision(10)
214  //<< "iterated trace point: " << trace_x << " - "
215  //<< trace_y << std::endl;
216 
217  // For this reason I had to deactivate the related tests
218  // for i386 in tests/test_massspectrumcombiner.cpp
219 
220  // trace_x is the m/z value that we need to combine,
221  // so make sure we check if there is a mz shift to apply.
222 
223  // if(m_mzIntegrationParams.m_applyMzShift)
224  // trace_x += m_mzIntegrationParams.m_mzShift;
225 
226  // Now apply the rounding (if any).
227  if(m_decimalPlaces != -1)
228  trace_x = Utils::roundToDecimals(trace_x, m_decimalPlaces);
229 
230  if(trace_x <= current_bin_mz)
231  {
232 
233  // std::cout
234  //<< std::setprecision(10)
235  //<< "Matched, because trace point.x is <= the current "
236  //"bin; increment trace_iter"
237  //<< std::endl;
238 
239  new_data_point.y += trace_y;
240 
241  // std::cout << std::setprecision(10)
242  //<< "After incrementation of the intensity: "
243  //<< new_data_point.y << std::endl;
244 
245  // Let's record that we matched.
246  trace_matched = true;
247 
248  // Because we matched, we can step-up with the
249  // iterator.
250  ++trace_iter;
251  }
252  // else
253  //{
254  // We did have a non-0 y value, but that did not
255  // match. So we do not step-up with the iterator.
256  //}
257  }
258  // End of
259  // if(trace_iter->y)
260  else
261  {
262  // std::cout << std::setprecision(10)
263  //<< "itered trace point intensity is 0: " << trace_x
264  //<< " - " << trace_y << std::endl;
265 
266 
267  // We iterated into a y=0 data point, so just skip it. Let
268  // the below code think that we have matched the point and
269  // iterate one step up.
270 
271  // qDebug() << "The y value is almost equal to 0, increment the "
272  //"trace iter but do nothing else.";
273 
274  trace_matched = true;
275  ++trace_iter;
276  }
277  // At this point, check if none of them matched.
278 
279  if(!trace_matched)
280  {
281  // None of the first and trace mass spectra data
282  // points were found to match the current bin. All we
283  // have to do is go to the next bin. We break and the
284  // bin vector iterator will be incremented.
285 
286  // However, if we had a valid new data point, that
287  // data point needs to be pushed back in the new mass
288  // spectrum.
289 
290  if(new_data_point.isValid())
291  {
292 
293  // We need to check if that bin value is present already in
294  // the map_trace object passed as parameter.
295 
296  std::pair<std::map<pappso_double, pappso_double>::iterator,
297  bool>
298  result =
299  map_trace.insert(std::pair<pappso_double, pappso_double>(
300  new_data_point.x, new_data_point.y));
301 
302  if(!result.second)
303  {
304  // The key already existed! The item was not inserted. We
305  // need to update the value.
306 
307  result.first->second += new_data_point.y;
308 
309  // qDebug()
310  //<< "Incremented the data point in the map trace.";
311  }
312  // else
313  //{
314  // qDebug()
315  //<< "Inserted a new data point into the map trace.";
316  //}
317  }
318 
319  // We need to break this loop! That will increment the
320  // bin iterator.
321 
322  break;
323  }
324  }
325  // End of
326  // while(trace_iter != trace_iter_end)
327 
328  // Each time we get here, that means that we have consumed all
329  // the mass spectra data points that matched the current bin.
330  // So go to the next bin.
331 
332  if(trace_iter == trace_iter_end)
333  {
334 
335  // Make sure a last check is done in case one data point was
336  // cooking...
337 
338  if(new_data_point.isValid())
339  {
340 
341  std::pair<std::map<pappso_double, pappso_double>::iterator, bool>
342  result =
343  map_trace.insert(std::pair<pappso_double, pappso_double>(
344  new_data_point.x, new_data_point.y));
345 
346  if(!result.second)
347  {
348  result.first->second += new_data_point.y;
349  }
350  }
351 
352  // Now truly exit the loops...
353  break;
354  }
355 
356  ++bin_iter;
357  }
358  // End of
359  // while(bin_iter != bin_end_iter)
360 
361  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()"
362  //<< "The combination result mass spectrum being returned has TIC:"
363  //<< new_trace.sumY();
364 
365  return map_trace;
366 }
367 
368 
369 MapTrace &
371  const MapTrace &map_trace_in) const
372 {
373  // qDebug();
374 
375  if(!map_trace_in.size())
376  {
377  // qDebug() << "Thread:" << QThread::currentThreadId()
378  //<< "Returning right away because map_trace_in is empty.";
379  return map_trace_out;
380  }
381 
382  Trace trace(map_trace_in);
383 
384  return combine(map_trace_out, trace);
385 }
386 
387 
388 } // namespace pappso
389 
int m_decimalPlaces
Number of decimals to use for the keys (x values)
std::vector< pappso_double > m_bins
MassSpectrumPlusCombiner()
Construct an uninitialized instance.
virtual ~MassSpectrumPlusCombiner()
Destruct the instance.
virtual MapTrace & combine(MapTrace &map_trace, const Trace &trace) const override
MassSpectrumPlusCombiner & operator=(const MassSpectrumPlusCombiner &other)
A simple container of DataPoint instances.
Definition: trace.h:148
static pappso_double roundToDecimals(pappso_double value, int decimal_places)
Definition: utils.cpp:120
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
double pappso_double
A type definition for doubles.
Definition: types.h:49
std::shared_ptr< const MassSpectrumPlusCombiner > MassSpectrumPlusCombinerCstSPtr
pappso_double x
Definition: datapoint.h:23
bool isValid() const
Definition: datapoint.cpp:132
pappso_double y
Definition: datapoint.h:24