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

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

public class AmtExtraInfoDef
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 double	NO_MATCH_PROBABILITY
static double	NO_OBSERVED_HYDROPHOBICITY
protected static AmtExtraInfoDef	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

AmtExtraInfoDef()

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 double	getFeatureSetEstimatedTruePositives(FeatureSet featureSet)
static double	getFeatureSetFalseAssignmentRate(FeatureSet featureSet)
static java.lang.String	getFeatureSetMatchedDatabaseName(FeatureSet featureSet)
static java.util.List<java.lang.String>	getFeatureSetRunsMatched(FeatureSet featureSet)
static double	getMatchProbability(Feature feature)
static double	getObservedHydrophobicity(Feature feature)
static AmtExtraInfoDef	getSingletonInstance()
static boolean	hasMatchProbability(Feature feature)
static boolean	hasObservedHydrophobicity(Feature feature)
static void	setFeatureSetEstimatedTruePositives(FeatureSet featureSet, double estTruePos)
static void	setFeatureSetFalseAssignmentRate(FeatureSet featureSet, double estTruePos)
static void	setFeatureSetMatchedDatabaseName(FeatureSet featureSet, java.lang.String matchedDatabaseName)
static void	setFeatureSetRunsMatched(FeatureSet featureSet, java.util.List<java.lang.String> runsMatched)
static void	setMatchProbability(Feature feature, double matchProbability)
static void	setObservedHydrophobicity(Feature feature, double hydrophobicity)

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_OBSERVED_HYDROPHOBICITY

public static final double NO_OBSERVED_HYDROPHOBICITY

See Also:

Constant Field Values

NO_MATCH_PROBABILITY

public static final double NO_MATCH_PROBABILITY

See Also:

Constant Field Values

singletonInstance

protected static AmtExtraInfoDef singletonInstance

Constructor Detail

AmtExtraInfoDef

public AmtExtraInfoDef()

Method Detail

getSingletonInstance

public static AmtExtraInfoDef getSingletonInstance()

getObservedHydrophobicity

public static double getObservedHydrophobicity(Feature feature)

setObservedHydrophobicity

public static void setObservedHydrophobicity(Feature feature,
                                             double hydrophobicity)

hasObservedHydrophobicity

public static boolean hasObservedHydrophobicity(Feature feature)

getMatchProbability

public static double getMatchProbability(Feature feature)

setMatchProbability

public static void setMatchProbability(Feature feature,
                                       double matchProbability)

hasMatchProbability

public static boolean hasMatchProbability(Feature feature)

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:

getFeatureSetRunsMatched

public static java.util.List<java.lang.String> getFeatureSetRunsMatched(FeatureSet featureSet)

setFeatureSetRunsMatched

public static void setFeatureSetRunsMatched(FeatureSet featureSet,
                                            java.util.List<java.lang.String> runsMatched)

getFeatureSetEstimatedTruePositives

public static double getFeatureSetEstimatedTruePositives(FeatureSet featureSet)

setFeatureSetEstimatedTruePositives

public static void setFeatureSetEstimatedTruePositives(FeatureSet featureSet,
                                                       double estTruePos)

getFeatureSetFalseAssignmentRate

public static double getFeatureSetFalseAssignmentRate(FeatureSet featureSet)

setFeatureSetFalseAssignmentRate

public static void setFeatureSetFalseAssignmentRate(FeatureSet featureSet,
                                                    double estTruePos)

getFeatureSetMatchedDatabaseName

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

setFeatureSetMatchedDatabaseName

public static void setFeatureSetMatchedDatabaseName(FeatureSet featureSet,
                                                    java.lang.String matchedDatabaseName)