org.fhcrc.cpl.toolbox.proteomics.feature
Class AnalyzeICAT

java.lang.Object
  org.fhcrc.cpl.toolbox.proteomics.feature.AnalyzeICAT

public class AnalyzeICAT
extends java.lang.Object

Created by IntelliJ IDEA. User: mbellew Date: May 23, 2005 Time: 11:30:21 AM

Nested Class Summary

static class

AnalyzeICAT.IsotopicLabel

Field Summary

static float	DEFAULT_DELTA_MASS
static int	DEFAULT_DELTA_MASS_TYPE
static float	DEFAULT_DELTA_TIME
static int	DEFAULT_MAX_LABEL_COUNT
static int	DELTA_MASS_ABSOLUTE
static int	DELTA_MASS_PPM
static AnalyzeICAT.IsotopicLabel	icatLabel
protected static java.util.ArrayList	prePopulatedTags

Constructor Summary

AnalyzeICAT()

Method Summary

static java.util.ArrayList	analyze(Feature[] featuresIN, AnalyzeICAT.IsotopicLabel label) Uses default values for mass and time tolerance
static java.util.ArrayList	analyze(Feature[] featuresIN, AnalyzeICAT.IsotopicLabel label, float deltaMass, int deltaMassType, float deltaTime) In some way this seems a lot like deconvolute (FeatureSet.deconvolute()).
static java.util.ArrayList	analyze1(Feature[] featuresIN, AnalyzeICAT.IsotopicLabel label) Uses default values for mass and time tolerance
static java.util.ArrayList	analyze1(Feature[] featuresIN, AnalyzeICAT.IsotopicLabel label, float deltaMass, int deltaMassType, float deltaTime) can be run on deconvoluted or non-deconvoluted feature set
protected static float	calculateAbsoluteDeltaMass(float centerMass, float deltaMass, int deltaMassType) Utility method to calculate the absolute mass tolerance, given a mass tolerance parameter that may be absolute or relative
static java.util.ArrayList	getPrePopulatedLabels() Returns an ArrayList of pre-populated IsotopicLabels.
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MAX_LABEL_COUNT

public static int DEFAULT_MAX_LABEL_COUNT

prePopulatedTags

protected static java.util.ArrayList prePopulatedTags

icatLabel

public static AnalyzeICAT.IsotopicLabel icatLabel

DELTA_MASS_ABSOLUTE

public static final int DELTA_MASS_ABSOLUTE

See Also:

Constant Field Values

DELTA_MASS_PPM

public static final int DELTA_MASS_PPM

See Also:

Constant Field Values

DEFAULT_DELTA_MASS

public static final float DEFAULT_DELTA_MASS

See Also:

Constant Field Values

DEFAULT_DELTA_TIME

public static final float DEFAULT_DELTA_TIME

See Also:

Constant Field Values

DEFAULT_DELTA_MASS_TYPE

public static final int DEFAULT_DELTA_MASS_TYPE

See Also:

Constant Field Values

Constructor Detail

AnalyzeICAT

public AnalyzeICAT()

Method Detail

calculateAbsoluteDeltaMass

protected static float calculateAbsoluteDeltaMass(float centerMass,
                                                  float deltaMass,
                                                  int deltaMassType)

Utility method to calculate the absolute mass tolerance, given a mass tolerance parameter that may be absolute or relative

Parameters:

centerMass -

deltaMass -

deltaMassType -

Returns:

analyze1

public static java.util.ArrayList analyze1(Feature[] featuresIN,
                                           AnalyzeICAT.IsotopicLabel label)

Uses default values for mass and time tolerance

Parameters:

featuresIN -

label -

Returns:

analyze1

public static java.util.ArrayList analyze1(Feature[] featuresIN,
                                           AnalyzeICAT.IsotopicLabel label,
                                           float deltaMass,
                                           int deltaMassType,
                                           float deltaTime)

can be run on deconvoluted or non-deconvoluted feature set

Parameters:

featuresIN -

label -

deltaMass -

deltaMassType - absolute or ppm

deltaTime -

Returns:

analyze

public static java.util.ArrayList analyze(Feature[] featuresIN,
                                          AnalyzeICAT.IsotopicLabel label)

Uses default values for mass and time tolerance

Parameters:

featuresIN -

label -

Returns:

analyze

public static java.util.ArrayList analyze(Feature[] featuresIN,
                                          AnalyzeICAT.IsotopicLabel label,
                                          float deltaMass,
                                          int deltaMassType,
                                          float deltaTime)

In some way this seems a lot like deconvolute (FeatureSet.deconvolute()). However, in that case we can group features by mass. In this case, we don't know the adjusted mass until after we align (we need to know the number of modifications).

Parameters:

featuresIN -

label -

deltaMass -

deltaMassType - absolute or ppm

deltaTime -

Returns:

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Throws:

java.lang.Exception

getPrePopulatedLabels

public static java.util.ArrayList getPrePopulatedLabels()

Returns an ArrayList of pre-populated IsotopicLabels. If the list isn't yet populated, populate it here

Returns:

an arraylist of pre-populated IsotopicLabels