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RevisionHistory.txt
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RevisionHistory.txt
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DeconTools DeconConsole / AutoProcessor Revision History
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