-
Notifications
You must be signed in to change notification settings - Fork 4
/
RevisionHistory.txt
235 lines (179 loc) · 10.6 KB
/
RevisionHistory.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
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
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
DeconTools DeconConsole / AutoProcessor Revision History
Version 1.1.7787; April 27, 2021 mem
- Always treat a period as a decimal point when parsing numbers
Version 1.1.7675; January 5, 2021 mem
- Add support for .UIMF files where the first frame has a frame number greater than 1
Version 1.1.7370; March 6, 2020 mem
- Update to .NET 4.7.2
- In DeconConsole, show the processing rate (scans/minute) and the the actual number of scans processed
- Update the old GUI to read Thermo .Raw files using ThermoRawFileReader
Version 1.1.7101; June 11, 2019 mem
- Use MathNet.Numerics.Statistics methods to compute average, median, standard deviation, and linear regression
Version 1.1.6946; January 7, 2019 mem
- New version of ThermoRawFileReader.dll that uses ThermoFisher.CommonCore.RawFileReader.dll
Version 1.1.6633; February 28, 2018 mem
- Use FileLogger in PRISM.dll instead of log4net
- Update TargetedWorkflowConsole to use CommandLineParser in Prism.dll
- Add option AppendTargetsFileNameToResultFile to TargetedWorkflowConsole
Version 1.1.6492; October 10, 2017 mem
- Additional scan number logic fixes for UIMF files
Version 1.1.6491; October 9, 2017 mem
- Fix bug determining the number of scans per frame
- Obtain log4net from NuGet
Version 1.1.6395; July 5, 2017 bcg
- Update the ProteowizardWrapper and fix the usages of the DependencyLoader
- Fix the 64-bit installer directory
- Remove some obsolete classes
- Pull some DLLs from NuGet instead of local copies
Version 1.1.6347; May 18, 2017 bcg
- Disable the IMS per-frame timeout if there are 10 or fewer frames
Version 1.1.6321; April 22, 2017 mem
- Updated to .NET 4.6.2
- Updated UIMFLibrary, obtained from NuGet
- See https://www.nuget.org/packages/UIMFLibrary
- Still using System.Data.SQLite v1.0.97, but obtaining from NuGet
Version 1.1.6262; February 22, 2017 mem
- Replace PRISM.dll with ShFolderBrowser.dll
- Remove references to obsolete file format .yafms
Version 1.1.6261; February 21, 2017 bcg
- Add support/translation from the old IMS parameter files.
Version 1.1.6148; October 31, 2016 mem
- Update app.config files to map SQLite versions to 1.0.97
Version 1.1.6053; July 28, 2016 mem
- The Miscellaneous section of the parameter file now has 3 new parameters for specifying runtime limits
MaxMinutesPerScan, default 4 minutes
MaxMinutesPerFrame, default 20 minutes
MaxHoursPerDataset, default 400 hours
Version 1.1.5990; May 26, 2016 mem
- Remove dependency on DeconEngineV2.dll, since the code has been ported from C++ to C# and the results validated to match
- See the files with namespace DeconTools.Backend.ProcessingTasks.Deconvoluters.HornDeconvolutor.ThrashV1
- HornDeconvolutor in namespace DeconTools.Backend.ProcessingTasks uses the new C#-based ThrashV1
- Specifying <DeconvolutionType>ThrashV1</DeconvolutionType> in the DeconTools parameter file will use the new C#-based ThrashV1
- Note that ThrashDeconvolutorV2 was a previous attempt to port the C++ code to C#, but the results from ThrashDeconvolutorV2 do not match the C++ results
Version 1.0.5945; April 11, 2016 mem
- Remove reference to pwiz_bindings_cli.dll since the presence of that file can interfere with ProteowizardWrapper searching for ProteoWizard DLLs
Version 1.0.5940; April 6, 2016 mem
- Update to UIMFLibrary.dll v3.0.5940
Version 1.0.5935; April 1, 2016 mem
- Update to ProteowizardWrapper v1.0.5934
- Update to System.Data.SQLite v1.0.97
- Now compiling as v4.5.1 (for compatibility with ProteoWizard)
Version 1.0.5799; November 17, 2015 bcg
- Updated ProteoWizard Wrapper DLL
- Throw an exception when ProteoWizard is needed and it's not available.
Version 1.0.5795; November 13, 2015 bcg
- Updated multiple DLLs
- Modified use of ProteowizardWrapper, to dynamically find (at runtime) the 32-bit ProteoWizard install
- Change the installer from a Visual Studio installer msi to an InnoSetup executable
Version 1.0.5753; October 2, 2015 mem
- Fixed bug in ZeroFiller that led to a divide-by-zero overflow when adjacent data points had the same mass value
Version 1.0.5700; August 10, 2015 mem
- Add additional exception handling
- Now using a period for decimal points, even if the system's language settings are configured to use a comma
Version 1.0.5674; July 15, 2015 mem
- Added DblToString() for formatting double values as strings, limiting the number of decimal places shown
Version 1.0.5518; February 9, 2015 mem
- Moved acqus and apexAcquisition.method file reading into BrukerDataReader.DLL
- BrukerCalibrationData now inherits from BrukerDataReader.GlobalParameters
- BrukerV3Run.GetMassSpectrum now uses the mass range used during data acquisition to define the range of data to return
- Fixed file paths in unit tests
- Updated ProteoWizard DLLs
Version 1.0.5513; February 4, 2015 mem
- Created 64-bit version of DeconConsole.exe and DeconTools.Backend.dll
- Does not depend on DeconEngineV2.dll, and thus does not support ThrashV1
Version 1.0.5504; January 26, 2015 mem
- New version of the UIMFLibrary that uses less memory when caching spectra
Version 1.0.5480; January 2, 2015 mem
- Added HandleProcessCorruptedStateExceptionsAttribute to GetMassSpectrum in XCaliburRun2 in an attempt to catch COM errors due to corrupt spectra
- New version of ThermoRawFileReader
Version 1.0.5326; August 1, 2014 mem
- DeconConsole no longer references SetConsoleMode in kernel32.dll
Version 1.0.5325; July 31, 2014 mem
- Removed dependency on DeconEngine.dll, which required Visual C++ from .NET 1.1 (MSVCP71.dll)
- DeconEngine.dll was included to support the Rapid deconvolution method, which we no longer use
Version 1.0.5291; June 27, 2014 mem
- Fixed bug in DeconToolsZeroFiller that dropped the final data point when zero filling
- Updated UIMFLibrary.dll
- Updated System.Data.SQLite.dll
Version 1.0.5280; June 16, 2014 mem
- Updated DeconEngineV2.dll
Version 1.0.5044; Oct 23, 2013 mem
- Now validating that the _peaks.txt file has usable data
- Now sorting data returned by msfileReader.GetMassListFromScanNum if not sorted by m/z
- Fixed bug in FWHM calculator
- Slight peak detector speed up
Version 1.0.5021; Sep 30, 2013 gslysz
- Bug fixes
Version 1.0.5003; Sep 12, 2013 gslysz
- Public release that supports ThrashV1 (C++ based) and ThrashV2 (C# based)
Version 1.0.4672; Oct 16, 2012 gslysz
- fixed total failure bug when trying to read mzXML data
- improved Bruker file reader
Version 1.0.4591; July 27, 2012 gslysz
- Upgraded to read Thermo .raw files using xrawfile2.dll v2.2
Version 1.0.4533; May 30, 2012 gslysz
- Support for mzML, large mzXML files, and mz5 (using Proteowizard)
- Support for BrukerTOF (Maxis)
Version 1.0.4412; Jan 30, 2012 gslysz
- 'SaturationThreshold' parameter added.
Version 1.0.4400; Jan 18, 2012 gslysz
- UIMF files with MS/MS now processed properly
- Summing fixed. Can sum across MS1 LC frames for MS/MS-containing UIMF files
Version 1.0.4364; Dec 13, 2011 gslysz
- Under-the-cover changes to support alternative workflows
- Rewrote workflow for peak output for multiple datasets (each consisting of a single scan)
- "UIMF saturation repair" workflow added
Version 1.0.4262; Sept 1, 2011 gslysz
- Incorporated Anoop's O16O18 program that extracts peak abundances for peaks that might be part of O16O18 labelled peptide
Version 1.0.4259; Aug 30, 2011 gslysz
- DeconConsole errors do not wait for user to hit enter; now program exits;
Version 1.0.4211; July 13, 2011 gslysz
- _scans files written after each scan, not at the end
- _isos file written to more frequently
Version 1.0.4210; July 12,2011 gslysz
- Improved logging. Fixed some glitches with the Autoprocessor GUI
Version 1.0.4129; Apr 22, 2011 gslysz
- UIMF Frames are 0-based instead of 1-based (this is a change in the UIMFLibrary)
Version 1.0.4062; Feb 14, 2011 gslysz
- Peak data exported with MSFeature associations
- Interference scoring added
Version 1.0.3980; Nov 24, 2010 gslysz
- overhaul how Bruker files are handled. No longer uses DeconEngine. Uses C# code instead.
- simply select the parent folder that contains the raw data.
- works with Bruker_9T; Bruker_Solarix (12T); Bruker_15T
Version 1.0.3817; June 14, 2010 gslysz
- incorporates re-written UIMFLibrary.dll
Version 1.0.3791; May 19, 2010 gslysz
- support for Agilent.D files (new generation TOF)
- UIMF calibration support
- Fit re-calculation for RAPID is much improved (faster)
Version 1.0.3631; Dec 10, 2009 gslysz
- revamped exporters to export during the processing instead of at very end. Writing to a temporary .bin no longer needed.
- added sqlite exporters for _isos, _scans, and _peaks.
- added new parameter (NumPeaksUsedInAbundance) to allow control over how abundance is calculated for a feature.
- support for Bruker 9T data
- support for summing Bruker 9T data
Version 1.0.XXXX; Nov 2, 2009 gslysz
- added support for mzXML processing
- added support for ICR2LS processing
- added 'Original Intensities' info to UIMF _isos result output. This column reports the unsummed intensities (Anoop's work).
Version 1.0.3490; July 22, 2009 gslysz
- Added 'Re-fitter', which re-calculates the fit. This can be used to calculate a THRASH-style fit value for data processed using RAPID. [this first version is very slow]
Version 1.0.3480; July 12, 2009 gslysz
- Stopped debugging info from being sent to console (this might slow Matt's DMS performance)
- Added info on processing % to log file (every 15 min will write to log file)
- Log file is written as the file is processed, instead of at the very end.
- Added new column 'Summed_abundance' (currently doesn't work with RAPID since RAPID does not reveal the isotopes in the isotopic profile)
- Fixed 'cumulative_drift_time'; should be reporting correctly now.
Version 1.0.3475; July 7, 2009 gslysz
- Fixed an unwanted conversion from Double to Float that was occurring for most file types
- Added ability to merge multiple runs into a single _isos and _scans file. (Initially made for Julia Laskin's requirements).
Version 1.0.3470; July 2, 2009 gslysz
- Added ability to output peak lists for each scan for IMF and RAW files.
Version 1.0.3463; June 25, 2009 gslysz
- prevented memory overload by serializing / deserializing result objects to disk.
- reduced sig figs in exported result files (_isos, _scans).
- added indicator on UI for total number of Features found.
- Log files are given name similar to the file that was processed.
- log files record version information of dlls.
- new file selection UI