org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo
Class IsotopicLabelExtraInfoDef

java.lang.Object
  org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.FeatureExtraInformationDef
      org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.IsotopicLabelExtraInfoDef

public class IsotopicLabelExtraInfoDef
extends FeatureExtraInformationDef

Contains column name and datatype information about each column. Each column datatype must be a class with a constructor that accepts one String argument.

Field Summary

static float	NO_RATIO_FOR_FEATURE
protected static IsotopicLabelExtraInfoDef	singletonInstance

Fields inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.FeatureExtraInformationDef

_columnInfoTypeMap, _knownColumnDataClassMap, _knownExtraInfoTypes, _standardExtraInformationTypes, cidExtraInfoDef, columnNameDatatypeMap, columnNames, featureSetPropertyNames, intensityWindowsInformationDef, MULTI_VALUE_LIST_SEPARATOR, textCode

Constructor Summary

IsotopicLabelExtraInfoDef()

Method Summary

java.lang.Object	convertFeatureSetPropertyStringValue(java.lang.String propertyName, java.lang.String value) Save as convertStringValue, but for feature set properties
java.lang.String	convertFeatureSetPropertyToString(java.lang.String propertyName, java.lang.Object value) Same as convertToString, but for feature set properties
static java.lang.String	getFeatureSetAlgorithm(FeatureSet featureSet)
static int	getHeavyFirstScan(Feature feature)
static double	getHeavyIntensity(Feature feature)
static int	getHeavyLastScan(Feature feature)
static double	getHeavyMass(Feature feature)
static AnalyzeICAT.IsotopicLabel	getLabel(Feature feature)
static int	getLabelCount(Feature feature)
static int	getLightFirstScan(Feature feature)
static double	getLightIntensity(Feature feature)
static int	getLightLastScan(Feature feature)
static double	getLightMass(Feature feature)
static double	getRatio(Feature feature)
static IsotopicLabelExtraInfoDef	getSingletonInstance()
static boolean	hasLabel(Feature feature)
static boolean	hasRatio(Feature feature)
static boolean	isHeavyLabeled(Feature feature, int labelType)
static boolean	isLightLabeled(Feature feature, int labelType)
static void	removeRatio(Feature feature)
static void	setFeatureSetAlgorithm(FeatureSet featureSet, java.lang.String baseName)
static void	setHeavyFirstScan(Feature feature, int scan)
static void	setHeavyIntensity(Feature feature, double intensity)
static void	setHeavyLastScan(Feature feature, int scan)
static void	setHeavyMass(Feature feature, double mass)
static void	setLabel(Feature feature, AnalyzeICAT.IsotopicLabel label)
static void	setLabelCount(Feature feature, int labelCount)
static void	setLightFirstScan(Feature feature, int scan)
static void	setLightIntensity(Feature feature, double intensity)
static void	setLightLastScan(Feature feature, int scan)
static void	setLightMass(Feature feature, double mass)
static void	setRatio(Feature feature, double ratio)

Methods inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.FeatureExtraInformationDef

addKnownExtraInfoType, convertIntListToString, convertStringArrayToString, convertStringArrayToString, convertStringListToString, convertStringListToString, convertStringValue, convertToString, createFeatureSetPropertyName, createPopupMenuItems, getColumnInfoTypeMap, getColumnNames, getDatatypeForColumnName, getFeatureSetProperty, getInfoTypeForColumn, getKnownColumnDataClassMap, getKnownDataClassForColumn, getKnownExtraInfoTypes, getStandardExtraInformationTypes, getTextCode, getTranslatedText, init, isThisTypeOfFeatureSetProperty, parseIntListString, parseStringListString, parseStringListString, setFeatureSetProperty, setTextCode, stripPrefixFromFeatureSetPropertyName, toString

Methods inherited from class java.lang.Object

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

Field Detail

NO_RATIO_FOR_FEATURE

public static final float NO_RATIO_FOR_FEATURE

See Also:

Constant Field Values

singletonInstance

protected static IsotopicLabelExtraInfoDef singletonInstance

Constructor Detail

IsotopicLabelExtraInfoDef

public IsotopicLabelExtraInfoDef()

Method Detail

convertFeatureSetPropertyToString

public java.lang.String convertFeatureSetPropertyToString(java.lang.String propertyName,
                                                          java.lang.Object value)

Same as convertToString, but for feature set properties

Overrides:

convertFeatureSetPropertyToString in class FeatureExtraInformationDef

Parameters:

propertyName -

value -

Returns:

convertFeatureSetPropertyStringValue

public java.lang.Object convertFeatureSetPropertyStringValue(java.lang.String propertyName,
                                                             java.lang.String value)

Save as convertStringValue, but for feature set properties

Overrides:

convertFeatureSetPropertyStringValue in class FeatureExtraInformationDef

Parameters:

propertyName -

value -

Returns:

getSingletonInstance

public static IsotopicLabelExtraInfoDef getSingletonInstance()

hasLabel

public static boolean hasLabel(Feature feature)

getLabelCount

public static int getLabelCount(Feature feature)

getLabel

public static AnalyzeICAT.IsotopicLabel getLabel(Feature feature)

setLabel

public static void setLabel(Feature feature,
                            AnalyzeICAT.IsotopicLabel label)

setHeavyIntensity

public static void setHeavyIntensity(Feature feature,
                                     double intensity)

setLightIntensity

public static void setLightIntensity(Feature feature,
                                     double intensity)

getHeavyIntensity

public static double getHeavyIntensity(Feature feature)

getLightIntensity

public static double getLightIntensity(Feature feature)

setHeavyMass

public static void setHeavyMass(Feature feature,
                                double mass)

getHeavyMass

public static double getHeavyMass(Feature feature)

setLightMass

public static void setLightMass(Feature feature,
                                double mass)

getLightMass

public static double getLightMass(Feature feature)

setLightFirstScan

public static void setLightFirstScan(Feature feature,
                                     int scan)

getLightFirstScan

public static int getLightFirstScan(Feature feature)

setLightLastScan

public static void setLightLastScan(Feature feature,
                                    int scan)

getLightLastScan

public static int getLightLastScan(Feature feature)

setHeavyFirstScan

public static void setHeavyFirstScan(Feature feature,
                                     int scan)

getHeavyFirstScan

public static int getHeavyFirstScan(Feature feature)

setHeavyLastScan

public static void setHeavyLastScan(Feature feature,
                                    int scan)

getHeavyLastScan

public static int getHeavyLastScan(Feature feature)

setRatio

public static void setRatio(Feature feature,
                            double ratio)

removeRatio

public static void removeRatio(Feature feature)

getRatio

public static double getRatio(Feature feature)

hasRatio

public static boolean hasRatio(Feature feature)

setLabelCount

public static void setLabelCount(Feature feature,
                                 int labelCount)

getFeatureSetAlgorithm

public static java.lang.String getFeatureSetAlgorithm(FeatureSet featureSet)

setFeatureSetAlgorithm

public static void setFeatureSetAlgorithm(FeatureSet featureSet,
                                          java.lang.String baseName)

isLightLabeled

public static boolean isLightLabeled(Feature feature,
                                     int labelType)

isHeavyLabeled

public static boolean isHeavyLabeled(Feature feature,
                                     int labelType)