org.fhcrc.cpl.toolbox.proteomics
Class QuantitationUtilities

java.lang.Object
  org.fhcrc.cpl.toolbox.proteomics.QuantitationUtilities

public class QuantitationUtilities
extends java.lang.Object

Utilities for working with quantitation

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 java.lang.String	ALGORITHM_Q3
static java.lang.String	ALGORITHM_XPRESS
static java.lang.String[]	ALL_LABEL_CODES
static java.lang.String[]	ALL_LABEL_EXPLANATIONS
static int	LABEL_ACRYLAMIDE
static java.lang.String	LABEL_ACRYLAMIDE_CODE
static java.lang.String	LABEL_ACRYLAMIDE_EXPLANATION
static int	LABEL_LYCINE
static java.lang.String	LABEL_LYCINE_CODE
static java.lang.String	LABEL_LYCINE_EXPLANATION
static float	SILAC_LABEL_MASS
static float	SILAC_LABEL_MASSDIFF_PERRESIDUE

Constructor Summary

QuantitationUtilities()

Method Summary

static float	calcHeavyLightMassDiff(java.lang.String peptide, int labelType) Calculate the difference between heavy and light masses of a completely heavy and completely light labeled version of this peptide
static int	inferLabelType(java.lang.String residue, float massDiff) Infer a label type by its residue and mass diff.

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

SILAC_LABEL_MASSDIFF_PERRESIDUE

public static final float SILAC_LABEL_MASSDIFF_PERRESIDUE

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Constant Field Values

ALGORITHM_Q3

public static final java.lang.String ALGORITHM_Q3

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Constant Field Values

ALGORITHM_XPRESS

public static final java.lang.String ALGORITHM_XPRESS

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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

SILAC_LABEL_MASS

public static final float SILAC_LABEL_MASS

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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

LABEL_ACRYLAMIDE

public static final int LABEL_ACRYLAMIDE

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Constant Field Values

LABEL_LYCINE

public static final int LABEL_LYCINE

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Constant Field Values

LABEL_ACRYLAMIDE_CODE

public static final java.lang.String LABEL_ACRYLAMIDE_CODE

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Constant Field Values

LABEL_LYCINE_CODE

public static final java.lang.String LABEL_LYCINE_CODE

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Constant Field Values

LABEL_ACRYLAMIDE_EXPLANATION

public static final java.lang.String LABEL_ACRYLAMIDE_EXPLANATION

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Constant Field Values

LABEL_LYCINE_EXPLANATION

public static final java.lang.String LABEL_LYCINE_EXPLANATION

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Constant Field Values

ALL_LABEL_CODES

public static final java.lang.String[] ALL_LABEL_CODES

ALL_LABEL_EXPLANATIONS

public static final java.lang.String[] ALL_LABEL_EXPLANATIONS

Constructor Detail

QuantitationUtilities

public QuantitationUtilities()

Method Detail

calcHeavyLightMassDiff

public static float calcHeavyLightMassDiff(java.lang.String peptide,
                                           int labelType)

Calculate the difference between heavy and light masses of a completely heavy and completely light labeled version of this peptide

Parameters:

peptide -

labelType -

Returns:

inferLabelType

public static int inferLabelType(java.lang.String residue,
                                 float massDiff)

Infer a label type by its residue and mass diff. If can't, return -1;

Parameters:

residue -

massDiff -

Returns: