Package org.fhcrc.cpl.viewer.commandline.modules

Class Summary

BaseViewerCommandLineModuleImpl	Base class for command line modules.
CalibrateFeatureMassesCLM	Command linemodule for mass calibration
CalibrateMzxmlMassesCLM	Command linemodule for Saving pieces of mzXML files
ConsensusFeatureFileCLM	Command linemodule for feature finding
ConvertFeatureFileCommandLineModule
CreateIndexCommandLineModule
DeconvoluteCommandLineModule	Command linemodule for deconvolution.
DetectAdductsCLM	Command linemodule for adduct detection.
DumpWindow2DCommandLineModule	Dump a 2D window (scans in rows, m/z in columns) around each feature.
FeatureSelectionParamsCommandLineModule	Command line module ancestor for modules that need feature selection parameters
FeatureSetMatcherCommandLineModule
FilterFeaturesCommandLineModule	Command Module for feature filtering
FindPeptidesCommandLineModule	Command Module for feature finding.
HydrophobicityAlgorithmAnalyzerCLM	Command line module for analyzing a hydrophobicity algorithm.
MassAccuracyCommandLineModule	Show a plot that lets the user determine the mass accuracy of the instrumentation
PeptidePeakModellerCLM	Show a plot that lets the user determine the mass accuracy of the instrumentation
PlotFeatureAttributesCLM	Command linemodule for plotting the mass calibration of a feature file
PlotMassCalibrationCLM	Command linemodule for plotting the mass calibration of a feature file
PlotMs1Ms2ScanCountsCLM	Command linemodule for plotting the mass calibration of a feature file
RunCommandFileCommandLineModule	Command linemodule for feature finding
SaveImageCommandLineModule	Command linemodule for feature finding
SaveMzxmlWindowCommandLineModule	Command linemodule for Saving pieces of mzXML files
SpreadsheetMergeCLM	This is an unwieldy jumble of code to help merge together two spreadsheets based on shared values in the 'mergecolumn' column.
UserManualCLM	Create and display a user manual
ViewSpectrumChartCLM	test