RevisionHistory.txt

UIMFLibrary Revision History

Version 3.6.3.0; January 23, 2019
	- Fix a math int vs. object problem in UpdateGlobalStats that only appeared at runtime
	- Mark DataReader.GetIntensityBlockForDemultiplexing as obsolete, to reduce code duplication and encourage such functions to be located in the project that uses them.

Version 3.6.2.0; November 6, 2018
	- Replace UpdateGlobalFrameCount with UpdateGlobalStats

Version 3.6.1.0; January 9, 2018
	- Consolidate some code to text templates, and separate the RlzEncoding and Compression
	- Add a couple reader functions to get bin-intensity values without expanding to the full array

Version 3.6.0.0; October 13, 2017
	- Fix a bug in the zero run length encoding (affecting the zero suppression, the count would be one too high for a gap)
	- Handle the bug when reading files that were encoded with the buggy zero suppression

Version 3.5.7.5; September 26, 2017
	- Add drift tube length and drift tube gas global parameters

Version 3.5.7.1; September 7, 2017 	
	- Use CLZF2 instead of custom class LZFCompressionUtil
	- Add NetStandard 2.0 support

Version 3.4.2; August 31, 2017
	- Add method RenumberFrames
	- Add Version_Info table

Version 3.4.1; August 26, 2017
	- Fix MzCalibrator when used on non-1GHz files

Version 3.4.0; April 27, 2017
	- Expand unit tests
	- Configure for Appveyor to auto-build

Version 3.1.0; March 31, 2017
	- Use new .csproj format and push to NuGet

Version 3.0.6270; March 2, 2017
	- Update the DataReader to allow reading .uimf files with empty Frame_Params and/or Frame_Parameters
	- Add method ValidateLegacyHPFColumnsExist to DataWriter
	- Add method ValidateLegacyHPFColumnsExist

Version 3.0.6220; January 11, 2017
	- Update CloneUIMF to copy views

Version 3.0.6215; January 6, 2017
	- Preferentially use lists of Tuples instead of lists of KeyValuePair
	- Raise an exception if binToIntensityMap is passed to InsertScan with intensity values of 0

Version 3.0.6180; December 2, 2016
	- Update TableExists to check for views in addition to tables
	- Add method GetTableColumnNames
	- Add unit tests

Version 3.0.6043; July 18, 2016
	- Fix bug in the SQL used by GetFrameNumbers that was not returning any results.

Version 3.0.6019; June 24, 2016
	- Add pagingFilterStartBin and pagingFilterCount to GetIntensityBlockForDemultiplexing

Version 3.0.5996; June 1, 2016
	-  Add properties HasFrameParamsTable, HasGlobalParamsTable, and HasLegacyParameterTables

Version 3.0.5989; May 25, 2016
	- Update mz calibrator to contain virtual methods that can be overriden by derived classes.

Version 3.0.5988; May 24, 2016
	- Now defining the ScanNum field as a 32-bit integer instead of a 16-bit integer in the Frame_Scans table
	- Add custom exception handlers to the reader

Version 3.0.5980; May 16, 2016
	- Update InsertScan to no longer return an int but to instead have output parameter nonZeroCount

Version 3.0.5970; May 6, 2016
	- Fix bug that failed to populate the cached GlobalParams when the writer opens an existing .uimf file

Version 3.0.5961; April 27, 2016
	- Update to SQLite v1.0.97 (previously used 1.0.93)
	- Update to .NET 4.5.1
	- Add ReaderWriterExtensions.cs to UIMFLibrary.csproj (was already used by UIMFLibraryAsync.csproj)

Version 3.0.5940; April 6, 2016
	- Update GetSpectrum to avoid an index out of range exception if the requested scan number does not exist in the spectrum cache

Version 3.0.5842; December 30, 2015
	- Add m/z-bin conversion functions to MzCalibrator

Version 3.0.5744; September 23, 2015
	- Add new GlobalParams: InstrumentClass, PpmBinBasedStartMz, and PpmBinBasedEndMz
	- Add property IsPpmBinBased to GlobalParams

Version 3.0.5654; June 25, 2015
	- Added check for out-of-range bin values in GetSpectrum in the reader
		- Errors reported via new event, ErrorEvent 
	- Added check for out-of-range bin values in InsertScan in the writer

Version 3.0.5653; June 24, 2015
	- Update several AddUpdate functions to return the instance of the class, thus allowing chaining function calls (i.e. the Fluent way)

Version 3.0.5652; June 23, 2015
	- The reader now explicitly uses the "en-US" CultureInfo for string to number conversions
	- MSConvert-specific version now uses SQLite v1.0.97 (previously used 1.0.90)

Version 3.0.5583; April 15, 2015
	- GetSpectrum will now always use GetSpectrumBinCentric if bin-centric tables are present
		- Previous only used the Bin-centric method if the number of bins being retrieved was greater than numFrames * numScans

Version 3.0.5564; March 27, 2015
	- Update AccumulateFrameData to not use compression if yCompression is 1 or smaller

Version 3.0.5556; March 19, 2015
	- Reader will now always report DateStarted with format code M/d/yyyy h:mm:ss tt, regardless of how the date is stored in the UIMF file
	- Fix bug storing DriftTime in GetFrameScans

Version 3.0.5540; March 3, 2015
	- Added method PreCacheAllFrameParams, which speeds up AddLegacyParameterTablesUsingExistingParamTables

Version 3.0.5536; February 27, 2015
	- The writer now has the option (enabled by default) to populate the legacy parameter tables (Global_Parameters and Frame_Parameters)

Version 3.0.5532; February 23, 2015
	- Updated GetDriftTime to have required parameter normalizeByPressure
	- Added PressureUnits frameter parameter

Version 3.0.5504; January 26, 2015
	- Reduced memory footprint by updating SpectrumCache to use a SortedList instead of a Dictionary

Version 3.0.5450; December 3, 2014
	- Added support for Agilent .D folders where the first scan is 1 instead of 0
	- Added frame parameters ScanNumFirst and ScanNumLast

Version 3.0.5442; November 25, 2014
	- Removed legacy InsertScan functions
	- Updated GetTicOrBpiByFrame to support the Frame_Params table
	- Added version of FlushUimf that supports closing/reopening the active transaction a minimum of 5 seconds apart

Version 3.0.5441; November 24, 2014
	- Refactored the global parameters and frame parameters into key-value pairs
		- New tables: Global_Params, Frame_Params, and Frame_Param_Keys
		- The reader supports both v2.0 and v3.0 .UIMF files
	- Added .NET 4.5.1 project with an asynchronous InsertFrame function
	- Extensive code and unit test cleanup

Version 2.1.5288; June 24, 2014
	- Standardized data type names for database fields to conform to standard SqLite types
	- Refactored shared code in UIMFWriter.CreateTables
	- Resharper code cleanup

Version 2.1.5287; June 23, 2014
	- UpdateGlobalParameter now supports updating a string field in Global_Parameters 
	- Updated the UIMFLibrary_Demo to use the latest DataReader and DataWriter classes
	- Expanded the code documentation throughout

Version 2.1.5214; April 11, 2014
	- Updated the DataWriter to implement System.IDisposable and to use a constructor that requires the UIMF file string
	- Removed the CloseUIMF() and OpenUIMF() methods

Version 2.0.4891; May 23, 2013
	- Added bin-centric functions

Version 2.0.4450; March 8, 2012
	- Added overloaded version of InsertScan that takes an integer array of intensities

Version 2.0.4434; February 21, 2012
	- Added xml file for 64-bit System.Data.SQLite

Version 2.0.4429; February 16, 2012
	- Replaced IMSCOMP.dll with LZFCompressionUtil

Version 2.0.4419; February 6, 2012
	- Fixed bug that causes an error if a bin value was seen that exceeded the maximum bin value of the file

Version 2.0.4373; December 22, 2011
	- Updated UIMFLibrary to automatically handle FrameType of 0 or 1 

Version 2.0.4365; December 14, 2011
	- More code cleanup, including renaming enum iFrameType to FrameTye

Version 2.0.4358; December 7, 2011
	- Removed all references of FrameIndex

Version 1.3.4212; July 14, 2011
	- Added support for the pressure columns in the Frame_Parameters having values with units of milliTorr instead of Torr
		- Auto-converting values to Torr when reading data with PopulateFrameParameters	
		- Example dataset is Sarc_ctrl_1ugul_Run2_4bit_23Sep11_Frodo from IMS_TOF_6
	- Renamed the voltEntrance and voltExit fields:
		voltEntranceIFTOut -> voltEntranceHPFOut
		voltEntranceIFTIn -> voltEntranceHPFIn
		voltExitIFTOut -> voltExitHPFOut
		voltExitIFTIn -> voltExitHPFIn

Version 1.3.4200; July 2, 2011
	- Overloaded AddFrameParameter to support defining a default integer or string value when adding a column

Version 1.3.4199; July 1, 2011
	- Added support to TryGetFrameParam and TryGetFrameParamInt32 for Null values

Version 1.3.4195; June 27, 2011
	- Added column Decoded to the Frame_Parameters table
	- Added functions IsCalibrated and TableHasColumn to the reader

Version 1.3.4178; June 10, 2011
	- Renamed description for FrameType 3 to be "MS/MS" instead of "Fragmentation"
	- Added ability to update the CalibrationDone column when calling update_CalibrationCoefficients or updateAll_CalibrationCoefficients
	- Added PostLogEntry function to the DataReader class

Version 1.3.4170; June 2, 2011
	- Overloaded CloneUIMF to include versions with parameter eFrameScanFrameTypeDataToAlwaysCopy

Version 1.3.4135; April 28, 2011
	- Updated CloneUIMF to skip the sqlite_sequence table (auto-generated by SQLite)
	- Updated CloneUIMF to attach the source DB to the target DB (instead of attaching the target DB to the source DB)

Version 1.3.4132; April 25, 2011
	- Changed the Entry_ID column in the Log_Entries table to INTEGER PRIMARY KEY
		- Was previously INTEGER PRIMARY KEY AUTOINCREMENT, which results in the creation of table sqlite_sequence

Version 1.3.4130; April 23, 2011
	- Added CloneDB() method to the UIMFReader
	- Copies all tables and data, though, by default, skips the data in the Frame_Scans table

Version 1.3.4128; April 21, 2011
	- Updated DataReader to reference frames using frame_index instead of FrameNum
		- Use set_FrameType() to change the frame type; it will return the number of frames of the given type
		- Then, obtain frame-related data by frame index instead of frame num
	- Cleaned up code in reader
	- Created FrameType enum (and constants):
			MS = 0
            Fragmentation = 1
            Prescan = 2
            Calibration = 3
	- Added UIMFViewer utility functions
	- Now building both 32-bit and 64-bit versions of the UIMFLibrary

Version 1.2; July 16, 2010
	- Added caching of spectra
	- Added caching of t values (used for converting bins to m/z values)
	- Added more prepared statements

Version 1.1; June 24, 2010
	- Updated to System.Data.SQLite
	- Created lib in project folders to store dlls (note: IMSCOMP.dll doesn't play nice with this method)
	- Reformated connection strings for new dll.

Version 1.0; June 23, 2010
	- Added Revision History
	- Updated to NUnit tests