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RenameFiles.bat
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RenameFiles.bat
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move AM_Program\clsAnalysisMgrSettings.cs AM_Program\AnalysisMgrSettings.cs
pause
move AM_Program\clsCleanupMgrErrors.cs AM_Program\CleanupMgrErrors.cs
move AM_Program\clsCodeTest.cs AM_Program\CodeTest.cs
move AM_Program\clsCodeTestAM.cs AM_Program\CodeTestAM.cs
pause
move AM_Program\clsMainProcess.cs AM_Program\MainProcess.cs
move AM_Program\clsPluginLoader.cs AM_Program\PluginLoader.cs
move AM_Shared\clsAnalysisJob.cs AM_Shared\AnalysisJob.cs
move AM_Shared\clsAnalysisMgrBase.cs AM_Shared\AnalysisMgrBase.cs
move AM_Shared\clsAnalysisResources.cs AM_Shared\AnalysisResources.cs
move AM_Shared\clsAnalysisResults.cs AM_Shared\AnalysisResults.cs
move AM_Shared\clsAnalysisToolRunnerBase.cs AM_Shared\AnalysisToolRunnerBase.cs
move AM_Shared\clsAssemblyTools.cs AM_Shared\AssemblyTools.cs
move AM_Shared\clsCDTAUtilities.cs AM_Shared\CDTAUtilities.cs
move AM_Shared\clsDataPackageDatasetInfo.cs AM_Shared\DataPackageDatasetInfo.cs
move AM_Shared\clsDataPackageFileHandler.cs AM_Shared\DataPackageFileHandler.cs
move AM_Shared\clsDataPackageInfoLoader.cs AM_Shared\DataPackageInfoLoader.cs
move AM_Shared\clsDataPackageJobInfo.cs AM_Shared\DataPackageJobInfo.cs
move AM_Shared\clsDBStatusLogger.cs AM_Shared\DBStatusLogger.cs
move AM_Shared\clsDBTask.cs AM_Shared\DBTask.cs
move AM_Shared\clsDirectorySearch.cs AM_Shared\DirectorySearch.cs
move AM_Shared\clsDotNetZipTools.cs AM_Shared\DotNetZipTools.cs
move AM_Shared\clsFileCopyUtilities.cs AM_Shared\FileCopyUtilities.cs
move AM_Shared\clsFileSearch.cs AM_Shared\FileSearch.cs
move AM_Shared\clsFormattedXMLWriter.cs AM_Shared\FormattedXMLWriter.cs
move AM_Shared\clsGlobal.cs AM_Shared\Global.cs
move AM_Shared\clsLoggerBase.cs AM_Shared\LoggerBase.cs
move AM_Shared\clsMemoryUsageLogger.cs AM_Shared\MemoryUsageLogger.cs
move AM_Shared\clsMessageContainer.cs AM_Shared\MessageContainer.cs
move AM_Shared\clsMessageQueueLogger.cs AM_Shared\MessageQueueLogger.cs
move AM_Shared\clsMessageSender.cs AM_Shared\MessageSender.cs
move AM_Shared\clsMyEMSLUtilities.cs AM_Shared\MyEMSLUtilities.cs
move AM_Shared\clsOfflineProcessing.cs AM_Shared\OfflineProcessing.cs
move AM_Shared\clsProteinCollectionInfo.cs AM_Shared\ProteinCollectionInfo.cs
move AM_Shared\clsProteowizardTools.cs AM_Shared\ProteowizardTools.cs
move AM_Shared\clsRemoteMonitor.cs AM_Shared\RemoteMonitor.cs
move AM_Shared\clsRemoteTransferUtility.cs AM_Shared\RemoteTransferUtility.cs
move AM_Shared\clsRunDosProgram.cs AM_Shared\RunDosProgram.cs
move AM_Shared\clsScanStatsGenerator.cs AM_Shared\ScanStatsGenerator.cs
move AM_Shared\clsSplitCattedFiles.cs AM_Shared\SplitCattedFiles.cs
move AM_Shared\clsSplitFastaFileUtilities.cs AM_Shared\SplitFastaFileUtilities.cs
move AM_Shared\clsSplitMGFFile.cs AM_Shared\SplitMGFFile.cs
move AM_Shared\clsSqLiteUtilities.cs AM_Shared\SqLiteUtilities.cs
move AM_Shared\clsStatusFile.cs AM_Shared\StatusFile.cs
move AM_Shared\clsSummaryFile.cs AM_Shared\SummaryFile.cs
move AM_Shared\clsSystemProcessInfo.cs AM_Shared\SystemProcessInfo.cs
move AM_Shared\clsToolVersionUtilities.cs AM_Shared\ToolVersionUtilities.cs
move AM_Shared\clsXMLUtils.cs AM_Shared\XMLUtils.cs
move Plugins\AM_Ape_PlugIn\clsAnalysisResourcesApe.cs Plugins\AM_Ape_PlugIn\AnalysisResourcesApe.cs
move Plugins\AM_Ape_PlugIn\clsAnalysisToolRunnerApe.cs Plugins\AM_Ape_PlugIn\AnalysisToolRunnerApe.cs
move Plugins\AM_Ape_PlugIn\clsApeAMBase.cs Plugins\AM_Ape_PlugIn\ApeAMBase.cs
move Plugins\AM_Ape_PlugIn\clsApeAMGetImprovResults.cs Plugins\AM_Ape_PlugIn\ApeAMGetImprovResults.cs
move Plugins\AM_Ape_PlugIn\clsApeAMGetQRollupResults.cs Plugins\AM_Ape_PlugIn\ApeAMGetQRollupResults.cs
move Plugins\AM_Ape_PlugIn\clsApeAMGetViperResults.cs Plugins\AM_Ape_PlugIn\ApeAMGetViperResults.cs
move Plugins\AM_Ape_PlugIn\clsApeAMOperations.cs Plugins\AM_Ape_PlugIn\ApeAMOperations.cs
move Plugins\AM_Ape_PlugIn\clsApeAMRunWorkflow.cs Plugins\AM_Ape_PlugIn\ApeAMRunWorkflow.cs
move Plugins\AM_AScore_PlugIn\clsAnalysisResourcesAScore.cs Plugins\AM_AScore_PlugIn\AnalysisResourcesAScore.cs
move Plugins\AM_AScore_PlugIn\clsAnalysisToolRunnerAScore.cs Plugins\AM_AScore_PlugIn\AnalysisToolRunnerAScore.cs
move Plugins\AM_AScore_PlugIn\clsAScoreMage.cs Plugins\AM_AScore_PlugIn\AScoreMage.cs
move Plugins\AM_Bruker_DA_Export\clsAnalysisResourcesBrukerDAExport.cs Plugins\AM_Bruker_DA_Export\AnalysisResourcesBrukerDAExport.cs
move Plugins\AM_Bruker_DA_Export\clsAnalysisToolRunnerBrukerDAExport.cs Plugins\AM_Bruker_DA_Export\AnalysisToolRunnerBrukerDAExport.cs
move Plugins\AM_Cyclops_PlugIn\clsAnalysisResourcesCyclops.cs Plugins\AM_Cyclops_PlugIn\AnalysisResourcesCyclops.cs
move Plugins\AM_Cyclops_PlugIn\clsAnalysisToolRunnerCyclops.cs Plugins\AM_Cyclops_PlugIn\AnalysisToolRunnerCyclops.cs
move Plugins\AM_DataImport_Plugin\clsAnalysisResourcesDataImport.cs Plugins\AM_DataImport_Plugin\AnalysisResourcesDataImport.cs
pause
move Plugins\AM_DataImport_Plugin\clsAnalysisToolRunnerDataImport.cs Plugins\AM_DataImport_Plugin\AnalysisToolRunnerDataImport.cs
move Plugins\AM_Decon2ls_PlugIn_Decon2LSV2\clsAnalysisResourcesDecon2ls.cs Plugins\AM_Decon2ls_PlugIn_Decon2LSV2\AnalysisResourcesDecon2ls.cs
move Plugins\AM_Decon2ls_PlugIn_Decon2LSV2\clsAnalysisToolRunnerDecon2ls.cs Plugins\AM_Decon2ls_PlugIn_Decon2LSV2\AnalysisToolRunnerDecon2ls.cs
move Plugins\AM_Decon2ls_PlugIn_Decon2LSV2\clsDeconToolsQCPlotsGenerator.cs Plugins\AM_Decon2ls_PlugIn_Decon2LSV2\DeconToolsQCPlotsGenerator.cs
move Plugins\AM_Decon2ls_PlugIn_Decon2LSV2\clsXMLParamFileReader.cs Plugins\AM_Decon2ls_PlugIn_Decon2LSV2\XMLParamFileReader.cs
move Plugins\AM_DeconPeakDetector_PlugIn\clsAnalysisResourcesDeconPeakDetector.cs Plugins\AM_DeconPeakDetector_PlugIn\AnalysisResourcesDeconPeakDetector.cs
move Plugins\AM_DeconPeakDetector_PlugIn\clsAnalysisToolRunnerDeconPeakDetector.cs Plugins\AM_DeconPeakDetector_PlugIn\AnalysisToolRunnerDeconPeakDetector.cs
move Plugins\AM_DtaRefinery_PlugIn\clsAnalysisResourcesDtaRefinery.cs Plugins\AM_DtaRefinery_PlugIn\AnalysisResourcesDtaRefinery.cs
move Plugins\AM_DtaRefinery_PlugIn\clsAnalysisToolRunnerDtaRefinery.cs Plugins\AM_DtaRefinery_PlugIn\AnalysisToolRunnerDtaRefinery.cs
move Plugins\AM_DtaRefinery_PlugIn\clsDeconMSnLogFileValidator.cs Plugins\AM_DtaRefinery_PlugIn\DeconMSnLogFileValidator.cs
move Plugins\AM_DtaRefinery_PlugIn\clsDtaRefLogMassErrorExtractor.cs Plugins\AM_DtaRefinery_PlugIn\DtaRefLogMassErrorExtractor.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsConcatToolWrapper.cs Plugins\AM_DTASpectraFileGen_PlugIn\ConcatToolWrapper.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsDtaGen.cs Plugins\AM_DTASpectraFileGen_PlugIn\DtaGen.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsDtaGenDeconConsole.cs Plugins\AM_DTASpectraFileGen_PlugIn\DtaGenDeconConsole.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsDtaGenMSConvert.cs Plugins\AM_DTASpectraFileGen_PlugIn\DtaGenMSConvert.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsDtaGenRawConverter.cs Plugins\AM_DTASpectraFileGen_PlugIn\DtaGenRawConverter.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsDtaGenResources.cs Plugins\AM_DTASpectraFileGen_PlugIn\DtaGenResources.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsDtaGenThermoRaw.cs Plugins\AM_DTASpectraFileGen_PlugIn\DtaGenThermoRaw.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsDtaGenToolRunner.cs Plugins\AM_DTASpectraFileGen_PlugIn\DtaGenToolRunner.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsMGFConverter.cs Plugins\AM_DTASpectraFileGen_PlugIn\MGFConverter.cs
move Plugins\AM_DTASpectraFileGen_PlugIn\clsMGFtoDtaGenMainProcess.cs Plugins\AM_DTASpectraFileGen_PlugIn\MGFtoDtaGenMainProcess.cs
move Plugins\AM_DTA_Import_PlugIn\clsAnalysisResourcesDtaImport.cs Plugins\AM_DTA_Import_PlugIn\AnalysisResourcesDtaImport.cs
move Plugins\AM_DTA_Import_PlugIn\clsAnalysisToolRunnerDtaImport.cs Plugins\AM_DTA_Import_PlugIn\AnalysisToolRunnerDtaImport.cs
move Plugins\AM_DTA_Split_PlugIn\clsAnalysisResourcesDtaSplit.cs Plugins\AM_DTA_Split_PlugIn\AnalysisResourcesDtaSplit.cs
move Plugins\AM_DTA_Split_PlugIn\clsAnalysisToolRunnerDtaSplit.cs Plugins\AM_DTA_Split_PlugIn\AnalysisToolRunnerDtaSplit.cs
move Plugins\AM_Extraction_PlugIn\clsAnalysisResourcesExtraction.cs Plugins\AM_Extraction_PlugIn\AnalysisResourcesExtraction.cs
move Plugins\AM_Extraction_PlugIn\clsExtractToolRunner.cs Plugins\AM_Extraction_PlugIn\ExtractToolRunner.cs
move Plugins\AM_Extraction_PlugIn\clsMSGFPlusPSMs.cs Plugins\AM_Extraction_PlugIn\MSGFPlusPSMs.cs
move Plugins\AM_Extraction_PlugIn\clsPepHitResultsProcWrapper.cs Plugins\AM_Extraction_PlugIn\PepHitResultsProcWrapper.cs
move Plugins\AM_Extraction_PlugIn\clsPeptideExtractWrapper.cs Plugins\AM_Extraction_PlugIn\PeptideExtractWrapper.cs
move Plugins\AM_Extraction_PlugIn\clsPeptideProphetWrapper.cs Plugins\AM_Extraction_PlugIn\PeptideProphetWrapper.cs
move Plugins\AM_Extraction_PlugIn\clsPHRPMassErrorValidator.cs Plugins\AM_Extraction_PlugIn\PHRPMassErrorValidator.cs
move Plugins\AM_Formularity\clsAnalysisResourcesFormularity.cs Plugins\AM_Formularity\AnalysisResourcesFormularity.cs
move Plugins\AM_Formularity\clsAnalysisToolRunnerFormularity.cs Plugins\AM_Formularity\AnalysisToolRunnerFormularity.cs
move Plugins\AM_Formularity\clsPdfPageInfo.cs Plugins\AM_Formularity\PdfPageInfo.cs
move Plugins\AM_Formularity\clsPngToPdfConverter.cs Plugins\AM_Formularity\PngToPdfConverter.cs
move Plugins\AM_GlyQIQ_Plugin\clsAnalysisResourcesGlyQIQ.cs Plugins\AM_GlyQIQ_Plugin\AnalysisResourcesGlyQIQ.cs
move Plugins\AM_GlyQIQ_Plugin\clsAnalysisToolRunnerGlyQIQ.cs Plugins\AM_GlyQIQ_Plugin\AnalysisToolRunnerGlyQIQ.cs
move Plugins\AM_GlyQIQ_Plugin\clsGlyQIqRunner.cs Plugins\AM_GlyQIQ_Plugin\GlyQIqRunner.cs
move Plugins\AM_ICR2LS_PlugIn\clsAnalysisResourcesIcr2ls.cs Plugins\AM_ICR2LS_PlugIn\AnalysisResourcesIcr2ls.cs
move Plugins\AM_ICR2LS_PlugIn\clsAnalysisToolRunnerICR.cs Plugins\AM_ICR2LS_PlugIn\AnalysisToolRunnerICR.cs
move Plugins\AM_ICR2LS_PlugIn\clsAnalysisToolRunnerICRBase.cs Plugins\AM_ICR2LS_PlugIn\AnalysisToolRunnerICRBase.cs
move Plugins\AM_ICR2LS_PlugIn\clsAnalysisToolRunnerLTQ_FTPek.cs Plugins\AM_ICR2LS_PlugIn\AnalysisToolRunnerLTQ_FTPek.cs
move Plugins\AM_IDM_Plugin\clsAnalysisResourcesIDM.cs Plugins\AM_IDM_Plugin\AnalysisResourcesIDM.cs
move Plugins\AM_IDM_Plugin\clsAnalysisToolRunnerIDM.cs Plugins\AM_IDM_Plugin\AnalysisToolRunnerIDM.cs
move Plugins\AM_IDPicker_PlugIn\clsAnalysisResourcesIDPicker.cs Plugins\AM_IDPicker_PlugIn\AnalysisResourcesIDPicker.cs
move Plugins\AM_IDPicker_PlugIn\clsAnalysisToolRunnerIDPicker.cs Plugins\AM_IDPicker_PlugIn\AnalysisToolRunnerIDPicker.cs
move Plugins\AM_InspectResultsAssembly_PlugIn\clsAnalysisResourcesInspResultsAssembly.cs Plugins\AM_InspectResultsAssembly_PlugIn\AnalysisResourcesInspResultsAssembly.cs
move Plugins\AM_InspectResultsAssembly_PlugIn\clsAnalysisToolRunnerInspResultsAssembly.cs Plugins\AM_InspectResultsAssembly_PlugIn\AnalysisToolRunnerInspResultsAssembly.cs
move Plugins\AM_InSpecT_PlugIn\clsAnalysisResourcesIN.cs Plugins\AM_InSpecT_PlugIn\AnalysisResourcesIN.cs
move Plugins\AM_InSpecT_PlugIn\clsAnalysisToolRunnerIN.cs Plugins\AM_InSpecT_PlugIn\AnalysisToolRunnerIN.cs
move Plugins\AM_InSpecT_PlugIn\clsCreateInspectIndexedDB.cs Plugins\AM_InSpecT_PlugIn\CreateInspectIndexedDB.cs
move Plugins\AM_LCMSFeatureFinder_Plugin\clsAnalysisResourcesLCMSFF.cs Plugins\AM_LCMSFeatureFinder_Plugin\AnalysisResourcesLCMSFF.cs
move Plugins\AM_LCMSFeatureFinder_Plugin\clsAnalysisToolRunnerLCMSFF.cs Plugins\AM_LCMSFeatureFinder_Plugin\AnalysisToolRunnerLCMSFF.cs
move Plugins\AM_LipidMapSearch_Plugin\clsAnalysisResourcesLipidMapSearch.cs Plugins\AM_LipidMapSearch_Plugin\AnalysisResourcesLipidMapSearch.cs
move Plugins\AM_LipidMapSearch_Plugin\clsAnalysisToolRunnerLipidMapSearch.cs Plugins\AM_LipidMapSearch_Plugin\AnalysisToolRunnerLipidMapSearch.cs
move Plugins\AM_Mage_PlugIn\clsAnalysisResourcesMAC.cs Plugins\AM_Mage_PlugIn\AnalysisResourcesMAC.cs
move Plugins\AM_Mage_PlugIn\clsAnalysisResourcesMage.cs Plugins\AM_Mage_PlugIn\AnalysisResourcesMage.cs
move Plugins\AM_Mage_PlugIn\clsAnalysisToolRunnerMAC.cs Plugins\AM_Mage_PlugIn\AnalysisToolRunnerMAC.cs
move Plugins\AM_Mage_PlugIn\clsAnalysisToolRunnerMage.cs Plugins\AM_Mage_PlugIn\AnalysisToolRunnerMage.cs
move Plugins\AM_Masic_Plugin\clsAnalysisResourcesMASIC.cs Plugins\AM_Masic_Plugin\AnalysisResourcesMASIC.cs
move Plugins\AM_Masic_Plugin\clsAnalysisToolRunnerMASICAgilent.cs Plugins\AM_Masic_Plugin\AnalysisToolRunnerMASICAgilent.cs
move Plugins\AM_Masic_Plugin\clsAnalysisToolRunnerMASICBase.cs Plugins\AM_Masic_Plugin\AnalysisToolRunnerMASICBase.cs
move Plugins\AM_Masic_Plugin\clsAnalysisToolRunnerMASICFinnigan.cs Plugins\AM_Masic_Plugin\AnalysisToolRunnerMASICFinnigan.cs
move Plugins\AM_MetaboliteDetector_Plugin\clsAnalysisResourcesMetaboliteDetector.cs Plugins\AM_MetaboliteDetector_Plugin\AnalysisResourcesMetaboliteDetector.cs
move Plugins\AM_MetaboliteDetector_Plugin\clsAnalysisToolRunnerMetaboliteDetector.cs Plugins\AM_MetaboliteDetector_Plugin\AnalysisToolRunnerMetaboliteDetector.cs
move Plugins\AM_MODa_PlugIn\clsAnalysisResourcesMODa.cs Plugins\AM_MODa_PlugIn\AnalysisResourcesMODa.cs
move Plugins\AM_MODa_PlugIn\clsAnalysisToolRunnerMODa.cs Plugins\AM_MODa_PlugIn\AnalysisToolRunnerMODa.cs
move Plugins\AM_MODPlus_Plugin\clsAnalysisResourcesMODPlus.cs Plugins\AM_MODPlus_Plugin\AnalysisResourcesMODPlus.cs
move Plugins\AM_MODPlus_Plugin\clsAnalysisToolRunnerMODPlus.cs Plugins\AM_MODPlus_Plugin\AnalysisToolRunnerMODPlus.cs
move Plugins\AM_MODPlus_Plugin\clsMODPlusResultsReader.cs Plugins\AM_MODPlus_Plugin\MODPlusResultsReader.cs
move Plugins\AM_MODPlus_Plugin\clsMODPlusRunner.cs Plugins\AM_MODPlus_Plugin\MODPlusRunner.cs
move Plugins\AM_MSAlign_Histone_Plugin\clsAnalysisResourcesMSAlignHistone.cs Plugins\AM_MSAlign_Histone_Plugin\AnalysisResourcesMSAlignHistone.cs
move Plugins\AM_MSAlign_Histone_Plugin\clsAnalysisToolRunnerMSAlignHistone.cs Plugins\AM_MSAlign_Histone_Plugin\AnalysisToolRunnerMSAlignHistone.cs
move Plugins\AM_MSAlign_Plugin\clsAnalysisResourcesMSAlign.cs Plugins\AM_MSAlign_Plugin\AnalysisResourcesMSAlign.cs
move Plugins\AM_MSAlign_Plugin\clsAnalysisToolRunnerMSAlign.cs Plugins\AM_MSAlign_Plugin\AnalysisToolRunnerMSAlign.cs
move Plugins\AM_MSAlign_Quant_Plugin\clsAnalysisResourcesMSAlignQuant.cs Plugins\AM_MSAlign_Quant_Plugin\AnalysisResourcesMSAlignQuant.cs
move Plugins\AM_MSAlign_Quant_Plugin\clsAnalysisToolRunnerMSAlignQuant.cs Plugins\AM_MSAlign_Quant_Plugin\AnalysisToolRunnerMSAlignQuant.cs
move Plugins\AM_MSDeconv_Plugin\clsAnalysisResourcesMSDeconv.cs Plugins\AM_MSDeconv_Plugin\AnalysisResourcesMSDeconv.cs
move Plugins\AM_MSDeconv_Plugin\clsAnalysisToolRunnerMSDeconv.cs Plugins\AM_MSDeconv_Plugin\AnalysisToolRunnerMSDeconv.cs
move Plugins\AM_MSDeconv_Plugin\clsRenumberMzXMLScans.cs Plugins\AM_MSDeconv_Plugin\RenumberMzXMLScans.cs
move Plugins\AM_MSFragger_Plugin\clsAnalysisResourcesMSFragger.cs Plugins\AM_MSFragger_Plugin\AnalysisResourcesMSFragger.cs
move Plugins\AM_MSFragger_Plugin\clsAnalysisToolRunnerMSFragger.cs Plugins\AM_MSFragger_Plugin\AnalysisToolRunnerMSFragger.cs
move Plugins\AM_MSGFDB_PlugIn\clsAnalysisResourcesMSGFDB.cs Plugins\AM_MSGFDB_PlugIn\AnalysisResourcesMSGFDB.cs
move Plugins\AM_MSGFDB_PlugIn\clsAnalysisToolRunnerMSGFDB.cs Plugins\AM_MSGFDB_PlugIn\AnalysisToolRunnerMSGFDB.cs
move Plugins\AM_MSGFDB_PlugIn\clsCreateMSGFDBSuffixArrayFiles.cs Plugins\AM_MSGFDB_PlugIn\CreateMSGFDBSuffixArrayFiles.cs
move Plugins\AM_MSGFDB_PlugIn\clsFastaContaminantUtility.cs Plugins\AM_MSGFDB_PlugIn\FastaContaminantUtility.cs
move Plugins\AM_MSGFDB_PlugIn\clsMSGFPlusUtils.cs Plugins\AM_MSGFDB_PlugIn\MSGFPlusUtils.cs
move Plugins\AM_MSGFDB_PlugIn\clsScanTypeFileCreator.cs Plugins\AM_MSGFDB_PlugIn\ScanTypeFileCreator.cs
pause
move Plugins\AM_MSGF_PlugIn\clsAnalysisResourcesMSGF.cs Plugins\AM_MSGF_PlugIn\AnalysisResourcesMSGF.cs
move Plugins\AM_MSGF_PlugIn\clsMSGFInputCreator.cs Plugins\AM_MSGF_PlugIn\MSGFInputCreator.cs
move Plugins\AM_MSGF_PlugIn\clsMSGFInputCreatorInspect.cs Plugins\AM_MSGF_PlugIn\MSGFInputCreatorInspect.cs
move Plugins\AM_MSGF_PlugIn\clsMSGFInputCreatorMODa.cs Plugins\AM_MSGF_PlugIn\MSGFInputCreatorMODa.cs
move Plugins\AM_MSGF_PlugIn\clsMSGFInputCreatorMODPlus.cs Plugins\AM_MSGF_PlugIn\MSGFInputCreatorMODPlus.cs
move Plugins\AM_MSGF_PlugIn\clsMSGFInputCreatorMSGFDB.cs Plugins\AM_MSGF_PlugIn\MSGFInputCreatorMSGFDB.cs
move Plugins\AM_MSGF_PlugIn\clsMSGFInputCreatorSequest.cs Plugins\AM_MSGF_PlugIn\MSGFInputCreatorSequest.cs
move Plugins\AM_MSGF_PlugIn\clsMSGFInputCreatorXTandem.cs Plugins\AM_MSGF_PlugIn\MSGFInputCreatorXTandem.cs
move Plugins\AM_MSGF_PlugIn\clsMSGFToolRunner.cs Plugins\AM_MSGF_PlugIn\MSGFToolRunner.cs
move Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\clsMSGFResultsSummarizer.cs Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\MSGFResultsSummarizer.cs
move Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\clsNormalizedPeptideInfo.cs Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\NormalizedPeptideInfo.cs
move Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\clsPSMInfo.cs Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\PSMInfo.cs
move Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\clsPSMStats.cs Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\PSMStats.cs
move Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\clsUniqueSeqInfo.cs Plugins\AM_MSGF_PlugIn\MSGFResultsSummarizerDLL\UniqueSeqInfo.cs
move Plugins\AM_MSMSSpectrumFilter_PlugIn\clsAnalysisResourcesMsMsSpectrumFilter.cs Plugins\AM_MSMSSpectrumFilter_PlugIn\AnalysisResourcesMsMsSpectrumFilter.cs
move Plugins\AM_MSMSSpectrumFilter_PlugIn\clsAnalysisToolRunnerMsMsSpectrumFilter.cs Plugins\AM_MSMSSpectrumFilter_PlugIn\AnalysisToolRunnerMsMsSpectrumFilter.cs
move Plugins\AM_MSPathFinder_Plugin\clsAnalysisResourcesMSPathFinder.cs Plugins\AM_MSPathFinder_Plugin\AnalysisResourcesMSPathFinder.cs
move Plugins\AM_MSPathFinder_Plugin\clsAnalysisToolRunnerMSPathFinder.cs Plugins\AM_MSPathFinder_Plugin\AnalysisToolRunnerMSPathFinder.cs
move Plugins\AM_MSXML_Bruker_PlugIn\clsAnalysisResourcesMSXMLBruker.cs Plugins\AM_MSXML_Bruker_PlugIn\AnalysisResourcesMSXMLBruker.cs
move Plugins\AM_MSXML_Bruker_PlugIn\clsAnalysisToolRunnerMSXMLBruker.cs Plugins\AM_MSXML_Bruker_PlugIn\AnalysisToolRunnerMSXMLBruker.cs
move Plugins\AM_MSXML_Bruker_PlugIn\clsCompassXportRunner.cs Plugins\AM_MSXML_Bruker_PlugIn\CompassXportRunner.cs
move Plugins\AM_MSXML_Gen_PlugIn\clsAnalysisResourcesMSXMLGen.cs Plugins\AM_MSXML_Gen_PlugIn\AnalysisResourcesMSXMLGen.cs
move Plugins\AM_MSXML_Gen_PlugIn\clsAnalysisToolRunnerMSXMLGen.cs Plugins\AM_MSXML_Gen_PlugIn\AnalysisToolRunnerMSXMLGen.cs
move Plugins\AM_MSXML_Gen_PlugIn\clsMSXmlCreator.cs Plugins\AM_MSXML_Gen_PlugIn\MSXmlCreator.cs
move Plugins\AM_MSXML_Gen_PlugIn\clsMSXmlGen.cs Plugins\AM_MSXML_Gen_PlugIn\MSXmlGen.cs
move Plugins\AM_MSXML_Gen_PlugIn\clsMSXmlGenMSConvert.cs Plugins\AM_MSXML_Gen_PlugIn\MSXmlGenMSConvert.cs
move Plugins\AM_MSXML_Gen_PlugIn\clsMSXMLGenReadW.cs Plugins\AM_MSXML_Gen_PlugIn\MSXMLGenReadW.cs
move Plugins\AM_MSXML_Gen_PlugIn\clsParentIonUpdater.cs Plugins\AM_MSXML_Gen_PlugIn\ParentIonUpdater.cs
move Plugins\AM_MSXML_Gen_PlugIn\clsRawConverterRunner.cs Plugins\AM_MSXML_Gen_PlugIn\RawConverterRunner.cs
move Plugins\AM_MultiAlign_Aggregator_PlugIn\clsAnalysisResourcesMultiAlignAggregator.cs Plugins\AM_MultiAlign_Aggregator_PlugIn\AnalysisResourcesMultiAlignAggregator.cs
move Plugins\AM_MultiAlign_Aggregator_PlugIn\clsAnalysisToolRunnerMultiAlignAggregator.cs Plugins\AM_MultiAlign_Aggregator_PlugIn\AnalysisToolRunnerMultiAlignAggregator.cs
move Plugins\AM_MultiAlign_Aggregator_PlugIn\clsMultiAlignMage.cs Plugins\AM_MultiAlign_Aggregator_PlugIn\MultiAlignMage.cs
move Plugins\AM_MultiAlign_Plugin\clsAnalysisResourcesMultiAlign.cs Plugins\AM_MultiAlign_Plugin\AnalysisResourcesMultiAlign.cs
move Plugins\AM_MultiAlign_Plugin\clsAnalysisToolRunnerMultiAlign.cs Plugins\AM_MultiAlign_Plugin\AnalysisToolRunnerMultiAlign.cs
move Plugins\AM_Mz_Refinery_Plugin\clsAnalysisResourcesMzRefinery.cs Plugins\AM_Mz_Refinery_Plugin\AnalysisResourcesMzRefinery.cs
move Plugins\AM_Mz_Refinery_Plugin\clsAnalysisToolRunnerMzRefinery.cs Plugins\AM_Mz_Refinery_Plugin\AnalysisToolRunnerMzRefinery.cs
move Plugins\AM_Mz_Refinery_Plugin\clsMassErrorInfo.cs Plugins\AM_Mz_Refinery_Plugin\MassErrorInfo.cs
move Plugins\AM_Mz_Refinery_Plugin\clsMzRefineryMassErrorStatsExtractor.cs Plugins\AM_Mz_Refinery_Plugin\MzRefineryMassErrorStatsExtractor.cs
move Plugins\AM_NOMSI\clsAnalysisResourcesNOMSI.cs Plugins\AM_NOMSI\AnalysisResourcesNOMSI.cs
move Plugins\AM_NOMSI\clsAnalysisToolRunnerNOMSI.cs Plugins\AM_NOMSI\AnalysisToolRunnerNOMSI.cs
move Plugins\AM_OMSSA_PlugIn\clsAnalysisResourcesOM.cs Plugins\AM_OMSSA_PlugIn\AnalysisResourcesOM.cs
move Plugins\AM_OMSSA_PlugIn\clsAnalysisToolRunnerOM.cs Plugins\AM_OMSSA_PlugIn\AnalysisToolRunnerOM.cs
move Plugins\AM_PBFSpectraFileGen_PlugIn\clsAnalysisResourcesPBFGenerator.cs Plugins\AM_PBFSpectraFileGen_PlugIn\AnalysisResourcesPBFGenerator.cs
move Plugins\AM_PBFSpectraFileGen_PlugIn\clsAnalysisToolRunnerPBFGenerator.cs Plugins\AM_PBFSpectraFileGen_PlugIn\AnalysisToolRunnerPBFGenerator.cs
move Plugins\AM_PepProtProphet_Plugin\clsAnalysisResourcesPepProtProphet.cs Plugins\AM_PepProtProphet_Plugin\AnalysisResourcesPepProtProphet.cs
move Plugins\AM_PepProtProphet_Plugin\clsAnalysisToolRunnerPepProtProphet.cs Plugins\AM_PepProtProphet_Plugin\AnalysisToolRunnerPepProtProphet.cs
move Plugins\AM_Phospho_FDR_Aggregator_PlugIn\clsAnalysisResourcesPhosphoFdrAggregator.cs Plugins\AM_Phospho_FDR_Aggregator_PlugIn\AnalysisResourcesPhosphoFdrAggregator.cs
move Plugins\AM_Phospho_FDR_Aggregator_PlugIn\clsAnalysisToolRunnerPhosphoFdrAggregator.cs Plugins\AM_Phospho_FDR_Aggregator_PlugIn\AnalysisToolRunnerPhosphoFdrAggregator.cs
move Plugins\AM_PRIDE_Converter_PlugIn\clsAnalysisResourcesPRIDEConverter.cs Plugins\AM_PRIDE_Converter_PlugIn\AnalysisResourcesPRIDEConverter.cs
move Plugins\AM_PRIDE_Converter_PlugIn\clsAnalysisToolRunnerPRIDEConverter.cs Plugins\AM_PRIDE_Converter_PlugIn\AnalysisToolRunnerPRIDEConverter.cs
move Plugins\AM_PRIDE_Converter_PlugIn\clsPXFileInfo.cs Plugins\AM_PRIDE_Converter_PlugIn\PXFileInfo.cs
move Plugins\AM_PRIDE_Converter_PlugIn\clsPXFileInfoBase.cs Plugins\AM_PRIDE_Converter_PlugIn\PXFileInfoBase.cs
move Plugins\AM_PRIDE_Converter_PlugIn\clsResultFileContainer.cs Plugins\AM_PRIDE_Converter_PlugIn\ResultFileContainer.cs
move Plugins\AM_PRIDE_Converter_PlugIn\clsSampleMetadata.cs Plugins\AM_PRIDE_Converter_PlugIn\SampleMetadata.cs
move Plugins\AM_PRIDE_MzXML_PlugIn\clsAnalysisResourcesPRIDEMzXML.cs Plugins\AM_PRIDE_MzXML_PlugIn\AnalysisResourcesPRIDEMzXML.cs
move Plugins\AM_PRIDE_MzXML_PlugIn\clsAnalysisToolRunnerPRIDEMzXML.cs Plugins\AM_PRIDE_MzXML_PlugIn\AnalysisToolRunnerPRIDEMzXML.cs
move Plugins\AM_ProMex_Plugin\clsAnalysisResourcesProMex.cs Plugins\AM_ProMex_Plugin\AnalysisResourcesProMex.cs
move Plugins\AM_ProMex_Plugin\clsAnalysisToolRunnerProMex.cs Plugins\AM_ProMex_Plugin\AnalysisToolRunnerProMex.cs
move Plugins\AM_ProSightPC_Quant_Plugin\clsAnalysisResourcesProSightQuant.cs Plugins\AM_ProSightPC_Quant_Plugin\AnalysisResourcesProSightQuant.cs
move Plugins\AM_ProSightPC_Quant_Plugin\clsAnalysisToolRunnerProSightQuant.cs Plugins\AM_ProSightPC_Quant_Plugin\AnalysisToolRunnerProSightQuant.cs
move Plugins\AM_QC-ART_PlugIn\clsAnalysisResourcesQCART.cs Plugins\AM_QC-ART_PlugIn\AnalysisResourcesQCART.cs
move Plugins\AM_QC-ART_PlugIn\clsAnalysisToolRunnerQCART.cs Plugins\AM_QC-ART_PlugIn\AnalysisToolRunnerQCART.cs
move Plugins\AM_RepoPkgr_PlugIn\clsAnalysisResourcesRepoPkgr.cs Plugins\AM_RepoPkgr_PlugIn\AnalysisResourcesRepoPkgr.cs
move Plugins\AM_RepoPkgr_PlugIn\clsAnalysisToolRunnerRepoPkgr.cs Plugins\AM_RepoPkgr_PlugIn\AnalysisToolRunnerRepoPkgr.cs
move Plugins\AM_ResultsCleanup_PlugIn\clsAnalysisResourcesResultsCleanup.cs Plugins\AM_ResultsCleanup_PlugIn\AnalysisResourcesResultsCleanup.cs
move Plugins\AM_ResultsCleanup_PlugIn\clsAnalysisToolRunnerResultsCleanup.cs Plugins\AM_ResultsCleanup_PlugIn\AnalysisToolRunnerResultsCleanup.cs
move Plugins\AM_ResultsXfer_PlugIn\clsAnalysisResourcesResultXfer.cs Plugins\AM_ResultsXfer_PlugIn\AnalysisResourcesResultXfer.cs
move Plugins\AM_ResultsXfer_PlugIn\clsResultXferToolRunner.cs Plugins\AM_ResultsXfer_PlugIn\ResultXferToolRunner.cs
move Plugins\AM_Sequest_PlugIn\clsAnalysisResourcesSeq.cs Plugins\AM_Sequest_PlugIn\AnalysisResourcesSeq.cs
move Plugins\AM_Sequest_PlugIn\clsAnalysisToolRunnerAgilentSeq.cs Plugins\AM_Sequest_PlugIn\AnalysisToolRunnerAgilentSeq.cs
move Plugins\AM_Sequest_PlugIn\clsAnalysisToolRunnerSeqBase.cs Plugins\AM_Sequest_PlugIn\AnalysisToolRunnerSeqBase.cs
move Plugins\AM_Sequest_PlugIn\clsAnalysisToolRunnerSeqCluster.cs Plugins\AM_Sequest_PlugIn\AnalysisToolRunnerSeqCluster.cs
move Plugins\AM_SMAQC_PlugIn\clsAnalysisResourcesSMAQC.cs Plugins\AM_SMAQC_PlugIn\AnalysisResourcesSMAQC.cs
move Plugins\AM_SMAQC_PlugIn\clsAnalysisToolRunnerSMAQC.cs Plugins\AM_SMAQC_PlugIn\AnalysisToolRunnerSMAQC.cs
move Plugins\AM_ThermoPeakDataExporter\clsAnalysisResourcesThermoPeakDataExporter.cs Plugins\AM_ThermoPeakDataExporter\AnalysisResourcesThermoPeakDataExporter.cs
move Plugins\AM_ThermoPeakDataExporter\clsAnalysisToolRunnerThermoPeakDataExporter.cs Plugins\AM_ThermoPeakDataExporter\AnalysisToolRunnerThermoPeakDataExporter.cs
move Plugins\AM_TopFD_Plugin\clsAnalysisResourcesTopFD.cs Plugins\AM_TopFD_Plugin\AnalysisResourcesTopFD.cs
move Plugins\AM_TopFD_Plugin\clsAnalysisToolRunnerTopFD.cs Plugins\AM_TopFD_Plugin\AnalysisToolRunnerTopFD.cs
move Plugins\AM_TopPIC_Plugin\clsAnalysisResourcesTopPIC.cs Plugins\AM_TopPIC_Plugin\AnalysisResourcesTopPIC.cs
move Plugins\AM_TopPIC_Plugin\clsAnalysisToolRunnerTopPIC.cs Plugins\AM_TopPIC_Plugin\AnalysisToolRunnerTopPIC.cs
move Plugins\AM_UIMFtoMassHunter_Plugin\clsAnalysisResourcesUIMFtoMassHunter.cs Plugins\AM_UIMFtoMassHunter_Plugin\AnalysisResourcesUIMFtoMassHunter.cs
move Plugins\AM_UIMFtoMassHunter_Plugin\clsAnalysisToolRunnerUIMFtoMassHunter.cs Plugins\AM_UIMFtoMassHunter_Plugin\AnalysisToolRunnerUIMFtoMassHunter.cs
move Plugins\AM_XTandem_PlugIn\clsAnalysisResourcesXT.cs Plugins\AM_XTandem_PlugIn\AnalysisResourcesXT.cs
move Plugins\AM_XTandem_PlugIn\clsAnalysisToolRunnerXT.cs Plugins\AM_XTandem_PlugIn\AnalysisToolRunnerXT.cs
move Plugins\_Unused\AM_IDP_PlugIn\AM_IDP_PlugIn\clsAnalysisResourcesIDP.cs Plugins\_Unused\AM_IDP_PlugIn\AM_IDP_PlugIn\AnalysisResourcesIDP.cs
move Plugins\_Unused\AM_IDP_PlugIn\AM_IDP_PlugIn\clsAnalysisToolRunnerIDP.cs Plugins\_Unused\AM_IDP_PlugIn\AM_IDP_PlugIn\AnalysisToolRunnerIDP.cs