changelog 25 KB
Newer Older
Langella Olivier's avatar
Langella Olivier committed
1
2
3
4
5
6
xtpcpp (0.4.8-1) buster; urgency=medium

  * fix for issues masschroqml, ptm island view

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 02 Nov 2020 11:10:53 +0100

Langella Olivier's avatar
Langella Olivier committed
7
8
9
10
11
12
xtpcpp (0.4.7-1) buster; urgency=medium

  * deep refactoring concerning msrun statistics

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 15 Oct 2020 16:48:37 +0200

Langella Olivier's avatar
Langella Olivier committed
13
14
15
16
17
18
19
xtpcpp (0.4.6-1) buster; urgency=medium

  * mfg support for timsdata temporarily removed
  * more checks tandemwrapper run

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 09 Oct 2020 16:07:27 +0200

Langella Olivier's avatar
Langella Olivier committed
20
21
22
23
24
25
26
xtpcpp (0.4.5-1) buster; urgency=medium

  * alginment GUI stuff
  * timstof support

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 08 Oct 2020 11:35:20 +0200

Langella Olivier's avatar
Langella Olivier committed
27
28
29
30
31
32
xtpcpp (0.4.4-6) buster; urgency=medium

  * new fix for issue #31

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 01 Oct 2020 10:07:36 +0200

33
34
35
36
37
38
xtpcpp (0.4.4-5) buster; urgency=medium

  * new point mutation notation feature fix #32

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 29 Sep 2020 16:24:05 +0200

Langella Olivier's avatar
Langella Olivier committed
39
40
41
42
43
44
xtpcpp (0.4.4-4) buster; urgency=medium

  * fix for issue #31

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 28 Sep 2020 10:20:55 +0200

45
46
47
48
49
50
xtpcpp (0.4.4-3) buster; urgency=medium

  * new package to fix issue #31

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 24 Sep 2020 16:05:03 +0200

Langella Olivier's avatar
Langella Olivier committed
51
52
53
54
55
56
xtpcpp (0.4.4-2) buster; urgency=medium

  * new package to fix issue #31

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 24 Sep 2020 15:20:04 +0200

57
58
59
60
61
62
xtpcpp (0.4.4-1) buster; urgency=medium

  * maximum number of file reached, test for issue #31

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 24 Sep 2020 13:21:31 +0200

Langella Olivier's avatar
Langella Olivier committed
63
64
65
66
67
68
xtpcpp (0.4.3-1) buster; urgency=medium

  * fix for issue #28 : new column in PTM tables and exports to count spectra bearing modifications

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 16 Sep 2020 10:55:19 +0200

Langella Olivier's avatar
Langella Olivier committed
69
70
71
72
73
74
xtpcpp (0.4.2-1) buster; urgency=medium

  * fix for issue #26 : bug in compar specific unique sequence sheet

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 02 Sep 2020 09:14:53 +0200

Langella Olivier's avatar
Langella Olivier committed
75
76
77
78
79
80
81
82
83
84
xtpcpp (0.4.1-1) buster; urgency=medium

  * better PTM support
  * no tims preset required
  * boost not needed
  * loss of mzIdentML support
  * export chemical formula in masschroqML output

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 22 Jul 2020 16:53:04 +0200

Langella Olivier's avatar
Langella Olivier committed
85
86
87
88
89
90
xtpcpp (0.4.0-2) buster; urgency=medium

  * display all digits of XIC areas

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 08 Jun 2020 17:59:22 +0200

Langella Olivier's avatar
Langella Olivier committed
91
92
93
94
95
96
xtpcpp (0.4.0-1) buster; urgency=medium

  * fixed issue #23

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 29 May 2020 16:58:10 +0200

Langella Olivier's avatar
Langella Olivier committed
97
98
99
100
101
102
103
xtpcpp (0.3.9-2) buster; urgency=medium

  * fix issue #22
  * no more dependency with libpwiz and libboost

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 28 May 2020 09:46:44 +0200

Langella Olivier's avatar
Langella Olivier committed
104
105
106
107
108
109
xtpcpp (0.3.9-1) buster; urgency=medium

  * lots of improvements made by Thomas Renne

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 19 May 2020 16:25:15 +0200

110
111
112
113
114
115
xtpcpp (0.3.8-1) unreleased; urgency=low

  * New upstream version. Packaging tweaks.

 -- Filippo Rusconi <lopippo@debian.org>  Mon, 04 May 2020 11:37:03 +0200

Langella Olivier's avatar
Langella Olivier committed
116
117
118
119
120
121
122
xtpcpp (0.3.7-3) buster; urgency=medium

  * no console in windows version
  * pseudo centroid for tandem wrapper

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 20 Apr 2020 08:31:29 +0200

Langella Olivier's avatar
Langella Olivier committed
123
124
125
126
127
128
xtpcpp (0.3.7-2) buster; urgency=medium

  * important fix in lib PAPPSOms++

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sun, 12 Apr 2020 17:14:51 +0200

Langella Olivier's avatar
Langella Olivier committed
129
130
131
132
133
134
135
136
137
xtpcpp (0.3.7-1) buster; urgency=medium

  * allow column move (peptide list, protein list, ptm list, ptm peptide list)
  * edition of centroid parameters in tandem settings for tims tof reader
  * defining alignment groups
  * cross compilation with MXE

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 10 Apr 2020 22:05:08 +0200

Langella Olivier's avatar
Langella Olivier committed
138
139
140
141
142
143
xtpcpp (0.3.6-1) buster; urgency=medium

  * timstof support

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 04 Mar 2020 16:59:21 +0100

144
145
146
147
148
149
xtpcpp (0.3.5-1ubuntu1) bionic; urgency=medium

  * tandem error messages

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 10 Feb 2020 10:58:19 +0100

Langella Olivier's avatar
Langella Olivier committed
150
151
152
153
154
155
156
xtpcpp (0.3.4-1) buster; urgency=medium

  * several issues fixed by Thomas Renne
  * mascot dat parser work

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 29 Jan 2020 10:22:48 +0100

Langella Olivier's avatar
Langella Olivier committed
157
158
159
160
161
162
xtpcpp (0.3.3-1) buster; urgency=medium

  * new spreadsheet output for PSMs

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 14 Jan 2020 10:33:42 +0100

163
164
165
166
167
168
xtpcpp (0.3.2-2ubuntu1) bionic; urgency=medium

  * ubuntu 18.04 package 

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 10 Jan 2020 22:39:39 +0000

Langella Olivier's avatar
Langella Olivier committed
169
170
171
172
173
174
xtpcpp (0.3.2-2) buster; urgency=medium

  * new pappsoms++ library

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 08 Jan 2020 22:22:40 +0100

Langella Olivier's avatar
Langella Olivier committed
175
176
177
178
179
180
181
xtpcpp (0.3.2-1) buster; urgency=medium

  * better ms run identification view
  * prapagation of the project name

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 06 Jan 2020 11:26:14 +0100

Langella Olivier's avatar
Langella Olivier committed
182
183
184
185
186
187
xtpcpp (0.3.1-3) buster; urgency=medium

  * bunch of little bug fix

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 20 Dec 2019 14:21:34 +0100

Langella Olivier's avatar
Langella Olivier committed
188
189
190
191
192
193
xtpcpp (0.3.1-2) buster; urgency=medium

  * merge of latest changes from forge mia

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 19 Dec 2019 22:34:59 +0100

Langella Olivier's avatar
Langella Olivier committed
194
195
196
197
198
xtpcpp (0.3.1-1) buster; urgency=medium

  * new features coded by Thomas Renne
  * new msrun list windows
  * instant msrun statistics
Langella Olivier's avatar
Langella Olivier committed
199
  * many GUI  fix
Langella Olivier's avatar
Langella Olivier committed
200
201
202

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 19 Dec 2019 22:26:05 +0100

Langella Olivier's avatar
Langella Olivier committed
203
204
205
206
207
208
xtpcpp (0.2.40-2) buster; urgency=medium

  * buster package

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 12 Sep 2019 20:25:49 +0200

Langella Olivier's avatar
Langella Olivier committed
209
210
211
212
213
214
215
216
217
218
xtpcpp (0.2.40-1) stretch; urgency=medium

  * find spectrum directly by index if scan numbers are not supported
  * MassChroqML output without peptide labels in comments
  * new UI to choose removal contaminant mode
  * new FDR computation : decoy/target
  * FDR driven peptide theshold, available for Tandem and Mascot results

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 12 Sep 2019 09:10:45 +0200

Langella Olivier's avatar
Langella Olivier committed
219
220
221
222
223
224
xtpcpp (0.2.38-4) stretch; urgency=medium

  * scoring, pluggable scoring added

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 18 Jun 2019 13:37:52 +0200

Langella Olivier's avatar
Langella Olivier committed
225
226
227
228
229
230
xtpcpp (0.2.38-3) stretch; urgency=medium

  * refine, maximum missed cleavage sites added

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 18 Jun 2019 13:28:02 +0200

Langella Olivier's avatar
Langella Olivier committed
231
232
233
234
235
236
xtpcpp (0.2.38-2) stretch; urgency=medium

  * protein, use minimal annotation parameter added

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 18 Jun 2019 11:43:37 +0200

Langella Olivier's avatar
Langella Olivier committed
237
238
239
240
241
242
243
244
245
xtpcpp (0.2.38-1) stretch; urgency=medium

  * new button to look for the best MS run to use as reference in alignment
  * accepts to run TPP modified version of X!Tandem, using specific parameters
  (DIA requirements)
  * new PAPPSOms++ library

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 17 Jun 2019 13:53:16 +0200

Langella Olivier's avatar
Langella Olivier committed
246
247
248
249
250
251
xtpcpp (0.2.37-2) stretch; urgency=medium

  * sum/max extraction bug fixed, thanks to Marlène and Thierry

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 28 May 2019 16:06:10 +0200

Langella Olivier's avatar
Langella Olivier committed
252
253
254
255
256
257
xtpcpp (0.2.37-1) stretch; urgency=medium

  * new PAPPSOms++ library

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 24 May 2019 11:53:47 +0200

Langella Olivier's avatar
Langella Olivier committed
258
259
260
261
262
263
264
265
xtpcpp (0.2.36-1) stretch; urgency=medium

  * proticdbml fix
  * new tandem.exe setup control
  * better error message for tandem run process

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 16 Apr 2019 15:03:10 +0200

Langella Olivier's avatar
Langella Olivier committed
266
267
268
269
270
271
xtpcpp (0.2.35-2) stretch; urgency=medium

  * fix libodsstream problem

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 25 Mar 2019 11:27:19 +0100

Langella Olivier's avatar
Langella Olivier committed
272
273
274
275
276
277
278
xtpcpp (0.2.35-1) stretch; urgency=medium

  * mutation support
  * peprepro filter

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 25 Mar 2019 10:46:03 +0100

Langella Olivier's avatar
Langella Olivier committed
279
280
281
282
283
284
xtpcpp (0.2.34-2) stretch; urgency=medium

  * fix filename bug

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 19 Mar 2019 08:53:24 +0100

Langella Olivier's avatar
Langella Olivier committed
285
286
287
288
289
290
291
292
293
294
295
296
297
xtpcpp (0.2.34-1) stretch; urgency=medium

  * fix ppm range in MassChroqML export (thanks to Thierry Balliau)
  * new features asked by Plateforme Post-génomique de la Pitié Salpétrière - P3S 
  (Solenne Chardonnet, Cédric Pionneau)
  * write protein list view as is in ODS file
  * write peptide list view as is in ODS file
  * new ui menu in peptide and protein list wiew
  * ppm delta added in ODS spectra sheet export
  * display Nter and Cter peptide flanking regions in ODS and list views

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 18 Mar 2019 11:06:11 +0100

Langella Olivier's avatar
Langella Olivier committed
298
299
300
301
302
303
304
305
306
307
xtpcpp (0.2.33-1) stretch; urgency=medium

  * scroll area for small screens
  * xic extraction method (sum or max)
  * resilient ODS on failure
  * global settings windows
  * xic extractor reader choice

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 25 Feb 2019 13:29:57 +0100

Langella Olivier's avatar
Langella Olivier committed
308
309
310
311
312
313
314
xtpcpp (0.2.32-1) stretch; urgency=medium

  * moving to refactored PAPPSOms++ library
  * bug fixed in FASTA exports

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 06 Feb 2019 11:48:02 +0100

Langella Olivier's avatar
Langella Olivier committed
315
316
317
318
319
320
xtpcpp (0.2.31-2) stretch; urgency=medium

  * user agent created, variable to disable htpp get version

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 01 Feb 2019 14:36:56 +0100

Langella Olivier's avatar
Langella Olivier committed
321
322
323
324
325
326
327
xtpcpp (0.2.31-1) stretch; urgency=medium

  * new Fasta file exports by groups and subgroups
  * better MassChroqML output : check MS run file paths, set output result files, set alignment/xic exctraction/peak detection parameters

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 28 Jan 2019 15:13:20 +0100

Langella Olivier's avatar
Langella Olivier committed
328
329
330
331
332
333
334
xtpcpp (0.2.30-1) stretch; urgency=medium

  * new ODS spreadsheet dedicated to peptidomic : comparison of the
    number of spectra for each peptide in each sample

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 14 Jan 2019 10:43:00 +0100

Langella Olivier's avatar
Langella Olivier committed
335
336
337
338
339
340
xtpcpp (0.2.29-4) stretch; urgency=medium

  * new PAPPSOms++ library

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 08 Jan 2019 16:19:34 +0100

Langella Olivier's avatar
Langella Olivier committed
341
342
343
344
345
346
347
348
349
350
351
352
353
xtpcpp (0.2.29-3) stretch; urgency=medium

  * new pappsomspp library

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 02 Jan 2019 21:52:00 +0100

xtpcpp (0.2.29-1) stretch; urgency=medium

  * modification to be qcustomplot 2.0.1 compliant
  * accept labeling method containing an empty label

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sat, 15 Dec 2018 16:51:44 +0100

Langella Olivier's avatar
Langella Olivier committed
354
355
356
357
358
359
360
xtpcpp (0.2.28-3) stretch; urgency=medium

  * mascot takes all query candidates
  * fix thread wait loading spectrum

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 07 Dec 2018 10:44:46 +0100

Langella Olivier's avatar
Langella Olivier committed
361
362
363
364
365
366
xtpcpp (0.2.28-2) stretch; urgency=medium

  * take only first spectrum psm in mascot parser

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 27 Nov 2018 09:21:43 +0100

367
368
369
370
371
372
373
374
375
376
xtpcpp (0.2.28-1) stretch; urgency=medium

  * improved mascot dat parser
  * ability to choose TSV as export file format
  * icon added for Windows
  * more checks on tandem binary path
  * dependency added on package tandem-mass

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 26 Nov 2018 15:29:21 +0100

Langella Olivier's avatar
Langella Olivier committed
377
378
379
380
381
382
xtpcpp (0.2.27-1) stretch; urgency=medium

  * look for sequence LI

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 13 Nov 2018 14:58:53 +0100

Langella Olivier's avatar
Langella Olivier committed
383
384
385
386
387
388
xtpcpp (0.2.26-1) stretch; urgency=medium

  * display distinctively the FDR on peptides and on PSM

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 09 Nov 2018 10:50:11 +0100

Langella Olivier's avatar
Langella Olivier committed
389
390
391
392
393
394
xtpcpp (0.2.25-2) stretch; urgency=medium

  * new version number 0.2.25

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 02 Nov 2018 15:31:01 +0100

Langella Olivier's avatar
Langella Olivier committed
395
396
397
398
399
400
401
402
403
404
xtpcpp (0.2.25-1) stretch; urgency=medium

  * mascot parser fix for single fasta file
  * protein mass including alanine
  * X!Tandem version check
  * FDR written as percentage in ODS files
  * compute peptide FDR directly on peptides (no protein validation)

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 02 Nov 2018 14:26:19 +0100

Langella Olivier's avatar
Langella Olivier committed
405
406
407
408
409
410
xtpcpp (0.2.24-3) stretch; urgency=medium

  * fix for temporary directory under condor

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 29 Oct 2018 11:14:33 +0100

Langella Olivier's avatar
Langella Olivier committed
411
412
413
414
415
416
xtpcpp (0.2.24-2) stretch; urgency=medium

  * ODS output fix

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 19 Oct 2018 16:57:33 +0200

Langella Olivier's avatar
Langella Olivier committed
417
418
419
420
421
422
423
xtpcpp (0.2.24-1) stretch; urgency=medium

  * new compar ODS output dedicated to labeled experiments
  * SEVERE bug fix concerning protein Evalue computation (reported by T. Balliau) 

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 19 Oct 2018 16:13:10 +0200

Langella Olivier's avatar
Langella Olivier committed
424
425
426
427
428
429
xtpcpp (0.2.23-2) stretch; urgency=medium

  * fix version number

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 16 Oct 2018 11:13:36 +0200

Langella Olivier's avatar
Langella Olivier committed
430
431
432
433
434
435
436
437
xtpcpp (0.2.23-1) stretch; urgency=medium

  * checking tandem.exe installation
  * new controls to select decoy sequences and avoid bug signaled by C. Henry and T. Balliau
  * new temporary folder handler for HTCondor jobs 

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 16 Oct 2018 10:57:47 +0200

Langella Olivier's avatar
Langella Olivier committed
438
439
440
441
442
443
xtpcpp (0.2.22-3) stretch; urgency=medium

  * major mzIdentML improvements for MS-GF+

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 03 Oct 2018 22:32:56 +0200

Langella Olivier's avatar
Langella Olivier committed
444
445
446
447
448
449
xtpcpp (0.2.22-2) stretch; urgency=medium

  * minor fix

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 03 Oct 2018 11:08:30 +0200

Langella Olivier's avatar
Langella Olivier committed
450
451
452
453
454
455
456
457
458
459
xtpcpp (0.2.22-1) stretch; urgency=medium

  * better Mascot parser
  * new placeholder for contaminant widget
  * refresh evalue when choosing threshold
  * display contaminant checkbox in protein view
  * release MSrun after reading

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 02 Oct 2018 13:56:06 +0200

Langella Olivier's avatar
Langella Olivier committed
460
461
462
463
464
465
xtpcpp (0.2.21-4) stretch; urgency=medium

  * make sure that we look for MSrun in the right place

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 03 Sep 2018 16:29:47 +0200

Langella Olivier's avatar
Langella Olivier committed
466
467
468
469
470
471
xtpcpp (0.2.21-3) stretch; urgency=medium

  * smart file path guess

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 31 Aug 2018 11:49:39 +0200

Langella Olivier's avatar
Langella Olivier committed
472
473
474
475
476
477
478
xtpcpp (0.2.21-2) stretch; urgency=medium

  * gui text fix (proteins => peptides)
  * find readable msRun file

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 29 Aug 2018 09:26:21 +0200

Langella Olivier's avatar
Langella Olivier committed
479
480
481
482
483
484
xtpcpp (0.2.21-1) stretch; urgency=medium

  * ODS column consistency checked, more auto documentation

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 17 Aug 2018 13:51:19 +0200

485
486
487
488
489
490
xtpcpp (0.2.20-1) stretch; urgency=medium

  * TIC columns added in ODS report

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 13 Jul 2018 09:31:03 +0200

Langella Olivier's avatar
Langella Olivier committed
491
492
493
494
495
496
497
xtpcpp (0.2.19-1) stretch; urgency=medium

  * fix in mzidentml reader and pepxml reader to be able to load files
    from MSfragger

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 09 Jul 2018 13:36:40 +0200

Langella Olivier's avatar
Langella Olivier committed
498
499
500
501
502
503
504
505
506
xtpcpp (0.2.18-1) stretch; urgency=medium

  * pepxml support
  * XPIP change : each peptide is related has is own identification engine id
  * better xic extractor cache by msrun
  * possibility to display specific identification engine attributes (omssa, comet,msgf+...)

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 05 Jul 2018 13:50:31 +0200

Langella Olivier's avatar
Langella Olivier committed
507
508
509
510
511
512
513
514
xtpcpp (0.2.17-1) stretch; urgency=medium

  * new window to edit detection parameters
  * new PAPPSO library API to 
    read MS run files

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sat, 02 Jun 2018 18:09:53 +0200

Langella Olivier's avatar
Langella Olivier committed
515
516
517
518
519
520
xtpcpp (0.2.16-3) stretch; urgency=medium

  * fix masschroq out put msrun reference

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sat, 26 May 2018 07:05:21 +0200

Langella Olivier's avatar
Langella Olivier committed
521
522
523
524
525
526
xtpcpp (0.2.16-2) stretch; urgency=medium

  * falling back to simple pwiz xic extractor

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sat, 26 May 2018 06:47:15 +0200

Langella Olivier's avatar
Langella Olivier committed
527
528
529
530
531
532
xtpcpp (0.2.16-1) stretch; urgency=medium

  * new buffered XIC extractor

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 25 May 2018 09:08:47 +0200

Langella Olivier's avatar
Langella Olivier committed
533
534
535
536
537
538
xtpcpp (0.2.15-2) stretch; urgency=medium

  * lib pappsomspp change

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 17 May 2018 22:18:27 +0200

Langella Olivier's avatar
Langella Olivier committed
539
540
541
542
543
544
545
xtpcpp (0.2.15-1) stretch; urgency=medium

  * new xic extractor API, spectral count export fallback, compar bug
    fixed

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 16 May 2018 11:36:53 +0200

Langella Olivier's avatar
Langella Olivier committed
546
547
548
549
550
551
xtpcpp (0.2.14-2) stretch; urgency=medium

  * avoid libodsstream bug in compar sheets

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 14 May 2018 13:01:39 +0200

Langella Olivier's avatar
Langella Olivier committed
552
553
554
555
556
557
xtpcpp (0.2.14-1) stretch; urgency=medium

  * NSAF compar export

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 04 May 2018 09:14:35 +0200

Langella Olivier's avatar
Langella Olivier committed
558
559
560
561
562
563
xtpcpp (0.2.13-1) stretch; urgency=medium

  * XIC peak borders

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 16 Apr 2018 13:34:17 +0200

Langella Olivier's avatar
Langella Olivier committed
564
565
566
567
568
569
xtpcpp (0.2.12-2) stretch; urgency=medium

  * ppm delta bug fix

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 28 Mar 2018 10:55:01 +0200

Langella Olivier's avatar
Langella Olivier committed
570
571
572
573
574
575
xtpcpp (0.2.12-1) stretch; urgency=medium

  * GUI improvements

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 26 Mar 2018 16:14:42 +0200

Langella Olivier's avatar
Langella Olivier committed
576
577
578
579
580
581
582
xtpcpp (0.2.11-1) stretch; urgency=medium

  * MASCOT dat parser
  * contaminant widget

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 13 Mar 2018 16:01:10 +0100

Langella Olivier's avatar
Langella Olivier committed
583
584
585
586
587
588
xtpcpp (0.2.10-4) stretch; urgency=medium

  * bug fix when no peak has been detected for a peptide

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 14 Feb 2018 10:20:28 +0100

Langella Olivier's avatar
Langella Olivier committed
589
590
591
592
593
594
xtpcpp (0.2.10-3) stretch; urgency=medium

  * new PAPPSOms++ library

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 12 Feb 2018 16:45:57 +0100

Langella Olivier's avatar
Langella Olivier committed
595
596
597
598
599
600
xtpcpp (0.2.10-2) stretch; urgency=medium

  * fix library package name

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sun, 11 Feb 2018 18:08:26 +0100

Langella Olivier's avatar
Langella Olivier committed
601
602
603
604
605
606
xtpcpp (0.2.10-1) stretch; urgency=medium

  * better UI and XIC viewer

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sun, 11 Feb 2018 08:02:37 +0100

Langella Olivier's avatar
Langella Olivier committed
607
xtpcpp (0.2.9-2) stretch; urgency=medium
Langella Olivier's avatar
Langella Olivier committed
608
609
610
611
612

  * extract XIC in other MS runs

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 29 Jan 2018 09:53:12 +0100

Langella Olivier's avatar
Langella Olivier committed
613
614
615
616
617
618
xtpcpp (0.2.8-1) stretch; urgency=medium

  * better PTM island mode

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 25 Jan 2018 10:06:17 +0100

Langella Olivier's avatar
Langella Olivier committed
619
620
621
622
623
624
xtpcpp (0.2.7-1) stretch; urgency=medium

  * bug fixed on long protein label with reversed sequences

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 23 Jan 2018 15:57:47 +0100

Langella Olivier's avatar
Langella Olivier committed
625
626
627
628
629
630
xtpcpp (0.2.6-1) stretch; urgency=medium

  * new XIC viewer

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 18 Jan 2018 16:28:07 +0100

Langella Olivier's avatar
Langella Olivier committed
631
xtpcpp (0.2.5-2) stretch; urgency=medium
Langella Olivier's avatar
Langella Olivier committed
632
633
634
635
636

  * disable warning message in xpip export

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 10 Jan 2018 16:19:17 +0100

Langella Olivier's avatar
Langella Olivier committed
637
638
639
640
641
642
xtpcpp (0.2.5-1) stretch; urgency=medium

  * search on msrun and scan, better individual mode, better widgets

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 10 Jan 2018 14:50:52 +0100

Langella Olivier's avatar
Langella Olivier committed
643
644
645
646
647
648
xtpcpp (0.2.4-1) stretch; urgency=medium

  * new peptide widget

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 03 Jan 2018 11:44:36 +0100

Langella Olivier's avatar
Langella Olivier committed
649
650
651
652
653
654
xtpcpp (0.2.3-2) stretch; urgency=medium

  * new mass delta, new FDR, new histogram

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 20 Dec 2017 11:20:52 +0100

Langella Olivier's avatar
Langella Olivier committed
655
656
657
658
659
660
xtpcpp (0.2.3-1) stretch; urgency=medium

  * better FDR and mass delta computing

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sun, 17 Dec 2017 18:19:11 +0100

Langella Olivier's avatar
Langella Olivier committed
661
662
663
664
665
666
xtpcpp (0.2.2-2) stretch; urgency=medium

  * new pappsomspp library

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 15 Dec 2017 11:38:38 +0100

Langella Olivier's avatar
Langella Olivier committed
667
668
669
670
671
672
xtpcpp (0.2.2-1) stretch; urgency=medium

  * better xpip format input and output

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 04 Dec 2017 10:54:31 +0100

Langella Olivier's avatar
Langella Olivier committed
673
674
675
676
677
678
679
680
xtpcpp (0.2.1-1) stretch; urgency=medium

  * huge refactoring
  * new xpip output file
  * clear mz file list in tandem run dialog

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 22 Nov 2017 15:56:02 +0100

Langella Olivier's avatar
Langella Olivier committed
681
682
683
684
685
686
687
688
xtpcpp (0.1.23-1) stretch; urgency=medium

  * better ODS and XPIP file
  * compute mass and number of tryptic
    peptides on non regular protein sequences

 -- Olivier Langella <olivier.langella@u-psud.fr>  Wed, 15 Nov 2017 12:57:36 +0100

Langella Olivier's avatar
Langella Olivier committed
689
690
691
692
693
694
xtpcpp (0.1.22-2) stretch; urgency=medium

  * HTCondor parameter edition

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 06 Nov 2017 08:44:17 +0100

Langella Olivier's avatar
Langella Olivier committed
695
696
697
698
699
700
701
702
703
xtpcpp (0.1.22-1) stretch; urgency=medium

  * new buttons in central widget
  * xpip file creation
  * tandem parameters added
  * avoid non amino acid chars in tryptic peptide count

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 27 Oct 2017 16:40:50 +0200

Langella Olivier's avatar
Langella Olivier committed
704
705
706
707
708
709
710
711
712
xtpcpp (0.1.21-1) stretch; urgency=medium

  * tandem file check
  * better tandem form
  * multiple directory upload
  * monitoring grouping (and faster grouping)

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sat, 21 Oct 2017 11:58:51 +0200

Langella Olivier's avatar
Langella Olivier committed
713
714
715
716
717
718
xtpcpp (0.1.20-2) stretch; urgency=medium

  * tandem parameter form hardened

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sun, 15 Oct 2017 20:32:27 +0200

Langella Olivier's avatar
Langella Olivier committed
719
720
721
722
723
724
xtpcpp (0.1.20-1) stretch; urgency=medium

  * tandem parameters editor

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sun, 15 Oct 2017 07:50:50 +0200

Langella Olivier's avatar
Langella Olivier committed
725
726
727
728
729
730
731
xtpcpp (0.1.19-1) stretch; urgency=medium

  * new preset window (for tandem parameters)
  * divizion by zero fixed and exception added

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 09 Oct 2017 09:03:30 +0200

Olivier Langella's avatar
Olivier Langella committed
732
733
734
735
736
737
xtpcpp (0.1.18-1) stretch; urgency=medium

  * MS run and identification statistics

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 26 Sep 2017 10:07:10 +0200

Olivier Langella's avatar
Olivier Langella committed
738
739
740
741
742
743
xtpcpp (0.1.17-2) stretch; urgency=medium

  * fix desktop file

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 22 Sep 2017 15:42:11 +0200

Olivier Langella's avatar
Olivier Langella committed
744
745
746
747
748
749
750
751
752
753
xtpcpp (0.1.17-1) stretch; urgency=medium

  * better tandem run dialog box
  * success message after tandem run (thanks T. Balliau)
  * condor/tmp_dir_autoremove parameter to keep log files
  * choose number of threads for tandem run
  * XPIP mime type associated to xtpcpp

 -- Olivier Langella <olivier.langella@u-psud.fr>  Fri, 22 Sep 2017 14:36:15 +0200

Olivier Langella's avatar
Olivier Langella committed
754
755
756
757
758
759
760
761
xtpcpp (0.1.16-1) stretch; urgency=medium

  * qt5 switch
  * about dialog window
  * Tandem run window (local and HTCondor)

 -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 18 Sep 2017 12:07:33 +0200

Langella Olivier's avatar
Langella Olivier committed
762
763
764
765
766
767
xtpcpp (0.1.15-1) stretch; urgency=medium

  * ptm peptide list

 -- Olivier Langella <olivier.langella@u-psud.fr>  Thu, 17 Aug 2017 15:40:53 +0200

Olivier Langella's avatar
Olivier Langella committed
768
769
770
771
772
773
xtpcpp (0.1.14-2) stretch; urgency=medium

  * utf8 pwiz library bug workaround

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sat, 01 Jul 2017 10:37:11 +0200

Olivier Langella's avatar
Olivier Langella committed
774
775
776
777
778
779
xtpcpp (0.1.14-1) stretch; urgency=medium

  * mzidentml and pepxml support

 -- Olivier Langella <olivier.langella@u-psud.fr>  Sat, 24 Jun 2017 22:43:53 +0200

Olivier Langella's avatar
Olivier Langella committed
780
781
782
783
784
785
xtpcpp (0.1.13-1) jessie; urgency=medium

  * progress bar, now spectral count output

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Mon, 12 Jun 2017 08:59:00 +0200

Olivier Langella's avatar
Olivier Langella committed
786
787
788
789
790
791
xtpcpp (0.1.12-1) jessie; urgency=medium

  * first PTM island support

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Wed, 31 May 2017 10:51:11 +0200

Olivier Langella's avatar
Olivier Langella committed
792
793
794
795
796
797
xtpcpp (0.1.11-2) jessie; urgency=medium

  * new odsstream library

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Tue, 23 May 2017 23:09:30 +0200

798
799
800
801
802
803
xtpcpp (0.1.11-1) jessie; urgency=medium

  * proticdbml output

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Sat, 20 May 2017 17:36:09 +0200

Olivier Langella's avatar
Olivier Langella committed
804
805
806
807
808
809
xtpcpp (0.1.10-1) jessie; urgency=medium

  * trick to read MGF files

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Fri, 12 May 2017 10:26:42 +0200

Olivier Langella's avatar
Olivier Langella committed
810
811
812
813
814
815
xtpcpp (0.1.9-1) jessie; urgency=medium

  * MGF peak sorting, waiting dialog, new ODS sheets (samples, groups)

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Tue, 09 May 2017 11:30:23 +0200

Olivier Langella's avatar
Olivier Langella committed
816
817
818
819
820
821
xtpcpp (0.1.8-1) jessie; urgency=medium

  * better peptide viewer

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Fri, 05 May 2017 16:28:16 +0200

Olivier Langella's avatar
Olivier Langella committed
822
823
824
825
826
827
xtpcpp (0.1.7-1) jessie; urgency=medium

  * button to link with peptide viewer

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Thu, 04 May 2017 14:47:48 +0200

Olivier Langella's avatar
Olivier Langella committed
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
xtpcpp (0.1.6-1) jessie; urgency=medium

  * new ODS sheet in outputs

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Wed, 03 May 2017 10:28:25 +0200

xtpcpp (0.1.5-2) jessie; urgency=medium

  * new export options

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Fri, 28 Apr 2017 10:30:20 +0200

xtpcpp (0.1.5-1) jessie; urgency=medium

  * new export options

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Fri, 28 Apr 2017 10:18:20 +0200

Olivier Langella's avatar
Olivier Langella committed
846
847
848
849
850
851
xtpcpp (0.1.4-1) jessie; urgency=medium

  * FASTA export

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Thu, 27 Apr 2017 09:19:11 +0200

Olivier Langella's avatar
Olivier Langella committed
852
853
854
855
856
857
xtpcpp (0.1.3-1) jessie; urgency=medium

  * thanks Ariane and Thierry

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Tue, 25 Apr 2017 16:22:04 +0200

Olivier Langella's avatar
Olivier Langella committed
858
859
860
861
862
863
864
xtpcpp (0.1.2-1) jessie; urgency=medium

  * new modification editor, new FDR mass deviation behaviour, lots of
    improvements

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Mon, 24 Apr 2017 10:17:53 +0200

Olivier Langella's avatar
Olivier Langella committed
865
866
867
868
869
870
xtpcpp (0.1.1-1) jessie; urgency=medium

  * bug fix and new features

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Thu, 20 Apr 2017 11:32:40 +0200

Olivier Langella's avatar
Olivier Langella committed
871
872
873
874
875
876
877
xtpcpp (0.1.0-1) jessie; urgency=medium

  * first jessie package

 -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Wed, 19 Apr 2017 10:15:33 +0200

xtpcpp (0.1.0-1~stretch) stretch; urgency=medium
Olivier Langella's avatar
Olivier Langella committed
878
879
880
881
882

  * first package

 -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 18 Apr 2017 20:55:14 +0200