Package org.fhcrc.cpl.viewer.ms2.commandline

Class Summary

CalculateFDRCLM	Commandline module for FDR calculation and filtering This allows the user to take a feature file (which can be a pepXML file) and do an FDR calculation based on reverse database hits (rev_ prefix), using some single peptide quality score (PeptideProphet probability, or any arbitrary search_score).
CombinePepXmlFilesCLM	test
CompareFastasCLM	Command linemodule for plotting the mass calibration of a feature file
CorrectPrecursorMzCLM	Command line module for correcting mzXML precursor masses
ExtractRunsFromPepXmlCommandLineModule
FilterPeptideRegexpCLM	Command linemodule for feature finding
FilterPepXmlCLM	Command linemodule for feature finding
FilterReverseDBHitsCLM	Command linemodule for feature finding
FindIndistinguishableProteinsCLM	Command linemodule for plotting the mass calibration of a feature file
FindSearchScoreCutoffForFARCLM	Command linemodule for feature finding
FindSearchScoreCutoffForFARCLM.PeptideProphetComparatorDesc
FindSearchScoreCutoffForFARCLM.SearchScoreComparator
FlipPepXMLRatiosCLM	Flip peptide ratios and light/heavy areas
GuessProteinsFromFastaCLM	test
MS2ScanViewerCLM	test
PeptideCompareCommandLineModule
PickTargetedMS2CandidatesCLM	Command linemodule for plotting the mass calibration of a feature file
PickTargetedMS2CandidatesCLM.PeptideCountsComparatorDesc
PlotDeltaMassesCLM	Command linemodule for plotting the mass calibration of a feature file
PopulateMS2TimesCLM	Command linemodule for feature finding
PostProcessPepXMLCLM	post-process a pepxml file
ProteinFractionsSpreadsheetCLM	Command linemodule for plotting the mass calibration of a feature file
ProtXmlCompareCLM	Command linemodule for plotting the mass calibration of a feature file
ProtXmlCompareCLM.ProteinInfo
ReverseFastaCLM	Creates a forward-reverse fasta file from an input fasta file
SpectralCountCLM
SummarizeProtXmlCLM	Command linemodule for plotting the mass calibration of a feature file