org.fhcrc.cpl.viewer.quant
Class QuantEventAssessor

java.lang.Object
  org.fhcrc.cpl.viewer.quant.QuantEventAssessor

public class QuantEventAssessor
extends java.lang.Object

This uses a big HACK, adding a dummy search score to peptide features to store the flag reason description

Nested Class Summary

static class	QuantEventAssessor.QuantEventAssessment Class for communicating assessment results
static class	QuantEventAssessor.QuantPeakSetSummary Data structure to pass around summary information about one set of peaks (light or heavy)

Field Summary

protected static org.apache.log4j.Logger	_log
static float	ACRYLAMIDE_LABEL_HEAVYMASS
static float	ACRYLAMIDE_LABEL_LIGHTMASS
static float	ACRYLAMIDE_LABEL_MASSDIFF_PERRESIDUE
static int	DEFAULT_NUM_SCANS_AROUND_EVENT
static float	DEFAULT_PEAK_PPM_TOLERANCE
static float	DEFAULT_PEAKBELOW_INTENSITY_RATIO_CUTOFF
static int	FLAG_REASON_COELUTING
static int	FLAG_REASON_DISSIMILAR_KL
static int	FLAG_REASON_DISSIMILAR_MS1_RATIO
static int	FLAG_REASON_OK
static int	FLAG_REASON_UNEVALUATED
static java.lang.String[]	flagReasonCodes
static java.lang.String[]	flagReasonDescriptions
protected int	labelType
protected float	maxFlagRatio
protected float	maxKlDiff
protected float	maxLightHeavyOverlapToIgnore
protected float	maxLogRatioDiff
protected float	minFlagRatio
protected float	minKlRatio
protected float	minSignificantPeakContributionBelowMonoisotope
protected int	numPeaksToUse
protected int	numRawPeaksToKeep
protected int	numScansAroundEventToConsider
protected float	peakBelowIntensityRatioCutoff
protected float	peakPPMTolerance
static java.lang.String	REASON_DUMMY_SEARCH_SCORE_NAME
protected boolean	showCharts
static float	SILAC_LABEL_MASS
static float	SILAC_LABEL_MASSDIFF_PERRESIDUE

Constructor Summary

QuantEventAssessor()

Method Summary

QuantEventAssessor.QuantEventAssessment	assessFeature(Feature feature, MSRun run) Assess this feature as a quantitative event
QuantEventAssessor.QuantEventAssessment	assessQuantEvent(QuantEvent event, MSRun run) Assess this quantitative event.
protected float	calcKL(float[] idealPeaks, java.util.List<java.lang.Float> peakIntensities)
protected float	calcKL(float mass, java.util.List<java.lang.Float> peakIntensities) Calculate a KL score for a list of peak intensities.
protected QuantEventAssessor.QuantPeakSetSummary	calcPeakIntensities(int firstScan, int lastScan, float mass, float mz, float charge, MSRun run, int numPeaks) Return the peak quant summary, with intensities of all peaks.
int	getLabelType()
static org.apache.log4j.Logger	getLogger()
float	getMaxFlagRatio()
float	getMinFlagRatio()
float	getPeakPPMTolerance()
boolean	isShowCharts()
static int	parseAssessmentCodeString(java.lang.String curationStatusString)
void	setLabelType(int labelType)
void	setMaxFlagRatio(float maxFlagRatio)
void	setMinFlagRatio(float minFlagRatio)
void	setPeakPPMTolerance(float peakPPMTolerance)
void	setShowCharts(boolean showCharts)

Methods inherited from class java.lang.Object

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

Field Detail

_log

protected static org.apache.log4j.Logger _log

FLAG_REASON_OK

public static final int FLAG_REASON_OK

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Constant Field Values

FLAG_REASON_COELUTING

public static final int FLAG_REASON_COELUTING

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Constant Field Values

FLAG_REASON_DISSIMILAR_KL

public static final int FLAG_REASON_DISSIMILAR_KL

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Constant Field Values

FLAG_REASON_DISSIMILAR_MS1_RATIO

public static final int FLAG_REASON_DISSIMILAR_MS1_RATIO

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Constant Field Values

FLAG_REASON_UNEVALUATED

public static final int FLAG_REASON_UNEVALUATED

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Constant Field Values

flagReasonDescriptions

public static final java.lang.String[] flagReasonDescriptions

flagReasonCodes

public static final java.lang.String[] flagReasonCodes

REASON_DUMMY_SEARCH_SCORE_NAME

public static final java.lang.String REASON_DUMMY_SEARCH_SCORE_NAME

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Constant Field Values

DEFAULT_PEAKBELOW_INTENSITY_RATIO_CUTOFF

public static final float DEFAULT_PEAKBELOW_INTENSITY_RATIO_CUTOFF

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Constant Field Values

peakBelowIntensityRatioCutoff

protected float peakBelowIntensityRatioCutoff

DEFAULT_NUM_SCANS_AROUND_EVENT

public static final int DEFAULT_NUM_SCANS_AROUND_EVENT

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Constant Field Values

numScansAroundEventToConsider

protected int numScansAroundEventToConsider

DEFAULT_PEAK_PPM_TOLERANCE

public static final float DEFAULT_PEAK_PPM_TOLERANCE

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Constant Field Values

peakPPMTolerance

protected float peakPPMTolerance

labelType

protected int labelType

showCharts

protected boolean showCharts

SILAC_LABEL_MASS

public static final float SILAC_LABEL_MASS

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Constant Field Values

SILAC_LABEL_MASSDIFF_PERRESIDUE

public static final float SILAC_LABEL_MASSDIFF_PERRESIDUE

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Constant Field Values

ACRYLAMIDE_LABEL_LIGHTMASS

public static final float ACRYLAMIDE_LABEL_LIGHTMASS

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Constant Field Values

ACRYLAMIDE_LABEL_HEAVYMASS

public static final float ACRYLAMIDE_LABEL_HEAVYMASS

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Constant Field Values

ACRYLAMIDE_LABEL_MASSDIFF_PERRESIDUE

public static final float ACRYLAMIDE_LABEL_MASSDIFF_PERRESIDUE

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Constant Field Values

numPeaksToUse

protected int numPeaksToUse

numRawPeaksToKeep

protected int numRawPeaksToKeep

minSignificantPeakContributionBelowMonoisotope

protected float minSignificantPeakContributionBelowMonoisotope

maxLightHeavyOverlapToIgnore

protected float maxLightHeavyOverlapToIgnore

maxKlDiff

protected float maxKlDiff

minKlRatio

protected float minKlRatio

maxLogRatioDiff

protected float maxLogRatioDiff

minFlagRatio

protected float minFlagRatio

maxFlagRatio

protected float maxFlagRatio

Constructor Detail

QuantEventAssessor

public QuantEventAssessor()

Method Detail

parseAssessmentCodeString

public static int parseAssessmentCodeString(java.lang.String curationStatusString)

assessFeature

public QuantEventAssessor.QuantEventAssessment assessFeature(Feature feature,
                                                             MSRun run)

Assess this feature as a quantitative event

Parameters:

feature -

run -

Returns:

assessQuantEvent

public QuantEventAssessor.QuantEventAssessment assessQuantEvent(QuantEvent event,
                                                                MSRun run)

Assess this quantitative event. Return assessment. Side effect: set event.algorithmicAssessment

Parameters:

event -

run -

Returns:

calcKL

protected float calcKL(float mass,
                       java.util.List<java.lang.Float> peakIntensities)

Calculate a KL score for a list of peak intensities. Have to normalize intensity first by dividing by peak sum

Parameters:

mass -

peakIntensities -

Returns:

calcKL

protected float calcKL(float[] idealPeaks,
                       java.util.List<java.lang.Float> peakIntensities)

calcPeakIntensities

protected QuantEventAssessor.QuantPeakSetSummary calcPeakIntensities(int firstScan,
                                                                     int lastScan,
                                                                     float mass,
                                                                     float mz,
                                                                     float charge,
                                                                     MSRun run,
                                                                     int numPeaks)

Return the peak quant summary, with intensities of all peaks. Use raw intensities, NOT resampled

Parameters:

firstScan -

lastScan -

mass -

mz -

charge -

run -

numPeaks -

Returns:

getPeakPPMTolerance

public float getPeakPPMTolerance()

setPeakPPMTolerance

public void setPeakPPMTolerance(float peakPPMTolerance)

getLogger

public static org.apache.log4j.Logger getLogger()

getMinFlagRatio

public float getMinFlagRatio()

setMinFlagRatio

public void setMinFlagRatio(float minFlagRatio)

getMaxFlagRatio

public float getMaxFlagRatio()

setMaxFlagRatio

public void setMaxFlagRatio(float maxFlagRatio)

isShowCharts

public boolean isShowCharts()

setShowCharts

public void setShowCharts(boolean showCharts)

getLabelType

public int getLabelType()

setLabelType

public void setLabelType(int labelType)