tandemparameters.cpp 12.6 KB
Newer Older
1
2
3
4
5
6
7
8
/**
 * \file /core/tandem_run/tandemparameters.cpp
 * \date 19/9/2017
 * \author Olivier Langella
 * \brief handles X!Tandem parameters
 */

/*******************************************************************************
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
 * Copyright (c) 2017 Olivier Langella <olivier.langella@u-psud.fr>.
 *
 * This file is part of XTPcpp.
 *
 *     XTPcpp is free software: you can redistribute it and/or modify
 *     it under the terms of the GNU General Public License as published by
 *     the Free Software Foundation, either version 3 of the License, or
 *     (at your option) any later version.
 *
 *     XTPcpp is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Olivier Langella <olivier.langella@u-psud.fr> - initial API and
 *implementation
 ******************************************************************************/
30
31

#include "tandemparameters.h"
32
#include <QDebug>
33
#include <pappsomspp/exception/exceptionnotfound.h>
Langella Olivier's avatar
Langella Olivier committed
34
#include <pappsomspp/exception/exceptionnotpossible.h>
35

36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
/*
 *
specific parameters for the modified TPP tandem version :
http://tools.proteomecenter.org/wiki/index.php?title=TPP:X%21Tandem_and_the_TPP

<note label="scoring, algorithm" type="input">k-score</note>
<note label="spectrum, use conditioning" type="input">no</note>
<note label="scoring, minimum ion count" type="input">1</note>
new labels :
"protein, taxon" https://www.thegpm.org/TANDEM/api/pt.html
"protein, homolog management"
"refine, sequence path" https://www.thegpm.org/TANDEM/api/rsp.html
 "refine, tic percent" https://www.thegpm.org/TANDEM/api/rtp.html
 "output, log path" https://www.thegpm.org/TANDEM/api/olp.html
 "output, message" https://www.thegpm.org/TANDEM/api/om.html
  "output, sequence path" https://www.thegpm.org/TANDEM/api/osp.html
   "output, path" https://www.thegpm.org/TANDEM/api/opath.html
Langella Olivier's avatar
Langella Olivier committed
53
54
55
56
57
  "protein, use annotations" https://www.thegpm.org/TANDEM/api/pua.html


   obsolete :
   "protein, use minimal annotations" yes no
58
59
*/

60
61
TandemParameters::TandemParameters()
{
62
}
63
64
TandemParameters::~TandemParameters()
{
65
66
}

67
68
69
70
71
TandemParameters::TandemParameters(const TandemParameters &other)
{
  qDebug() << "TandemParameters::TandemParameters copy begin";
  //_map_label_value = other._map_label_value;
  _method_name = other._method_name;
Olivier Langella's avatar
Olivier Langella committed
72

73
74
75
76
77
78
79
80
  QMap<QString, QString>::const_iterator i =
    other._map_label_value.constBegin();
  while(i != other._map_label_value.constEnd())
    {
      qDebug() << "TandemParameters::TandemParameters copy " << i.key() << " "
               << i.value();
      _map_label_value.insert(i.key(), i.value());
      i++; // added
Olivier Langella's avatar
Olivier Langella committed
81
    }
82
  qDebug() << "TandemParameters::TandemParameters copy end";
83
}
Langella Olivier's avatar
Langella Olivier committed
84
85


86
87
88
89
90
91
bool
TandemParameters::equals(const TandemParameters &other) const
{
  if(_method_name != other._method_name)
    {
      return false;
Langella Olivier's avatar
Langella Olivier committed
92
    }
93
94
95
  if(_map_label_value.size() != other._map_label_value.size())
    {
      return false;
Langella Olivier's avatar
Langella Olivier committed
96
    }
97
98
99
100
101
102
  QMap<QString, QString>::const_iterator i = _map_label_value.constBegin();
  while(i != _map_label_value.constEnd())
    {
      if(i.value() != other.getValue(i.key()))
        {
          return false;
Langella Olivier's avatar
Langella Olivier committed
103
        }
104
      i++; // added
Langella Olivier's avatar
Langella Olivier committed
105
    }
106
  return true;
Langella Olivier's avatar
Langella Olivier committed
107
108
}

109
110
111
const QString
TandemParameters::getLabelCategory(const QString &value) const
{
112
113
114

  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
           << value;
115
  return value.split(", ").at(0);
116
}
117
118
119
const QString &
TandemParameters::getValue(const QString &label) const
{
120
121
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
           << label;
122
123
124
125
  QMap<QString, QString>::const_iterator it = _map_label_value.constFind(label);
  if(it == _map_label_value.end())
    {
      throw pappso::ExceptionNotFound(
126
        QObject::tr("X!Tandem preset label \"%1\" not found in method \"%2\"")
127
128
          .arg(label)
          .arg(_method_name));
129
    }
130
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
131
  return it.value();
132
}
133
134
135
void
TandemParameters::setParamLabelValue(const QString &label, const QString &value)
{
136
137
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
           << label;
138
139
  // list path
  //<note type="input" label="list path, default
Langella Olivier's avatar
Langella Olivier committed
140
  // parameters">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/QExactive_analysis_FDR_nosemi.xml</note>
141
  //<note type="input" label="list path, taxonomy
Langella Olivier's avatar
Langella Olivier committed
142
  // information">/gorgone/pappso/tmp/temp_condor_job24872841484824316495370334631825647/database.xml</note>
143
144
145
  if(getLabelCategory(label) == "list path")
    {
      return;
146
    }
147

148
149
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
           << label;
150
151
152
  if((label == "spectrum, parent monoisotopic mass error units") ||
     (label == "spectrum, fragment monoisotopic mass error units"))
    {
153
      if((value != "Da") && (value != "Daltons") && (value != "ppm"))
154
155
        {
          throw pappso::ExceptionNotPossible(
156
            QObject::tr("\"%1\" value must be Daltons or ppm (not \"%2\")")
157
158
              .arg(label)
              .arg(value));
Langella Olivier's avatar
Langella Olivier committed
159
160
        }
    }
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
  else if((label == "spectrum, parent monoisotopic mass isotope error") ||
          (label == "spectrum, use neutral loss window") ||
          (label == "spectrum, use contrast angle") ||
          (label == "protein, cleavage semi") ||
          (label == "protein, quick acetyl") ||
          (label == "protein, quick pyrolidone") ||
          (label == "protein, stP bias") ||
          (label == "scoring, cyclic permutation") ||
          (label == "scoring, include reverse") ||
          (label == "scoring, y ions") || (label == "scoring, b ions") ||
          (label == "scoring, c ions") || (label == "scoring, z ions") ||
          (label == "scoring, a ions") || (label == "scoring, x ions") ||
          (label == "refine") ||
          (label ==
           "refine, use potential modifications for full refinement") ||
          (label == "refine, cleavage semi") ||
          (label == "refine, unanticipated cleavage") ||
          (label == "refine, spectrum synthesis") ||
          (label == "refine, point mutations") || (label == "output, mzid") ||
          (label == "output, spectra") || (label == "output, proteins") ||
          (label == "output, sequences") ||
          (label == "output, one sequence copy") ||
          (label == "output, parameters") || (label == "output, performance") ||
          (label == "output, histograms") ||
          (label == "output, path hashing") ||
186
187
          (label == "spectrum, use noise suppression") ||
          (label == "spectrum, use conditioning") ||
Langella Olivier's avatar
Langella Olivier committed
188
189
190
          (label == "protein, homolog management") ||
          (label == "protein, use minimal annotations") ||
          (label == "protein, use annotations"))
191
192
193
194
195
196
197
    {
      if((value != "yes") && (value != "no"))
        {
          throw pappso::ExceptionNotPossible(
            QObject::tr("%1 value must be yes or no (not %2)")
              .arg(label)
              .arg(value));
Langella Olivier's avatar
Langella Olivier committed
198
199
        }
    }
Langella Olivier's avatar
Langella Olivier committed
200

201
202
203
204
205
206
207
208
209
210
211
212
213
214
  else if((label == "spectrum, parent monoisotopic mass error minus") ||
          (label == "spectrum, parent monoisotopic mass error plus") ||
          (label == "spectrum, dynamic range") ||
          (label == "spectrum, minimum parent m+h") ||
          (label == "protein, cleavage C-terminal mass change") ||
          (label == "protein, cleavage N-terminal mass change") ||
          (label == "protein, C-terminal residue modification mass") ||
          (label == "protein, N-terminal residue modification mass") ||
          (label == "refine, maximum valid expectation value") ||
          (label == "spectrum, fragment monoisotopic mass error") ||
          (label == "spectrum, neutral loss mass") ||
          (label == "spectrum, neutral loss window") ||
          (label == "spectrum, minimum fragment mz") ||
          (label == "output, maximum valid expectation value") ||
215
216
          (label == "output, maximum valid protein expectation value") ||
          (label == "refine, tic percent")
217
218
219


  )
Langella Olivier's avatar
Langella Olivier committed
220

221
    {
222

223
      bool ok;
224
225
226
227
228
229
      QString value_bis = value.simplified();
      if(value_bis.isEmpty())
        {
          value_bis = "0.0";
        }
      value_bis.toDouble(&ok);
230
231
232
      if(!ok)
        { // not an integer
          throw pappso::ExceptionNotPossible(
233
            QObject::tr("\"%1\" value must be a number (not \"%2\")")
234
235
              .arg(label)
              .arg(value));
Langella Olivier's avatar
Langella Olivier committed
236
237
        }
    }
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
  else if((label == "protein, cleavage site") ||
          (label == "protein, modified residue mass file") ||
          (label == "residue, modification mass") ||
          (label == "residue, modification mass 1") ||
          (label == "residue, modification mass 2") ||
          (label == "residue, potential modification mass") ||
          (label == "residue, potential modification mass 1") ||
          (label == "residue, potential modification mass 2") ||
          (label == "residue, potential modification motif") ||
          (label == "residue, potential modification motif 1") ||
          (label == "residue, potential modification motif 2") ||
          (label == "refine, potential N-terminus modifications") ||
          (label == "refine, potential C-terminus modifications") ||
          (label == "refine, modification mass") ||
          (label == "refine, modification mass 1") ||
          (label == "refine, modification mass 2") ||
          (label == "refine, potential modification mass") ||
          (label == "refine, potential modification mass 1") ||
          (label == "refine, potential modification mass 2") ||
          (label == "refine, potential modification motif") ||
          (label == "refine, potential modification motif 1") ||
          (label == "refine, potential modification motif 2") ||
          (label == "output, sort results by") ||
261
262
263
264
265
          (label == "output, xsl path") || (label == "spectrum, path") ||
          (label == "scoring, algorithm") || (label == "protein, taxon") ||
          (label == "refine, sequence path") || (label == "output, log path") ||
          (label == "output, message") || (label == "output, sequence path") ||
          (label == "output, path"))
266
267
268
269
270
271
272
273
274
    {
      // string
    }
  else if((label == "spectrum, maximum parent charge") ||
          (label == "spectrum, total peaks") ||
          (label == "spectrum, minimum peaks") ||
          (label == "spectrum, sequence batch size") ||
          (label == "spectrum, threads") ||
          (label == "scoring, minimum ion count") ||
275
          (label == "scoring, maximum missed cleavage sites") ||
276
          (label == "output, histogram column width"))
277
    {
278

279
280
281
282
283
      bool ok;
      value.toInt(&ok);
      if(!ok)
        { // not an integer
          throw pappso::ExceptionNotPossible(
284
            QObject::tr("\"%1\" value must be an integer (not \"%2\")")
285
286
              .arg(label)
              .arg(value));
Langella Olivier's avatar
Langella Olivier committed
287
288
        }
    }
289
  else if(label == "spectrum, fragment mass type")
290
291
292
293
    {
      if((value != "monoisotopic") && (value != "average"))
        {
          throw pappso::ExceptionNotPossible(
294
295
            QObject::tr(
              "\"%1\" value must be monoisotopic or average (not \"%2\")")
296
297
              .arg(label)
              .arg(value));
Langella Olivier's avatar
Langella Olivier committed
298
299
        }
    }
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
  // tandem input parameter label "output, results" for value "valid" not known.

  else if(label == "output, results")
    {
      /*
    if((value != "all") && (value != "valid"))
      {
        throw pappso::ExceptionNotPossible(
          QObject::tr("\"%1\" value must be valid or all (not \"%2\")")
            .arg(label)
            .arg(value));
      }
      */
    }
  else
    {

      throw pappso::ExceptionNotPossible(
        QObject::tr(
          "tandem input parameter label \"%1\" for value \"%2\" not known.")
          .arg(label)
          .arg(value));
    }

Langella Olivier's avatar
Langella Olivier committed
324

325
326
327
328
329
  // text "protein, cleavage site" "protein, modified residue mass file"
  // "residue, modification mass"  || (label == "refine, potential N-terminus
  // modifications") || (label == "refine, potential C-terminus modifications")
  // spectrum, neutral loss mass
  // spectrum, neutral loss window
330
331
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
           << label;
332
  _map_label_value.insert(label, value);
333
334
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
           << label;
335
}
336
337
338
339
void
TandemParameters::setMethodName(const QString &method)
{
  _method_name = method;
340
}
341
342
343
344
const QString &
TandemParameters::getMethodName() const
{
  return _method_name;
345
}
346
347
348
349
const QMap<QString, QString> &
TandemParameters::getMapLabelValue() const
{
  return _map_label_value;
350
}