org.fhcrc.cpl.viewer.amt
Class AmtLabeledQuant

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

public class AmtLabeledQuant
extends java.lang.Object

Methods for performing labeled quantitation on AMT data. This is very simple. After AMT matching, we simply locate all peptides for which we've found both the light and heavy pair (given an isotopic label definition) with the same modification state and charge. We consider that one feature and record the light area, heavy area, and ratio

Field Summary

protected static org.apache.log4j.Logger	_log
static double	ACRYLAMIDE_MASS_DIFF
static java.lang.Character	ACRYLAMIDE_RESIDUE
static AnalyzeICAT.IsotopicLabel	DEFAULT_ISOTOPIC_LABEL
protected static double	DEFAULT_MASS_SLOP
static float	DEFAULT_MAX_SECOND_BEST_PROB_WITHIN_STATE
static float	DEFAULT_MIN_PROB_DIFF_WITHIN_STATE
static float	DEFAULT_MIN_RATIO_HIGH_PROB
static float	DEFAULT_MIN_RATIO_LOW_PROB
static MS2Modification[]	DEFAULT_OTHER_MODS
protected AnalyzeICAT.IsotopicLabel	isotopicLabel
protected java.util.List<java.lang.Float>	logRatiosAllFiles
protected double	massSlop
protected float	maxSecondBestProbWithinState
protected float	minProbDifferenceWithinState
protected float	minRatioHigherProbability
protected float	minRatioLowerProbability
protected MS2Modification[]	otherModifications
protected boolean	perCharge
protected boolean	showCharts

Constructor Summary

AmtLabeledQuant()

Method Summary

protected java.util.List<java.lang.Float>	calculateHeavyLabelResidueMasses() calculate the masses that represent a heavy label on the relevant residue Warning -- we're not handling the case in which there are THREE variable modifications -- the label and two others.
AnalyzeICAT.IsotopicLabel	getIsotopicLabel()
double	getMassSlop()
float	getMinRatioHigherProbability()
float	getMinRatioLowerProbability()
MS2Modification[]	getOtherModifications()
protected Feature	pickWinnerForModState(java.util.List<Feature> featuresInModState) Returns the highest-probability feature in the list, or null if no feature stands out above the rest enough
protected Feature	processFeaturePair(Feature lightFeature, Feature heavyFeature)
void	quantitate(FeatureSet featureSet) do the actual work
void	setIsotopicLabel(AnalyzeICAT.IsotopicLabel isotopicLabel)
void	setMassSlop(double massSlop)
void	setMinRatioHigherProbability(float minRatioHigherProbability)
void	setMinRatioLowerProbability(float minRatioLowerProbability)
void	setOtherModifications(MS2Modification[] otherModifications)

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

ACRYLAMIDE_MASS_DIFF

public static final double ACRYLAMIDE_MASS_DIFF

See Also:

Constant Field Values

ACRYLAMIDE_RESIDUE

public static final java.lang.Character ACRYLAMIDE_RESIDUE

isotopicLabel

protected AnalyzeICAT.IsotopicLabel isotopicLabel

DEFAULT_ISOTOPIC_LABEL

public static final AnalyzeICAT.IsotopicLabel DEFAULT_ISOTOPIC_LABEL

DEFAULT_OTHER_MODS

public static final MS2Modification[] DEFAULT_OTHER_MODS

otherModifications

protected MS2Modification[] otherModifications

DEFAULT_MASS_SLOP

protected static final double DEFAULT_MASS_SLOP

See Also:

Constant Field Values

DEFAULT_MIN_RATIO_HIGH_PROB

public static final float DEFAULT_MIN_RATIO_HIGH_PROB

See Also:

Constant Field Values

DEFAULT_MIN_RATIO_LOW_PROB

public static final float DEFAULT_MIN_RATIO_LOW_PROB

See Also:

Constant Field Values

minRatioHigherProbability

protected float minRatioHigherProbability

minRatioLowerProbability

protected float minRatioLowerProbability

massSlop

protected double massSlop

showCharts

protected boolean showCharts

logRatiosAllFiles

protected java.util.List<java.lang.Float> logRatiosAllFiles

perCharge

protected boolean perCharge

DEFAULT_MIN_PROB_DIFF_WITHIN_STATE

public static final float DEFAULT_MIN_PROB_DIFF_WITHIN_STATE

See Also:

Constant Field Values

minProbDifferenceWithinState

protected float minProbDifferenceWithinState

DEFAULT_MAX_SECOND_BEST_PROB_WITHIN_STATE

public static final float DEFAULT_MAX_SECOND_BEST_PROB_WITHIN_STATE

See Also:

Constant Field Values

maxSecondBestProbWithinState

protected float maxSecondBestProbWithinState

Constructor Detail

AmtLabeledQuant

public AmtLabeledQuant()

Method Detail

quantitate

public void quantitate(FeatureSet featureSet)

do the actual work

pickWinnerForModState

protected Feature pickWinnerForModState(java.util.List<Feature> featuresInModState)

Returns the highest-probability feature in the list, or null if no feature stands out above the rest enough

Parameters:

featuresInModState -

Returns:

processFeaturePair

protected Feature processFeaturePair(Feature lightFeature,
                                     Feature heavyFeature)

calculateHeavyLabelResidueMasses

protected java.util.List<java.lang.Float> calculateHeavyLabelResidueMasses()

calculate the masses that represent a heavy label on the relevant residue Warning -- we're not handling the case in which there are THREE variable modifications -- the label and two others. But, come on, that's, you know, crazy.

Returns:

getIsotopicLabel

public AnalyzeICAT.IsotopicLabel getIsotopicLabel()

setIsotopicLabel

public void setIsotopicLabel(AnalyzeICAT.IsotopicLabel isotopicLabel)

getMassSlop

public double getMassSlop()

setMassSlop

public void setMassSlop(double massSlop)

getMinRatioHigherProbability

public float getMinRatioHigherProbability()

setMinRatioHigherProbability

public void setMinRatioHigherProbability(float minRatioHigherProbability)

getMinRatioLowerProbability

public float getMinRatioLowerProbability()

setMinRatioLowerProbability

public void setMinRatioLowerProbability(float minRatioLowerProbability)

getOtherModifications

public MS2Modification[] getOtherModifications()

setOtherModifications

public void setOtherModifications(MS2Modification[] otherModifications)