RevisionHistory.txt

Analysis Tool Manager History

February 22, 2019
	- When retrieving MS-GF+ results from a remote host, MSGFPlus_Mods.txt is now optional

February 20, 2019
	- ParseMSGFPlusParameterFile now creates a new MS-GF+ parameter file with updated parameters
		- Previously it parsed the parameter file and converted the parameters to MS-GF+ command line arguments

February 8, 2019
	- Add support for EnzymeDef in MSGF+ parameter files
		- If defined, creates enzymes.txt in the params directory below the working directory

January 17, 2019
	- New ThermoRawFileReader that uses ThermoFisher.CommonCore

December 13, 2018
	- Add support for Formularity processing _peaks.txt files from DeconTools or .csv files from ThermoPeakDataExporter

October 18, 2018
	- Use ThermoRawFileReader to determine the maximum scan number

September 25, 2018
	- Add support for updating parent ion info in a .mzML file using a _dta.txt file from DeconMSn

September 17, 2018
	- Add ThermoPeakDataExporter plugin

September 7, 2018
	- Call NOMSI to create plot files from Formularity results

August 16, 2018
	- Add TopPIC and TopFD plugins

July 27, 2018
	- Add logic to check whether a FASTA file needs to be split again because previously created split FASTA files were deleted from the central share

July 19, 2018
	- Keep track of multiple shared results folders for data package jobs
	- In the FDR_Aggregator plugin, skip invalid jobs but continue processing valid jobs

June 28, 2018
	- Add support for MS-GF+ option MaxMissedCleavages

June 26, 2018
	- Keep track of Tissue ID and Tissue Name for each experiment in a data package

June 5, 2018
	- Add AnalysisManagerFormularityPlugin

May 25, 2018
	- Update to use FileSyncUtils and HashUtilities in PRISM.dll

May 15, 2018
	- Switch from BRENDA to BTO when writing out tissue type in the sample metadata section of a ProteomeXchange .px file

May 1, 2018
	- Always retrieve .mzid.gz files during data extraction of MSGF+ split fasta results

April 26, 2018
	- During data extraction, skip finding protein mods if the FASTA file is over 2 GB

April 25, 2018
	- Use elapsed MSGF+ processing time to update remote start and remote finish values when using existing MSGF+ results

April 19, 2018
	- Always use the progress value reported by the MSGF+ console output file

April 13, 2018
	- Configure tool DataExtractorSplitFasta to load the standard data extraction plugin
	- Skip running PHRP if the PHRP result files are all newer than the search result file(s)
	- Use the MzidMerger to combine .mzid files in a SplitFASTA analysis

March 30, 2018
	- Extensively improve offline job processing, including monitoring job progress and reporting runtime stats to the database

February 16, 2018
	- Use DMSUpdateManager to push new/updated DMS_Programs files to a remote Linux host

February 5, 2018
	- Use class LogTools in PRISM.dll instead of local clsLogTools

January 4, 2018
	- Add standalone logging classes that replace Log4Net

December 19, 2017
	- Enable Python Plotting when generating plots with MSFileInfoScanner after running DeconTools

November 15, 2017
	- Use GetFreeMemoryMB in PRISM.dll instead of class SystemMemoryInfo

October 30, 2017
	- Increase MSGF+ memory usage when processing large .mzML files

July 11, 2017
	- Add support for pushing jobs to a remote Linux host
	- Add offline mode option for processing jobs on a Linux host, independent of other servers

April 12, 2017
	- Update to .NET 4.6.2
	- Obtain PRISM.dll and PRISMWin.dll from NuGet
	- Use PRISMWin.dll for core count , core usage, clsDotNETVersionChecker, and GetDiskFreeSpace

February 14, 2017
	- Converted from VB.NET to C#
	- Updated to .NET 4.6.1

April 22, 2016
	- Update to .NET 4.5.1 due to new MSFileInfoScannerInterfaces.dll that is compiled against v4.5.1 and
	  uses System.Data.SQLite v1.0.97 compiled for .NET 4.5.1

February 19, 2016
	- Now purging old FASTA files before downloading the FASTA file for the current job

February 17, 2016
	- Refactored MyEMSL code into clsMyEMSLUtilities; shared by both clsAnalysisResources and clsAnalysisToolRunnerBase
	- Updated IAnalysisResources and IToolRunner to require passing in an instance of clsMyEMSLUtilities

November 23, 2015
	- Added support for monitoring actual CPU usage of processes spawned by clsRunDosProgram

November 5, 2015
	- Added lock file functions to clsAnalysisResources

October 20, 2015
	- LoadMgrSettingsFromDBWork now checks for pending monthly Windows updates to decide whether to log an "excessive failures" error to the database

September 15, 2015
	- Added manager parameters AuroraAvailable and MyEmslAvailable

July 27, 2015
	- Now logging errors to DMS5 if they occur when reading configuration options from the Manager Control DB

May 10, 2015
	- Updated the .exe and all DLLs to AnyCPU

January 31, 2015
	- Added ProMex plugin
	- Updated to .NET 4.0 version of Log4net

August 15, 2014
	- Updated IAnalysisResources to include methods GetOption and SetOption 

January 9, 2013
	- New version of PRISM.dll; requires instantiating PRISM.Files.clsFileTools to use most of the functions
		- Includes function CopyFileUsingLocks

August 15, 2012
	- Now aborting the message queue thread if stuck for over 15 seconds
	- Updated DTASpectraFileGen program to use MascotGenericFileToDTA.dll for conversion of MGF files to DTA.txt files

July 27, 2012
	- Updated to support the MgrSettingsGroupName parameter
		- Defines a ghost analysis manager that tracks settings shared by a group of analysis managers

July 26, 2012
	- Added command line switch /EL, which can be used to create the DMS_AnalysisMgr Windows event log, then exit the program

July 17, 2012
	- Added the LipidMapSearch plugin
	- Added MD5 and Sha-1 hash computation functions to clsGlobal
	- Updated the ICR-2LS plugin to check the archive for the ser file

May 7, 2012
	- Added clsScanStatsGenerator to AM_Shared
	- Updated MSGFDB plugin to check for phosphorylation search of HCD data and using -protocol 1
	- Updated MSGFDB plugin to use GenerateScanStatsFile in the Analysis Resources base class
	- Updated MSGF plugin to use PHRPReader
	- Added IDPicker plugin (also creates .pepXML file)

May 1, 2012
	- Updated the Analysis Manager Extraction Pluginto validate that computed mass errors are reasonable
		- Large mass errors likely indicate a problem with the ModDefs.txt file
		- Uses PHRPReader to read the _syn.txt files
	- Updated the SMAQC plugin to use switch -db to specify the location of the SQLite database

April 26, 2012
	- Updated the MSGF Plugin to use a new version of PHRPReader.dll

April 18, 2012
	- Updated Sequest plugin to auto-restart PVM if too many nodes stop responding

April 17, 2012
	- Updated Sequest plugin to create a temporary _out.txt file as .out files are created
		- File is copied up to the transfer folder every 5 minutes
	- Updated Sequest plugin to allow resuming analysis using the _out.txt.tmp file

April 13, 2012
	- Updated the MSGF Plugin to support creating .mzXML files using MSConvert
		- Uses AnalysisManagerMsXmlGenPlugIn.dll
	- New version of MsMsDataFileReader.dll
		- Supports MGF files created by ProteoWizard, where the title line contains file name, start scan, end scan, and charge (if known)

April 11, 2012
	- Split out much of the code from AnalysisManagerProg.exe and placed in AM_Shared.dll
	- Updated all of the plugins to use AM_Shared.dll instead of AnalysisManagerProg.exe

April 6, 2012
	- Updated MSGF Plugin to use PHRPReader.dll

April 2, 2012
	- Updated the MSGFDB plugin to dynamically load clsMSFileInfoScanner from within MSFileInfoScannerInterfaces.dll, which is stored at C:\DMS_Programs\MSFileInfoScanner

March 19, 2012
	- New versions of MSFileInfoScanner.dll and ThermoRawFileReaderDLL.dll
		- Switched from xrawfile2.dll to MSFileReader.XRawfile2.dll, which supports Xcalibur v2.2
	- No longer deleting the _ScanType.txt file when running MSGF via the MSGFDB_PlugIn

February 29, 2012
	- Updated the MSGF plugin to auto-create empty ResultToSeqMap and SeqToProteinMap files if the synopsis file is empty

February 21, 2012
	- Updated the MSGF Plugin to summarize the results having MSGF < 1E-10
	- Added MSGF_Results_Summarizer.exe program to allow for summarizing existing results and storing in DMS

February 17, 2012
	- Now reporting "Exception generating OrgDb file" in the completion code if a an exception occurs while creating the fasta file
	- Updated clsSplitCattedFiles to support receiving a list of DTA files to skip when de-concatenating a _DTA.txt file
	- Now dynamically adjusting the amount of memory reserved for BuildSA based on the source Fasta file size
	- Updated Sequest plugin to generate a list of DTA files to skip if resuming a failed job using existing .out files

February 14, 2012
	- Moved verification of the working directory (including auto-deleting old files) to after the managers checks if it is active

February 13, 2012
	- Updated SMAQC to support version 1.0.4423
	- Converted MultiAlign Aggregator plugin from VB to C# and added a test harness

February 7, 2012
	- Updated MultiAlign Aggregator plugin to parse the Multialign log file to estimate processing progress
	- Now parsing out exception messages from the DeconTools log file
	- Updated MSGF Plugin to skip the validation of RawDataType if parsing a .mzXML file

January 31, 2012
	- Updated MSXml plugin to support Bruker Amazon Ion Trap .D folders (which have an analysis.yep file instead of an analysis.baf file)
	- Updated MSGFDB plugin to obtain the .mxML file when running script MSGFDB_Bruker

January 24, 2012
	- Updated MSGFDB plugin to support AssumedScanType in the settings file

January 19, 2012
	- Added validation for various job parameters to assure they're not blank.

January 18, 2012
	- Updated Decon2LSV2 plugin to support DeconConsole v4400 (which only requires dataset file path and parameter file path, and not dataset type)
	- Updated MSGF plugin to use the _ModDefs.txt file if the synopsis file is 0 bytes and the _ModSummary.txt file is missing

January 16, 2012
	- Updated MSDeconv plugin to support paameters MSDeconvIncludeMS1 and MSDeconvOutputFormat

January 12, 2012
	- Updated the PRIDE_MZXML and Phospho_FDR_Aggregator plugins to redefine the dataset name and transfer folder path so that results are stored directly below the data package instead of in a subfolder named Aggregation

January 8, 2012
	- Updated MSGF plugin to simply copy the MSGFDB-based SpecProb value into the _fht_MSGF.txt and _syn_MSGF.txt files, rather than re-running MSGF

January 5, 2012
	- Updated functions FindAndRetrieveMiscFiles and FindDataFile to include option SearchArchivedDatasetFolder 
		- Allows to specify that only the Proto storage server should be searched for a file; skip the Archive
	- Updated the DataExtractor plugin to not search the Archive when looking for the _ModDefs.txt file or MassCorrectionTags file
	- Updated MSGF plugin to support MSGFDB v7097, which now treats the -m switch the same for both MSGFDB and MSGF
		- Now always using -m 0 when processing mzXML files with MSGF via MSGFDB
	- Updated MSGFDB plugin to support the -showDecoy switch
		- When TDA=1 and showDecoy=1 are present in the parameter file, then the results will contain peptides from reverse proteins (protein name starts with REV_)
		- Consequently, we use ProteinFileReader.dll to generate a decoy version of the source Fasta file prior to calling the PeptideToProteinMapEngine
	- Updated ValidateFreeDiskSpace to use the parent folder if the dataset storage path doesn't exist 

January 4, 2012
	- Updated MSAlign plugin to support MSAlign v0.7
		- The eValueThreshold parameter has been replaced with two parameters, cutoffType and cutoff

December 22, 2011
	- Now validating drive free space in key places
		- For Results_Transfer, simply validating the dataset storage path
		- For other analysis tools, validating:
			- Working directory
			- OrgDB directory
			- Remote transfer directory
		- Disables the manager locally if the working directory or OrgDB directory free space falls below 750 MB
		- Fails out the job if the Remote Transfer Directory free space is below 10 GB
		- Fails out the job if the Dataset storage Path free space is below 10 GB
	- Updated to abort requesting new tasks if 3 requests in a row result in a deadlock error
	- Updated MSGF to use "MSGFDB.jar ui.MSGF"

December 19, 2011
	- Updated MSAlign plugin to validate that the activation key (or instrument key for v0.5) is not FILE when running a MSAlign_Bruker dataset
		- Required since the mzXML file created by Bruker's compass program does not include the scantype information (CID, ETD, etc.)

December 14, 2011
	- Updated MSGFDB plugin to abort processing if a parameter file parsing error occurs
	- Updated MSGFDB plugin to validate that the _PepToProtMap.txt file does not have any __NoMatch__ entries

November 28, 2011
	- Updated MSAlign plugin to ignore the etc folder when running v0.5 of MSAlign

November 23, 2011
	- Now validating that the MSDeconv results file is not empty

November 20, 2011
	- Updated MultiAlign plugins to use StoreToolVersionInfoOneFile64Bit
	- Updated MSGFDB to support processing a .mzXML file instead of a _DTA.txt file

November 14, 2011
	- Added function StoreToolVersionInfoOneFile64Bit, which uses 64-bit app DLLVersionInspector.exe to determine the version of a 64-bit DLL or .Exe
		- Updated LCMSFeatureFinder plugin to use this function instead of looking for a folder named 32BitDLLs

November 7, 2011
	- Updated the job parameter objects to track section name
		- Can lookup job parameter by name alone, or using section name and parameter name

October 27, 2011
	- Updated MSGFDB to create the ScanStats.txt file from a .Raw file if the ScanStats.txt file cannot be found in a MASIC results folder

October 24, 2011
	- Updated MSGF plugin to use n/a for the Collision_Mode column when processing non-MSGFDB results
		- Necessary, since if the Collision_Mode column is empty, then MSGF reports the computed SpecProb values in the wrong results column
	- Now reading the tool version from the MSAlign console output file
	- Updated MSGF Plugin to delete the Console_Output.txt file if it is empty

October 20, 2011
	- Updated MSGF plugin to keep temporary files if KeepMSGFInputFile=True in the job parameters

October 19, 2011
	- Now creating a _ScanType.txt file when running MSGFDB
		- Allows for analysis of CID, ETD, and HCD spectra in a single analysis
		- Created using MASIC ScanStats files
	- Updated MSGF to support MSGFDB results having a mix of CID, ETD, and HCD spectra
		- Must run MSGF twice; first on the CID and HCD spectra, and then on the ETD spectra
	- New version of Ionic.Zip.dll

October 17, 2011
	- Now adding header line to MSAlign_ResultTable.txt file if we use MSAlign v0.5

October 15, 2011
	- Added MSAlign plugin
		- Supports MSAlign v0.5 and v0.6
		- In addition to the text result files, zips the files that MSAlign creates in the html and xml folders

October 13, 2011
	- Added MSDeconv plugin
	- Moved ValidateFreeMemorySize into clsAnalysisResources
	- Updated function RetrieveMZXmlFile to also look for MSXML_Gen_1_126_DatasetID
	- Streamlined the text in the _AnalysisSummary.txt file created by clsStatusFile
	- Updated MSGF plugin to delete the MSGF_ConsoleOutput.txt file if it is empty

October 6, 2011
	- Updated AnalysisManagerInspResultsAssemblyPlugIn.dll to report CLOSEOUT_NO_DATA when assembled results file is empty

September 26, 2011
	- Update the Extraction plugin to copy the _msgfdb_PepToProtMap.txt file to the local computer for MSGFDB analysis jobs.

September 13, 2011
	- Replaced calls to m_Completions_Msg to instead use clsAnalysisToolRunnerBase.m_message

September 13, 2011
	- DTA_Refinery updates
		- Now validating the _DeconMSn_Log.txt file to look for intensity values of 0
		- Now parsing DTA Refinery log file to look for known error messages

September 09, 2011
	- MSGF Plugin Updates:
		- Renamed SpecProb to MSGFDB_SpecProb
		- Renamed RankSpecProb to Rank_MSGFDB_SpecProb

September 09, 2011
	- Now deleting temp.tsv files in MSGFDB plugin

September 02, 2011
	- Now parsing the MSGF console output file in the MSGF plugin to determine the program version

September 01, 2011
	- In MSGF plugin, No logging error messages to MSGFInputCreator_Log.txt
	- In Sequest Plugin, now keeping _out.txt file if error occurs while zipping it

September 01, 2011
	- New closeout type: CLOSEOUT_ERROR_ZIPPING_FILE
	- When finding .mzXML files, now looking for either MSXML_Gen_1_39_DatasetID or MSXML_Gen_1_93_DatasetID

August 30, 2011
	- Updated MSGFDB plugin to send -tda 0 to BuildSA if using a decoy fasta file
	- Now checking for sufficient free memory before running BuildSA (which now uses 2 GB of ram)

August 30, 2011
	- Updated ValidateFreeMemorySize in MSGF plugin to match MSGFDB plugin

August 29, 2011
	- Updated MSGFDB plugin to include switch -Xmx4000M when calling BuildSA

August 26, 2011
	- Extraction plugin updates:
		- Now using lowercase _msgfdb for filenames
		- Fixed bug that caused validation errors when processing Inspect data

August 24, 2011
	- Now parsing out the %Complete messages from the MSGFDB log file.

August 24, 2011
	- Updated SetBioworksVersion() to support MSGFDB

August 24, 2011
	- Updated for 8/22/2011 version of MSGFDB

August 24, 2011
	- Updated Extraction plugin to use the ParamFileGenerator to make the _ModDefs.txt file if not found
	- Now verifying that the expected PHRP result files have been created

August 22, 2011
	- Updated the Extraction plugin to support MSGF-DB results (type MSG_Peptide_Hit)

August 22, 2011
	- Updated the MSGF plugin support for MSGF-DB results

August 19, 2011
	- Updated the MSGF plugin to support columns Ions_Observed, Ions_Expected, and DelM_PPM (though they're not actually used by the plugin)
	- Now determining the location of ReadW using ReAdWProgLoc

August 17, 2011
	- Updated the MSXML Generator plugin to support specifying a specific version of ReAdW.exe

August 12, 2011
	- New version of PeptideToProteinMapEngine.dll and ProteinCoverageSummarizer.dll
	- MSGFDBPlugin now creates a _PepToProtMap.txt file

August 10, 2011
	- Updated the Extract to use the .Exe version of the PeptideHitResultsProcessor (previously called a DLL)

August 01, 2011
	- Add CondenseCDTAFile.dll to the MSGF-DB plugin
	- New version of Protein_Exporter
	- Switch from StringDictionary to Generic.Dictionary
	- Add MSGFDB plugin

July 28, 2011
	- Fixed bug that truncated tool version to 256 characters when calling SP SetStepTaskToolVersion
	- Now recording the version of various DLLs that the PeptideToProteinMapEngine uses

July 27, 2011
	- Updated MultiAlignAggregator step tool to support using a specific version of the tool
	- Updated MultiAlign step tool to support using a specific version of the tool
	- Added DetermineProgramLocation and StoreToolVersionInfoOneFile to clsAnalysisToolRunnerBase

July 26, 2011
	- Now calling DeconConsole.exe instead of the DeconTools backend
		- Removed all the code related to DeconTools looping since no longer used

July 26, 2011
	- Plugin AnalysisManagerDecon2lsV2PlugIn now uses class clsAnalysisToolRunnerDecon2ls
	- Added AbortProgramNow to clsRunDosProgram
	- Now using String.IsNullOrWhiteSpace in GetParam for job and manager params
	- Updated LCMSFeatureFinder plugin to choosing a specific version of the LCMSFeatureFinder to run
		- Defined via settings file option

July 22, 2011
	- Altered logic when unable to delete files in the work directory

July 20, 2011
	- Made DeleteFileWithRetries a shared function
	- Tweaked calls to clsLogTools.WriteLog() to pass the exception

July 20, 2011
	- The MSGF Plugin now splits MSGF input files into segments with 25,000 entries per segment

July 13, 2011
	- Now checking for empty _DTA.txt file in DTA_Split and Inspect plugins

July 08, 2011
	- Updated to .NET 4
	- Added StoreToolVersionInfo function to all plugins

July 07, 2011
	- Updated Extraction plugin to use PeptideProphetRunner.exe instead of directly calling PeptideProphetLibrary.dll

June 02, 2011
	- Updated MultiAlign aggregator to support handling isos files or lcmsfeatures files.

June 02, 2011
	- New Protein Export DLLs

May 27, 2011
	- Added support for new command line switches for MultiAlign.  This includes adding plots.

May 19, 2011
	- Recompiled all plugins due to update to interface
		- Added property NeedToAbortProcessing to interface IToolRunner and clsAnalysisToolRunnerBase
	- Added post-build event to auto-copy DLLs to the AM_Common folder

May 18, 2011
	- Updated results transfer tool to create the parent folder of a dataset folder, if missing

May 18, 2011
	- Updated LCMSFeatureFinder plugin to copy the file specified by DeconToolsFilterFileName in the .ini file to the working directory (so that we can save an archive copy)

May 16, 2011
	- Fixed bug in Decon2LS plugin that returned CloseOutType.CLOSEOUT_SUCCESS instead of eReturnCode

May 16, 2011
	- Updated DoAnalysisJob to more closely resemble the capture task manager

May 10, 2011
	- Add support for MSConvert, which can create mzML or mzXML files

May 02, 2011
	- Adding new plugin for MultiAlign Aggregation.
		- This option uses a data package as its source.

April 25, 2011
	- Added support for renaming log file used by the MultiAlign plugin

April 21, 2011
	- Added MultiAlign plugin.
		- This plugin supports running MultiAlign in the DMS pipeline.

April 21, 2011
	- Updated CopyResultsFolderToServer to copy subfolders to the server (in addition to copying files)

April 01, 2011
	- ICR2LS Plugin Updates
		- Remove PROCESS_SER_FOLDER_OVER_NETWORK
		- Switch to using DeleteRawDataFiles in clsAnalysisResources

April 01, 2011
	- Expand DeleteRawDataFiles in the ICR2LS Plugin based on code in AM_Decon2ls_PlugIn

March 30, 2011
	- Added the MSXml Bruker Plugin

March 30, 2011
	- Now retrieving the _scans.csv file for the LCMSFeatureFinder plugin
	- Now retrieving analysis.baf file when tool is MSXmlBruker
	- Added DeleteRawFiles to clsAnalysisToolRunnerBase
	- Added closeout code CLOSEOUT_FILE_NOT_FOUND

March 18, 2011
	- Updated CreatePeptideToProteinMapping in Inspect Results Assembly plugin to check for an empty input file (no valid results)

March 18, 2011
	- Added support for option MSGFIgnoreFilters

March 18, 2011
	- Updated clsIonicZipTools to dispose the zipper and call the garbage collector to assure the handle to the .zip file is released

March 17, 2011
	- Updated RetrieveAggregateFiles in clsAnalysisResources to use column SharedResultsFolder from view V_DMS_Data_Package_Aggregation_Jobs

March 17, 2011
	- Added support for Phospho FDR aggregation jobs when the settings file does not contain CID, ETD, or HCD in the name

February 05, 2011
	- New version of PeptideToProteinMapEngine and ProteinCoverageSummarizer (updated to use v1.0.66 of System.Data.SQLite)

January 31, 2011
	- Renamed RAW_DATA_TYPE_BRUKER_TOF_FOLDER to RAW_DATA_TYPE_BRUKER_MALDI_IMAGING
	- Now setting .UseZip64WhenSaving to Ionic.Zip.Zip64Option.AsNecessary
	- No longer changing the readonly bit on every file when cleaning the work directory
	- Updated SEQUEST plugin to delete .DTA files as the corresponding .Out files are created
		- Decreases the time required to delete files after the job finishes

January 31, 2011
	- No longer grabbing _scans.csv file for LCMSFeatureFinder plugin
	- No longer retrieving the _dta.zip file for the Extraction plugin since we stopped computing MScore component of Discriminant Score
	- Disabled creation of IRR and NLI files for Sequest extraction

January 19, 2011
	- New version of PRISM.dll

January 07, 2011
	- Updated all Plugins to use m_WorkDir and m_Dataset
	- Updated to use MyBase.ZipFile and MyBase.UnzipFile instead of PRISM ZipTools class

January 07, 2011
	- Switched from SharpZipLib to Ionic.zip (DotNetZip)

December 08, 2010
	- Change DeconTools.Backend reference to have SpecificVersion=False
	- Update MSDataFileTrimmer to create a log file

December 07, 2010
	- Updates in Decon2LSV2 plugin to support December 2010 version of DeconTools.Backend.dll

December 07, 2010
	- Added a Try/Catch block around the call to DoAnalysisJob() to catch "Could not load file or assembly" errors and allow the job to be failed out

December 03, 2010
	- New version of DeconTools.Backend.dll, which adds support for Bruker .D folders

December 03, 2010
	- Improved error checking in CBoolSafe and CIntSafe

November 22, 2010
	- Added new parameter to the Reporter Ion m/z Filter (Mode 4) in the MSMSSpectrumFilter: ReporterIonMaxIntensityThreshold
		- At least one of the reporter ions must have an intensity at/above this value in order for the spectrum to pass the filter
		- In contrast, ReporterIonMinimumIntensity defines the minimum intensity that a reporter ion must have in order for it to be counted when checking ReporterIonMatchCountMinimum

November 19, 2010
	- Updates in the Decon2LSV2 plugin for Bruker .D folders and Agilent TOF .D folders

November 19, 2010
	- Updated MSMSSpectrumFilter plugin to support new Reporter Ion m/z Filter (Mode 4)

November 15, 2010
	- Update the Decon2LSV2 plugin to support 12T .D folders (which have a ser file and an apexAcquisition.method file)

November 15, 2010
	- Now centroiding the data when creating .mzXML files for the MSGF plugin
		- Results in faster mzXML file generation time and smaller .mzXML files

November 02, 2010
	- Remove Decon2LSRemoter and Decon2LSCAOServer from the solution file for the Decon2LSV2 plugin 

October 29, 2010
	- New versions of DeconMSn, DeconMsnEngine.dll, and MSMSSpectrumFilterAM.dll

October 26, 2010
	- Added support to the MSGF plugin for C-terminal dynamic peptide mods

September 28, 2010
	- Fixed bug in overloaded version of FolderExistsWithRetry in clsAnalysisResults.vb

September 15, 2010
	- Added support for variations in phospho FDR aggregator analyses
		- All three types are no longer required (CID, ETD, HCD).  
		- If a parameter file is left blank, then it is skipped.

September 13, 2010
	- Added function FolderExistsWithRetry() which checks for the existence of a folder, but will retry several times if an error occurs
	- Altered CopyFileWithRetry() logic to increase the time to wait between each retry
		- Waits 10 seconds, then 15, then 22, then 33, then 50 seconds, etc.

September 03, 2010
	- New versions of Protein_Exporter.dll and Protein_Storage.dll

September 02, 2010
	- Fixed benign MoveResultFiles logic bug
	- Updated the DTA split plugin to write the spectra out in a round-robin fashion
		- Removed the SplitToEqualScanCounts mode
	- Added support for using a shuffled DB when running Inspect
	- Updated the LCMSFeatureFinder to copy the .UIMF file if processing an IMS dataset
	- Updated the MSGF plugin to compute MSGF SpecProb values for First-hits files in addition to Synopsis files
	- Updated the MSGF plugin to support for peptide-terminal and protein-terminal static mods

September 02, 2010
	- Added ability to specify the MaxRetryCount value when calling FindValidFolder

August 20, 2010
	- XTandem_HPC Updates

August 12, 2010
	- Now validating that a machine has enough free RAM to run MSGF
	- Updated DTARefinery plugin to use the Param File Generator to obtain the Sequest .Params files

August 05, 2010
	- Updated DLLs: FileConcatenator.dll and PeptideFileExtractor.dll

August 02, 2010
	- Added pre-check for existing .Out files at the start of the Sequest plugin

July 23, 2010
	- Added ability to retrieve a dataset's .mzXML file for use by the MSGF Plugin
		- Looks for folder MSXML_Gen_1_39_00000 off of the dataset folder, where 00000 is the DatasetID

July 23, 2010
	- Improved MSGF results validation

July 22, 2010
	- Now computing % complete when generating DTA files
	- Removed call to clsGlobal.RemoveNonResultFiles() in several plugins
	- Re-worked inspect workflow
	- New version of PeptideHitResultsProcessor
	- Initial commit of MSGF plugin

July 13, 2010
	- Now setting .CreateNoWindow to False when calling AScore_Console.exe
	- Increased AScore_Console thread count to 4

July 08, 2010
	- Changed HPC account name from emsl33210 to mscfidle
	- New MSMSSpectrumFilter that supports filtering by Scan Type (e.g., MSn, HMSn, CID-MSn, CID-HMSn)
	- Removed all MsgBox calls from MSMSSpectrumFilter
	- Synchronized clsProgRunnerThreaded.vb with clsProgRunner.vb in PRISM.Dll
	- Updated the code to add another entry in the AScore.xml (<scan_stats_file></scan_stats_file>) file to calculate the HCD Scan number using the _ScanStatsEx.txt file.

July 07, 2010
	- Now archiving results if the call to clsGlobal.RemoveNonResultFiles fails
	- Now copying MSMSSpectrumFilter.dll from the AM_Common folder
	- Updated to allow a job's "SharedResultsFolders" command to be a comma-delimited list of folder names
	- Updated clsRunDosProgram to support new parameters: CacheStandardOutput,  EchoOutputToConsole,  WriteConsoleOutputToFile, and ConsoleOutputFilePath
	- Now writing any text that XTandem writes to the console to file XTandem_ConsoleOutput.txt
	- Now echoing MASIC's console output to the Analysis Manager console (but not writing it to a file)
	- Now combining InspectConsoleOutput_*.txt files together when running a multi-segment Inspect job.
	- Now writing any text that Inspect writes to the console to file InspectConsoleOutput.txt

July 01, 2010
	- Removed extra Imports statements
	- Disabled looping when running DeconMSn

June 15, 2010
	- Added try/catch handling to function DeleteRawDataFiles

June 15, 2010
	- Added the Phospho FDR Aggregator plugin
	- Added the PRIDE MzXml submission plugin
	- Now using XRawfile to determine the number of spectra in a .Raw file (previously used ICR-2LS)

May 20, 2010
	- Added option to Resume Sequest processing by looking for a file named Resume.txt in the FailedResultsFolder

April 22, 2010
	- Updated MSMSSpectrumFilter to use a new version of MsMsDataFileReader.dll 
		- Optimized processing speed when only filtering by collision mode or MSLevel

March 30, 2010
	- Added additional checks to XTandem_HPC plugin
		- Checks include calling gbalance to get the remaining hours available if in blocked state

March 18, 2010
	- Fix WallTime string building code in MakeMSubFile of XTandem_HPC plugin to allow for WallTimes >= 24 hours.

February 25, 2010
	- Added the DTA_Refinery plugin

February 16, 2010
	- Added the OMSSA plugin

January 22, 2010
	- Updated to support 0.ser folder change from the capture manager.  The S folders are still supported.

January 6, 2010
	- Initial commit of the LCMSFeatureFinder plugin

December 10, 2009
	- Updated to shell to the command prompt to run ICR-2LS Lite
	- Improved logic of distributing .Fasta files to cluster nodes
		- Now performs file size and file date comparison, taking into account daylight savings time differences
	- Now parses the sequest.log file at the completion of a job to verify that the number of processing cores matches the expected value
		- Sets Evaluation_Code to > 0 and updates Evaluation_Message if a problem is found
	- Updated to pass Evaluation_Code and Evaluation_Message to the DMS_Pipeline DB
	- Updated to recognize tools as being Sequest, XTandem, or Inspect when they contain the expected tool name as part of their full name (e.g. Sequest_UseExistingExternalDTA)
	- Added modMain and changed the public classes from Shared to Non-shared in clsMainProcess
	- Now recognizes /T at the command line when performing code testing

September 10, 2009
	- Added support for ManagerErrorCleanupMode
	- Changed logging.config to not log to the DMS5 DB

August 6, 2008
	- Added Inspect plugin