org.fhcrc.cpl.viewer.amt.commandline
Class AmtDatabaseDiagnosticCommandLineModule

java.lang.Object
  org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl
      org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl
          org.fhcrc.cpl.viewer.amt.commandline.AmtDatabaseDiagnosticCommandLineModule

All Implemented Interfaces:

CommandLineModule

public class AmtDatabaseDiagnosticCommandLineModule
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Command line module for getting information and charts on an AMT database. Has an extra mode for saving all charts to a directory

Field Summary

protected static org.apache.log4j.Logger	_log
protected AmtDatabase	amtDB
protected int	mode
protected static int	MODE_BASIC_INFO
protected static int	MODE_COMPARE_CALC_H_TIME
protected static int	MODE_COMPARE_OBS_H_CALC_H
protected static int	MODE_HIST_HYDRO_STD_DEV
protected static int	MODE_HIST_ID_PROBS
protected static int	MODE_HIST_MASSES
protected static int	MODE_PEPTIDE_DETAILS
protected static int	MODE_PLOT_MASS_H
protected static int	MODE_PLOT_MASS_VS_OBS_HYDRO
protected static int	MODE_PLOT_RUN_H_VS_MEDIAN
protected static int	MODE_PLOT_RUN_HYDRO_DIFFS
protected static int	MODE_PLOT_T_H_MAPS
protected static int	MODE_SAVE_ALL_CHARTS
protected static java.lang.String[]	modeExplanations
protected static java.lang.String[]	modeStrings
protected FeatureSet	ms1FeatureSet
protected java.io.File	outDir
protected java.io.File	outFile
protected java.io.PrintWriter	outPW
protected java.lang.String	peptide
protected boolean	showCharts

Fields inherited from class org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl

mArgumentDefs, mArgumentValues, mArgumentValueStrings, mCommandName, mHelpMessage, mShortDescription, mUsageMessage

Fields inherited from interface org.fhcrc.cpl.toolbox.commandline.CommandLineModule

MODULE_HELP_AUTOMATIC, MODULE_USAGE_AUTOMATIC, UNNAMED_ARG_SERIES_SEPARATOR

Constructor Summary

AmtDatabaseDiagnosticCommandLineModule()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
protected void	basicInfo()
protected org.jfree.chart.JFreeChart	compareCalculatedHAgainstTime() Plot time vs.
protected org.jfree.chart.JFreeChart	compareObservedHAgainstCalculatedH() Scatterplot observed hydrophobicity against calculated H, by run
void	execute() a great big switch statement
protected org.jfree.chart.JFreeChart	histogramHydroStdDev() Show a histogram of the standard deviations of hydrophobicity observations per peptide
protected org.jfree.chart.JFreeChart	histogramIDProbs()
protected org.jfree.chart.JFreeChart	histogramMasses() Histogram all masses in the database
protected void	init()
protected void	peptideDetails()
protected org.jfree.chart.JFreeChart	plotMassAndH()
protected org.jfree.chart.JFreeChart	plotMassVersusObsHydroByRun() Plot peptide mass vs.
protected org.jfree.chart.JFreeChart	plotRunHvsMedian() Plot observed H values in each individual run vs.
protected org.jfree.chart.JFreeChart	showMeanHydroDiffByRun() Show mean hydrophobicity deviation from prediction, on a handy bar chart.
protected org.jfree.chart.JFreeChart	showTimeHydMaps() Plot the T->H mappings of all runs.

Methods inherited from class org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl

createUnnamedFeatureFileArgumentDefinition, createUnnamedSeriesFeatureFileArgumentDefinition, getFastaFileArgumentValue, getFeatureSetArgumentValue, getModificationListArgumentValue

Methods inherited from class org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl

addArgumentDefinition, addArgumentDefinitions, addArgumentDefinitions, assertArgumentAbsent, assertArgumentAbsent, assertArgumentPresent, assertArgumentPresent, createArgsTableHTML, createUnnamedFileArgumentDefinition, createUnnamedSeriesFileArgumentDefinition, digestArguments, getAdvancedArgumentDefinitions, getArgumentDefinition, getArgumentDefinitions, getArgumentDefinitionsSortedForDisplay, getArgumentValue, getArgumentValues, getArgumentValueStrings, getBasicArgumentDefinitions, getBooleanArgumentValue, getCommandName, getDeltaMassArgumentValue, getDoubleArgumentValue, getDoubleArrayArgumentValue, getFileArgumentValue, getFileArrayArgumentValue, getFloatArgumentValue, getFullHelp, getHelpMessage, getHtmlHelpFragment, getIntegerArgumentValue, getPrintWriter, getShortDescription, getStringArgumentValue, getUnnamedArgumentValue, getUnnamedFileArgumentValue, getUnnamedSeriesArgumentValues, getUnnamedSeriesFileArgumentValues, getUsage, hasAdvancedArguments, hasArgumentValue, hasUnnamedArgumentValue, hasUnnamedSeriesArgumentValue, invoke, makeHtmlSafe, sortArgDefsForDisplay, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.fhcrc.cpl.toolbox.commandline.CommandLineModule

digestArguments, getAdvancedArgumentDefinitions, getArgumentDefinition, getArgumentDefinitions, getArgumentDefinitionsSortedForDisplay, getArgumentValueStrings, getBasicArgumentDefinitions, getCommandName, getFullHelp, getHelpMessage, getHtmlHelpFragment, getShortDescription, getUsage, invoke

Field Detail

_log

protected static org.apache.log4j.Logger _log

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

outPW

protected java.io.PrintWriter outPW

mode

protected int mode

amtDB

protected AmtDatabase amtDB

showCharts

protected boolean showCharts

ms1FeatureSet

protected FeatureSet ms1FeatureSet

peptide

protected java.lang.String peptide

modeStrings

protected static final java.lang.String[] modeStrings

modeExplanations

protected static final java.lang.String[] modeExplanations

MODE_COMPARE_OBS_H_CALC_H

protected static final int MODE_COMPARE_OBS_H_CALC_H

See Also:

Constant Field Values

MODE_COMPARE_CALC_H_TIME

protected static final int MODE_COMPARE_CALC_H_TIME

See Also:

Constant Field Values

MODE_PLOT_T_H_MAPS

protected static final int MODE_PLOT_T_H_MAPS

See Also:

Constant Field Values

MODE_HIST_HYDRO_STD_DEV

protected static final int MODE_HIST_HYDRO_STD_DEV

See Also:

Constant Field Values

MODE_PLOT_RUN_HYDRO_DIFFS

protected static final int MODE_PLOT_RUN_HYDRO_DIFFS

See Also:

Constant Field Values

MODE_SAVE_ALL_CHARTS

protected static final int MODE_SAVE_ALL_CHARTS

See Also:

Constant Field Values

MODE_PLOT_MASS_VS_OBS_HYDRO

protected static final int MODE_PLOT_MASS_VS_OBS_HYDRO

See Also:

Constant Field Values

MODE_BASIC_INFO

protected static final int MODE_BASIC_INFO

See Also:

Constant Field Values

MODE_HIST_MASSES

protected static final int MODE_HIST_MASSES

See Also:

Constant Field Values

MODE_PLOT_RUN_H_VS_MEDIAN

protected static final int MODE_PLOT_RUN_H_VS_MEDIAN

See Also:

Constant Field Values

MODE_PEPTIDE_DETAILS

protected static final int MODE_PEPTIDE_DETAILS

See Also:

Constant Field Values

MODE_PLOT_MASS_H

protected static final int MODE_PLOT_MASS_H

See Also:

Constant Field Values

MODE_HIST_ID_PROBS

protected static final int MODE_HIST_ID_PROBS

See Also:

Constant Field Values

Constructor Detail

AmtDatabaseDiagnosticCommandLineModule

public AmtDatabaseDiagnosticCommandLineModule()

Method Detail

init

protected void init()

assignArgumentValues

public void assignArgumentValues()
                          throws ArgumentValidationException

Description copied from interface: CommandLineModule

the first step in invoking your module. The values assigned to the various arguments by the user are passed to your module for storage and additional validation. Any communication with the user about their argument values should be done by this method.

Specified by:

assignArgumentValues in interface CommandLineModule

Throws:

ArgumentValidationException

execute

public void execute()
             throws CommandLineModuleExecutionException

a great big switch statement

Specified by:

execute in interface CommandLineModule

Throws:

CommandLineModuleExecutionException

basicInfo

protected void basicInfo()

peptideDetails

protected void peptideDetails()

plotRunHvsMedian

protected org.jfree.chart.JFreeChart plotRunHvsMedian()

Plot observed H values in each individual run vs. the median H value

Returns:

showMeanHydroDiffByRun

protected org.jfree.chart.JFreeChart showMeanHydroDiffByRun()

Show mean hydrophobicity deviation from prediction, on a handy bar chart. Useful for finding runs that are really wacked out.

Returns:

showTimeHydMaps

protected org.jfree.chart.JFreeChart showTimeHydMaps()

Plot the T->H mappings of all runs. Useful for showing up odd runs

Returns:

plotMassVersusObsHydroByRun

protected org.jfree.chart.JFreeChart plotMassVersusObsHydroByRun()

Plot peptide mass vs. observed hydrophobicity

Returns:

compareObservedHAgainstCalculatedH

protected org.jfree.chart.JFreeChart compareObservedHAgainstCalculatedH()

Scatterplot observed hydrophobicity against calculated H, by run

Returns:

compareCalculatedHAgainstTime

protected org.jfree.chart.JFreeChart compareCalculatedHAgainstTime()

Plot time vs. calculated H, per run

Returns:

histogramIDProbs

protected org.jfree.chart.JFreeChart histogramIDProbs()

Returns:

histogramHydroStdDev

protected org.jfree.chart.JFreeChart histogramHydroStdDev()

Show a histogram of the standard deviations of hydrophobicity observations per peptide

Returns:

histogramMasses

protected org.jfree.chart.JFreeChart histogramMasses()

Histogram all masses in the database

Returns:

plotMassAndH

protected org.jfree.chart.JFreeChart plotMassAndH()