org.fhcrc.cpl.viewer.amt
Class AmtDatabaseMatcher

java.lang.Object
  org.fhcrc.cpl.viewer.amt.AmtDatabaseMatcher

public class AmtDatabaseMatcher
extends java.lang.Object

This class performs simple matching between an AMT database and a feature files. It constructs a probability model for the matches based on mass and NRT deviation.

Nested Class Summary

static class

AmtDatabaseMatcher.PeptideProphetComparatorDesc

Field Summary

protected Fractionation2DUtilities.FractionatedAMTDatabaseStructure	amtDatabaseStructure
protected boolean	amtDBDimensionsDefined
protected double	amtFeatureMassAdjustment
protected boolean	buildCharts
static float	DEFAULT_2D_MATCH_DELTA_ELUTION
static float	DEFAULT_2D_MATCH_DELTA_MASS
static int	DEFAULT_2D_MATCH_DELTA_MASS_TYPE
static int	DEFAULT_DECOY_DB_MASS_ADJUSTMENT_DA
static double	DEFAULT_LEVERAGE_NUMERATOR
static float	DEFAULT_MASS_MATCH_DELTA_MASS
static int	DEFAULT_MASS_MATCH_DELTA_MASS_TYPE
static double	DEFAULT_MAX_LEVERAGE_NUMERATOR
static double	DEFAULT_MAX_STUDENTIZED_RESIDUAL
static int	DEFAULT_NONLINEAR_MAPPING_DEGREE
static int	DEFAULT_QUANTILE_REG_MIN_FEATURES
static float	DEFAULT_SIGNIFICANT_HYDRO_DIFFERENCE
static boolean	DEFAULT_USE_MS1_TIMES_FOR_ALIGNMENT
protected boolean	doDecoyMatch
FeatureSetMatcher.FeatureMatchingResult	featureMatchingResult
protected org.jfree.chart.JFreeChart	massCalibrationChart
org.jfree.chart.JFreeChart	massDeltaMassScatterPlot
protected float	massMatchDeltaMass
protected int	massMatchDeltaMassType
protected org.jfree.chart.JFreeChart	massMatchScatterplot
protected PanelWithRPerspectivePlot	massTimeErrorPerspectivePlot
protected int	maxEMIterations
protected double	maxRegressionLeverageNumerator
protected double	maxRegressionStudRes
protected float	maxSecondBestProbability
static int	MIN_MATCHED_FEATURES_FOR_REGRESSION
protected int	minEMIterations
protected float	minMatchProbabilityToKeep
protected float	minSecondBestProbabilityDifference
protected float	ms1Ms2MassTolerancePPM
protected float	ms1Ms2TimeToleranceSeconds
protected int	nonlinearMappingPolynomialDegree
protected AmtMatchProbabilityAssigner	probabilityAssigner
protected int	quantileRegressionMinFeatures
protected float	realMatchDeltaElution
protected float	realMatchDeltaMass
protected int	realMatchDeltaMassType
double[]	timeHydMapCoefficients
protected org.jfree.chart.JFreeChart	timeHydrophobicityMappingChart
protected boolean	useMs1TimesForAlignment

Constructor Summary

AmtDatabaseMatcher()

Method Summary

AmtDatabase	buildAmtDatabaseForGeographicRestriction(AmtDatabase amtDB, FeatureSet ms2FeatureSetToMatch, int maxEntries, int minRunMassMatchPercent, int maxRuns, boolean showCharts) This method removes runs from an AMT database based on distance in fraction space from the run we're matching to.
AmtDatabase	buildAmtDatabaseForPeptideMatches(AmtDatabase amtDB, FeatureSet ms2FeatureSetToMatch, int maxEntries, int minRunMassMatchPercent, int maxRuns, boolean showCharts, Feature[] ms1Features, MS2Modification[] ms2ModificationsForMatching) This is for paring down an AMT database by removing runs without many peptides in common with the MS2 features provided.
void	calculateFeatureHydrophobicities(Feature[] ms1Features, Feature[] alignmentGuideFeatures, FeatureSet amtDatabaseFeatureSet, int degree) Outermost method for calculating feature hydrophobicities.
double[]	calculateMassCalibrationParameters(FeatureSetMatcher.FeatureMatchingResult matchingResult, boolean showCharts) Calculate linear mass calibration parameters by doing robust linear regression of mass error in the matches vs.
double[]	calculateTHMapCoefficientsWithMassMatching(FeatureSet amtDatabaseFeatureSet, Feature[] ms1Features, int degree) Cover method
double[]	calculateTHMapCoefficientsWithMassMatching(FeatureSet amtDatabaseFeatureSet, Feature[] features, int degree, boolean onlyUseSamePeptideMatches) Use mass-only matching to calculate a time-hydrophobicity map.
double[]	calculateTHMapCoefficientsWithMatchedFeatures(Pair<Feature,Feature>[] matchedFeatures, int degree) Given pairs of matched features, map RT to H
double[]	calibrateMS1FeaturesWithMatches(Feature[] ms1Features, FeatureSetMatcher.FeatureMatchingResult matchingResult, boolean showCharts) Calibrate MS1 features based on an initial match to the AMT database.
FeatureSetMatcher.FeatureMatchingResult	callWindowMatcher(FeatureSet ms1FeatureSet, FeatureSet amtFeatureSet, float lowMassTolerance, float highMassTolerance, float lowHTolerance, float highHTolerance) Calls Window2DFeatureSetMatcher to do a dead-simple 2D match between two featuresets
void	createMassTimeErrorPlots(FeatureSetMatcher.FeatureMatchingResult matchingResult) Separating this out so the interesting code flows better
static java.util.Set<java.lang.String>	createPeptideSetFromFeatures(Feature[] features) Utility method
void	defineAMTDBStructure(Fractionation2DUtilities.FractionatedAMTDatabaseStructure amtDatabaseStructure) Define the "dimensions" of the AMT database.
Fractionation2DUtilities.FractionatedAMTDatabaseStructure	getAMTDBStructure()
double	getAmtFeatureMassAdjustment()
org.jfree.chart.JFreeChart	getMassCalibrationChart()
float	getMassMatchDeltaMass()
int	getMassMatchDeltaMassType()
org.jfree.chart.JFreeChart	getMassMatchScatterplot()
int	getMaxEMIterations()
double	getMaxRegressionLeverageNumerator()
double	getMaxRegressionStudentizedResidual()
float	getMaxSecondBestProbability()
int	getMinEMIterations()
float	getMinMatchProbabilityToKeep()
float	getMinSecondBestProbabilityDifference()
float	getMs1Ms2MassTolerancePPM()
float	getMs1Ms2TimeToleranceSeconds()
int	getNonlinearMappingPolynomialDegree()
AmtMatchProbabilityAssigner	getProbabilityAssigner()
int	getQuantileRegressionMinFeatures()
float	getRealMatchDeltaElution()
float	getRealMatchDeltaMass()
int	getRealMatchDeltaMassType()
org.jfree.chart.JFreeChart	getTimeHydrophobicityMappingChart()
boolean	isDecoyMatch()
boolean	isUseMs1TimesForAlignment()
java.util.List<Feature>	matchAgainstMs1(AmtDatabase amtDatabaseThisMatch, Feature[] amtDBFeaturesThisMatch, FeatureSet ms1FeatureSetToMatch, FeatureSet embeddedMs2FeatureSet, float minEmbeddedMs2PeptideProphet, MS2Modification[] ms2ModificationsArray, java.io.File matchingOutputFile, boolean removeFractions, int minRunsToKeep, int maxRunsToKeep, boolean calibrateMassesUsingMatches, boolean showCharts) Match an AMT database against a single MS1 feature file.
Pair<Feature,Feature>[]	matchOnMassOnly(FeatureSet amtDatabaseFeatureSet, Feature[] ms1Features, float massMatchDeltaMass, int massMatchDeltaMassType) Perform a mass-only match between MS1 features and AMT database.
void	matchWithFDRCalc(AmtDatabase amtDatabaseThisMatch, Feature[] amtDBFeaturesThisMatch, FeatureSet ms1FeatureSetToMatch, FeatureSet embeddedMs2FeatureSet, float minEmbeddedMs2PeptideProphet, MS2Modification[] ms2ModificationsArray, java.io.File matchingOutputFile, boolean removeFractions, int minRunsToKeep, int maxRunsToKeep, boolean calibrateMassesUsingMatches, boolean showCharts)
java.util.Map<Feature,java.lang.Float>	matchWithPortionDecoy(AmtDatabase amtDatabaseThisMatch, Feature[] amtDBFeaturesThisMatch, FeatureSet ms1FeatureSetToMatch, FeatureSet embeddedMs2FeatureSet, float minEmbeddedMs2PeptideProphet, MS2Modification[] ms2ModificationsArray, java.io.File matchingOutputFile, boolean removeFractions, int minRunsToKeep, int maxRunsToKeep, boolean calibrateMassesUsingMatches, boolean showCharts, java.util.Set<java.lang.String> decoyPeptides, float targetDecoyRatio) Change the masses of a random portion (portionDecoy) of the AMT database entries to make them decoy entries, perform the match, and report on the specificity of the match
AmtDatabase	reduceDatabaseByRunSimilarity(AmtDatabase amtDatabase, Feature[] ms2Features, FeatureSetMatcher.FeatureMatchingResult matchingResult, int minRunsToKeep, int maxRunsToKeep, boolean showCharts) Remove peptide entries from the AMT database that don't occur in runs that are similar, in peptide content, to ms2Features.
static void	representPeptidesWithMedianTimePerPeptidePerMod(FeatureSet featureSet) For each peptide, per modification state, remove all but one observation.
void	setAmtFeatureMassAdjustment(double amtFeatureMassAdjustment)
void	setBuildCharts(boolean buildCharts)
void	setDecoyMatch(boolean decoyMatch)
void	setMassMatchDeltaMass(float massMatchDeltaMass)
void	setMassMatchDeltaMassType(int massMatchDeltaMassType)
void	setMaxEMIterations(int maxEMIterations)
void	setMaxRegressionLeverageNumerator(double leverageNumeratorModalRegression)
void	setMaxRegressionStudentizedResidual(double maxRegressionStudRes)
void	setMaxSecondBestProbability(float maxSecondBestProbability)
void	setMinEMIterations(int minEMIterations)
void	setMinMatchProbabilityToKeep(float minMatchProbabilityToKeep)
void	setMinSecondBestProbabilityDifference(float minSecondBestProbabilityDifference)
void	setMs1Ms2MassTolerancePPM(float ms1Ms2MassTolerancePPM)
void	setMs1Ms2TimeToleranceSeconds(float ms1Ms2TimeToleranceSeconds)
void	setNonlinearMappingPolynomialDegree(int nonlinearMappingPolynomialDegree)
void	setProbabilityAssigner(AmtMatchProbabilityAssigner probabilityAssigner)
void	setQuantileRegressionMinFeatures(int quantileRegressionMinFeatures)
void	setRealMatchDeltaElution(float realMatchDeltaElution)
void	setRealMatchDeltaMass(float realMatchDeltaMass)
void	setRealMatchDeltaMassType(int realMatchDeltaMassType)
void	setUseMs1TimesForAlignment(boolean useMs1TimesForAlignment)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_LEVERAGE_NUMERATOR

public static final double DEFAULT_LEVERAGE_NUMERATOR

See Also:

Constant Field Values

DEFAULT_MAX_LEVERAGE_NUMERATOR

public static final double DEFAULT_MAX_LEVERAGE_NUMERATOR

See Also:

Constant Field Values

DEFAULT_MAX_STUDENTIZED_RESIDUAL

public static final double DEFAULT_MAX_STUDENTIZED_RESIDUAL

See Also:

Constant Field Values

DEFAULT_MASS_MATCH_DELTA_MASS

public static final float DEFAULT_MASS_MATCH_DELTA_MASS

See Also:

Constant Field Values

DEFAULT_MASS_MATCH_DELTA_MASS_TYPE

public static final int DEFAULT_MASS_MATCH_DELTA_MASS_TYPE

See Also:

Constant Field Values

DEFAULT_2D_MATCH_DELTA_MASS

public static final float DEFAULT_2D_MATCH_DELTA_MASS

See Also:

Constant Field Values

DEFAULT_2D_MATCH_DELTA_MASS_TYPE

public static final int DEFAULT_2D_MATCH_DELTA_MASS_TYPE

See Also:

Constant Field Values

DEFAULT_2D_MATCH_DELTA_ELUTION

public static final float DEFAULT_2D_MATCH_DELTA_ELUTION

See Also:

Constant Field Values

MIN_MATCHED_FEATURES_FOR_REGRESSION

public static final int MIN_MATCHED_FEATURES_FOR_REGRESSION

See Also:

Constant Field Values

DEFAULT_QUANTILE_REG_MIN_FEATURES

public static final int DEFAULT_QUANTILE_REG_MIN_FEATURES

See Also:

Constant Field Values

quantileRegressionMinFeatures

protected int quantileRegressionMinFeatures

DEFAULT_NONLINEAR_MAPPING_DEGREE

public static final int DEFAULT_NONLINEAR_MAPPING_DEGREE

See Also:

Constant Field Values

nonlinearMappingPolynomialDegree

protected int nonlinearMappingPolynomialDegree

DEFAULT_SIGNIFICANT_HYDRO_DIFFERENCE

public static final float DEFAULT_SIGNIFICANT_HYDRO_DIFFERENCE

See Also:

Constant Field Values

massMatchDeltaMass

protected float massMatchDeltaMass

massMatchDeltaMassType

protected int massMatchDeltaMassType

realMatchDeltaMass

protected float realMatchDeltaMass

realMatchDeltaMassType

protected int realMatchDeltaMassType

realMatchDeltaElution

protected float realMatchDeltaElution

minEMIterations

protected int minEMIterations

maxEMIterations

protected int maxEMIterations

DEFAULT_USE_MS1_TIMES_FOR_ALIGNMENT

public static final boolean DEFAULT_USE_MS1_TIMES_FOR_ALIGNMENT

See Also:

Constant Field Values

useMs1TimesForAlignment

protected boolean useMs1TimesForAlignment

ms1Ms2MassTolerancePPM

protected float ms1Ms2MassTolerancePPM

ms1Ms2TimeToleranceSeconds

protected float ms1Ms2TimeToleranceSeconds

doDecoyMatch

protected boolean doDecoyMatch

maxRegressionLeverageNumerator

protected double maxRegressionLeverageNumerator

maxRegressionStudRes

protected double maxRegressionStudRes

minMatchProbabilityToKeep

protected float minMatchProbabilityToKeep

maxSecondBestProbability

protected float maxSecondBestProbability

minSecondBestProbabilityDifference

protected float minSecondBestProbabilityDifference

DEFAULT_DECOY_DB_MASS_ADJUSTMENT_DA

public static final int DEFAULT_DECOY_DB_MASS_ADJUSTMENT_DA

See Also:

Constant Field Values

timeHydMapCoefficients

public double[] timeHydMapCoefficients

buildCharts

protected boolean buildCharts

featureMatchingResult

public FeatureSetMatcher.FeatureMatchingResult featureMatchingResult

massMatchScatterplot

protected org.jfree.chart.JFreeChart massMatchScatterplot

timeHydrophobicityMappingChart

protected org.jfree.chart.JFreeChart timeHydrophobicityMappingChart

massCalibrationChart

protected org.jfree.chart.JFreeChart massCalibrationChart

massTimeErrorPerspectivePlot

protected PanelWithRPerspectivePlot massTimeErrorPerspectivePlot

massDeltaMassScatterPlot

public org.jfree.chart.JFreeChart massDeltaMassScatterPlot

amtFeatureMassAdjustment

protected double amtFeatureMassAdjustment

amtDBDimensionsDefined

protected boolean amtDBDimensionsDefined

amtDatabaseStructure

protected Fractionation2DUtilities.FractionatedAMTDatabaseStructure amtDatabaseStructure

probabilityAssigner

protected AmtMatchProbabilityAssigner probabilityAssigner

Constructor Detail

AmtDatabaseMatcher

public AmtDatabaseMatcher()

Method Detail

matchWithFDRCalc

public void matchWithFDRCalc(AmtDatabase amtDatabaseThisMatch,
                             Feature[] amtDBFeaturesThisMatch,
                             FeatureSet ms1FeatureSetToMatch,
                             FeatureSet embeddedMs2FeatureSet,
                             float minEmbeddedMs2PeptideProphet,
                             MS2Modification[] ms2ModificationsArray,
                             java.io.File matchingOutputFile,
                             boolean removeFractions,
                             int minRunsToKeep,
                             int maxRunsToKeep,
                             boolean calibrateMassesUsingMatches,
                             boolean showCharts)
                      throws java.io.IOException

Throws:

java.io.IOException

matchWithPortionDecoy

public java.util.Map<Feature,java.lang.Float> matchWithPortionDecoy(AmtDatabase amtDatabaseThisMatch,
                                                                    Feature[] amtDBFeaturesThisMatch,
                                                                    FeatureSet ms1FeatureSetToMatch,
                                                                    FeatureSet embeddedMs2FeatureSet,
                                                                    float minEmbeddedMs2PeptideProphet,
                                                                    MS2Modification[] ms2ModificationsArray,
                                                                    java.io.File matchingOutputFile,
                                                                    boolean removeFractions,
                                                                    int minRunsToKeep,
                                                                    int maxRunsToKeep,
                                                                    boolean calibrateMassesUsingMatches,
                                                                    boolean showCharts,
                                                                    java.util.Set<java.lang.String> decoyPeptides,
                                                                    float targetDecoyRatio)
                                                             throws java.io.IOException

Change the masses of a random portion (portionDecoy) of the AMT database entries to make them decoy entries, perform the match, and report on the specificity of the match

Parameters:

amtDatabaseThisMatch -

amtDBFeaturesThisMatch -

ms1FeatureSetToMatch -

embeddedMs2FeatureSet -

minEmbeddedMs2PeptideProphet -

ms2ModificationsArray -

matchingOutputFile -

removeFractions -

minRunsToKeep -

maxRunsToKeep -

calibrateMassesUsingMatches -

showCharts -

decoyPeptides -

Throws:

java.io.IOException

representPeptidesWithMedianTimePerPeptidePerMod

public static void representPeptidesWithMedianTimePerPeptidePerMod(FeatureSet featureSet)

For each peptide, per modification state, remove all but one observation. That observation gets the median retention time of all of them

Parameters:

featureSet -

matchAgainstMs1

public java.util.List<Feature> matchAgainstMs1(AmtDatabase amtDatabaseThisMatch,
                                               Feature[] amtDBFeaturesThisMatch,
                                               FeatureSet ms1FeatureSetToMatch,
                                               FeatureSet embeddedMs2FeatureSet,
                                               float minEmbeddedMs2PeptideProphet,
                                               MS2Modification[] ms2ModificationsArray,
                                               java.io.File matchingOutputFile,
                                               boolean removeFractions,
                                               int minRunsToKeep,
                                               int maxRunsToKeep,
                                               boolean calibrateMassesUsingMatches,
                                               boolean showCharts)
                                        throws java.io.IOException

Match an AMT database against a single MS1 feature file. This is the master matching method

Returns:

a list of matched MS1 features

Throws:

java.io.IOException

matchOnMassOnly

public Pair<Feature,Feature>[] matchOnMassOnly(FeatureSet amtDatabaseFeatureSet,
                                               Feature[] ms1Features,
                                               float massMatchDeltaMass,
                                               int massMatchDeltaMassType)

Perform a mass-only match between MS1 features and AMT database. This is for determining alignment parameters when no embedded MS2 are available

Parameters:

amtDatabaseFeatureSet -

ms1Features -

massMatchDeltaMass -

massMatchDeltaMassType -

Returns:

calculateTHMapCoefficientsWithMassMatching

public double[] calculateTHMapCoefficientsWithMassMatching(FeatureSet amtDatabaseFeatureSet,
                                                           Feature[] ms1Features,
                                                           int degree)

Cover method

Parameters:

amtDatabaseFeatureSet -

ms1Features -

degree -

Returns:

calculateTHMapCoefficientsWithMassMatching

public double[] calculateTHMapCoefficientsWithMassMatching(FeatureSet amtDatabaseFeatureSet,
                                                           Feature[] features,
                                                           int degree,
                                                           boolean onlyUseSamePeptideMatches)

Use mass-only matching to calculate a time-hydrophobicity map. First we perform a simple mass-only matching. Plotted on a time-hydrophobicity chart, this will generally produce a uniformly distributed, diffuse noise of false positives, with a high-density line of true positives somewhere in the middle. We then look for that line. Simple regression won't do, because of all the noise -- it will tend to get dragged down unpredictably. We use Yan's modal regression to determine the high-density line. This requires an R installation, with the quantreg package installed. if onlyUseSamePeptideMatches is true, then we're doing same-peptide matching, but still checking mass (because of potential effects on RT due to modifications)

Parameters:

amtDatabaseFeatureSet -

features -

degree -

Returns:

calculateTHMapCoefficientsWithMatchedFeatures

public double[] calculateTHMapCoefficientsWithMatchedFeatures(Pair<Feature,Feature>[] matchedFeatures,
                                                              int degree)

Given pairs of matched features, map RT to H

Parameters:

matchedFeatures -

degree -

Returns:

calculateFeatureHydrophobicities

public void calculateFeatureHydrophobicities(Feature[] ms1Features,
                                             Feature[] alignmentGuideFeatures,
                                             FeatureSet amtDatabaseFeatureSet,
                                             int degree)

Outermost method for calculating feature hydrophobicities. Delegator.

Parameters:

ms1Features -

alignmentGuideFeatures -

amtDatabaseFeatureSet -

degree -

callWindowMatcher

public FeatureSetMatcher.FeatureMatchingResult callWindowMatcher(FeatureSet ms1FeatureSet,
                                                                 FeatureSet amtFeatureSet,
                                                                 float lowMassTolerance,
                                                                 float highMassTolerance,
                                                                 float lowHTolerance,
                                                                 float highHTolerance)

Calls Window2DFeatureSetMatcher to do a dead-simple 2D match between two featuresets

Parameters:

ms1FeatureSet -

amtFeatureSet -

lowMassTolerance -

highMassTolerance -

lowHTolerance -

highHTolerance -

Returns:

calibrateMS1FeaturesWithMatches

public double[] calibrateMS1FeaturesWithMatches(Feature[] ms1Features,
                                                FeatureSetMatcher.FeatureMatchingResult matchingResult,
                                                boolean showCharts)

Calibrate MS1 features based on an initial match to the AMT database. Warning! This will invalidate the hash keys in matchingResult when it updates the features. Do NOT try to use matchingResult after calling this.

Parameters:

ms1Features -

matchingResult -

showCharts -

Returns:

calculateMassCalibrationParameters

public double[] calculateMassCalibrationParameters(FeatureSetMatcher.FeatureMatchingResult matchingResult,
                                                   boolean showCharts)

Calculate linear mass calibration parameters by doing robust linear regression of mass error in the matches vs. MS1 feature mass.

Parameters:

matchingResult -

showCharts -

Returns:

createMassTimeErrorPlots

public void createMassTimeErrorPlots(FeatureSetMatcher.FeatureMatchingResult matchingResult)

Separating this out so the interesting code flows better

Parameters:

matchingResult -

createPeptideSetFromFeatures

public static java.util.Set<java.lang.String> createPeptideSetFromFeatures(Feature[] features)

Utility method

Parameters:

features -

Returns:

reduceDatabaseByRunSimilarity

public AmtDatabase reduceDatabaseByRunSimilarity(AmtDatabase amtDatabase,
                                                 Feature[] ms2Features,
                                                 FeatureSetMatcher.FeatureMatchingResult matchingResult,
                                                 int minRunsToKeep,
                                                 int maxRunsToKeep,
                                                 boolean showCharts)

Remove peptide entries from the AMT database that don't occur in runs that are similar, in peptide content, to ms2Features.

Parameters:

amtDatabase -

ms2Features -

matchingResult -

showCharts -

Returns:

getMassMatchDeltaMass

public float getMassMatchDeltaMass()

setMassMatchDeltaMass

public void setMassMatchDeltaMass(float massMatchDeltaMass)

getMassMatchDeltaMassType

public int getMassMatchDeltaMassType()

setMassMatchDeltaMassType

public void setMassMatchDeltaMassType(int massMatchDeltaMassType)

getRealMatchDeltaMass

public float getRealMatchDeltaMass()

setRealMatchDeltaMass

public void setRealMatchDeltaMass(float realMatchDeltaMass)

getRealMatchDeltaMassType

public int getRealMatchDeltaMassType()

setRealMatchDeltaMassType

public void setRealMatchDeltaMassType(int realMatchDeltaMassType)

getRealMatchDeltaElution

public float getRealMatchDeltaElution()

setRealMatchDeltaElution

public void setRealMatchDeltaElution(float realMatchDeltaElution)

setBuildCharts

public void setBuildCharts(boolean buildCharts)

getMassMatchScatterplot

public org.jfree.chart.JFreeChart getMassMatchScatterplot()

getTimeHydrophobicityMappingChart

public org.jfree.chart.JFreeChart getTimeHydrophobicityMappingChart()

getMaxRegressionLeverageNumerator

public double getMaxRegressionLeverageNumerator()

setMaxRegressionLeverageNumerator

public void setMaxRegressionLeverageNumerator(double leverageNumeratorModalRegression)

getMaxRegressionStudentizedResidual

public double getMaxRegressionStudentizedResidual()

setMaxRegressionStudentizedResidual

public void setMaxRegressionStudentizedResidual(double maxRegressionStudRes)

getAmtFeatureMassAdjustment

public double getAmtFeatureMassAdjustment()

setAmtFeatureMassAdjustment

public void setAmtFeatureMassAdjustment(double amtFeatureMassAdjustment)

getQuantileRegressionMinFeatures

public int getQuantileRegressionMinFeatures()

setQuantileRegressionMinFeatures

public void setQuantileRegressionMinFeatures(int quantileRegressionMinFeatures)

getMassCalibrationChart

public org.jfree.chart.JFreeChart getMassCalibrationChart()

defineAMTDBStructure

public void defineAMTDBStructure(Fractionation2DUtilities.FractionatedAMTDatabaseStructure amtDatabaseStructure)

Define the "dimensions" of the AMT database. This only has any meaning for a single multi-fraction database like an IPAS, with one- or (really) two-dimensional fractionation.

Parameters:

amtDatabaseStructure -

getAMTDBStructure

public Fractionation2DUtilities.FractionatedAMTDatabaseStructure getAMTDBStructure()

buildAmtDatabaseForPeptideMatches

public AmtDatabase buildAmtDatabaseForPeptideMatches(AmtDatabase amtDB,
                                                     FeatureSet ms2FeatureSetToMatch,
                                                     int maxEntries,
                                                     int minRunMassMatchPercent,
                                                     int maxRuns,
                                                     boolean showCharts,
                                                     Feature[] ms1Features,
                                                     MS2Modification[] ms2ModificationsForMatching)

This is for paring down an AMT database by removing runs without many peptides in common with the MS2 features provided. For getting rid of runs in a heavily fractionated database. Unnecessary?

Parameters:

amtDB -

ms2FeatureSetToMatch -

maxEntries -

minRunMassMatchPercent -

maxRuns -

showCharts -

ms1Features -

ms2ModificationsForMatching -

Returns:

The modified database, or null if it can't be done

buildAmtDatabaseForGeographicRestriction

public AmtDatabase buildAmtDatabaseForGeographicRestriction(AmtDatabase amtDB,
                                                            FeatureSet ms2FeatureSetToMatch,
                                                            int maxEntries,
                                                            int minRunMassMatchPercent,
                                                            int maxRuns,
                                                            boolean showCharts)

This method removes runs from an AMT database based on distance in fraction space from the run we're matching to. This is purely for demonstration of how well it doesn't work, should be discarded after paper is written.

Parameters:

amtDB -

ms2FeatureSetToMatch -

maxEntries -

minRunMassMatchPercent -

maxRuns -

showCharts -

Returns:

The modified database, or null if it can't be done

getMinMatchProbabilityToKeep

public float getMinMatchProbabilityToKeep()

setMinMatchProbabilityToKeep

public void setMinMatchProbabilityToKeep(float minMatchProbabilityToKeep)

getProbabilityAssigner

public AmtMatchProbabilityAssigner getProbabilityAssigner()

setProbabilityAssigner

public void setProbabilityAssigner(AmtMatchProbabilityAssigner probabilityAssigner)

isDecoyMatch

public boolean isDecoyMatch()

setDecoyMatch

public void setDecoyMatch(boolean decoyMatch)

getMinEMIterations

public int getMinEMIterations()

setMinEMIterations

public void setMinEMIterations(int minEMIterations)

getMaxEMIterations

public int getMaxEMIterations()

setMaxEMIterations

public void setMaxEMIterations(int maxEMIterations)

getMinSecondBestProbabilityDifference

public float getMinSecondBestProbabilityDifference()

setMinSecondBestProbabilityDifference

public void setMinSecondBestProbabilityDifference(float minSecondBestProbabilityDifference)

getMaxSecondBestProbability

public float getMaxSecondBestProbability()

setMaxSecondBestProbability

public void setMaxSecondBestProbability(float maxSecondBestProbability)

isUseMs1TimesForAlignment

public boolean isUseMs1TimesForAlignment()

setUseMs1TimesForAlignment

public void setUseMs1TimesForAlignment(boolean useMs1TimesForAlignment)

getMs1Ms2MassTolerancePPM

public float getMs1Ms2MassTolerancePPM()

setMs1Ms2MassTolerancePPM

public void setMs1Ms2MassTolerancePPM(float ms1Ms2MassTolerancePPM)

getMs1Ms2TimeToleranceSeconds

public float getMs1Ms2TimeToleranceSeconds()

setMs1Ms2TimeToleranceSeconds

public void setMs1Ms2TimeToleranceSeconds(float ms1Ms2TimeToleranceSeconds)

getNonlinearMappingPolynomialDegree

public int getNonlinearMappingPolynomialDegree()

setNonlinearMappingPolynomialDegree

public void setNonlinearMappingPolynomialDegree(int nonlinearMappingPolynomialDegree)