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

java.lang.Object
  org.fhcrc.cpl.toolbox.proteomics.feature.Spectrum.Peak
      org.fhcrc.cpl.toolbox.proteomics.feature.Feature
          org.fhcrc.cpl.toolbox.proteomics.feature.FeatureAsMap

All Implemented Interfaces:

java.lang.Cloneable, java.util.Map

Direct Known Subclasses:

PeptideArrayAnalyzer.FeatureAsMapWithIdAndFile

public class FeatureAsMap
extends Feature
implements java.util.Map

This is a subclass of Feature that implements Map. All the Map methods put values in and take values out of the properties Map. This class exists to allow TabLoader to populate arbitrary properties of a Feature. Those properties may be known at development time, and they may not. This is a separate class so that Feature isn't cluttered with all these Map methods, which really don't make a lot of sense for Feature.

Nested Class Summary

Nested classes/interfaces inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.Feature

Feature.IntensityDescComparator, Feature.MassAscComparator, Feature.MzAscComparator, Feature.MzDistAscComparator, Feature.MzScanAscComparator, Feature.PeaksKLComparatorDesc, Feature.ScanAscComparator, Feature.ScanChargeMzAscComparator

Nested classes/interfaces inherited from interface java.util.Map

java.util.Map.Entry<K,V>

Field Summary

protected static org.apache.log4j.Logger

_log

Fields inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.Feature

_propertyMap, accurateMZ, charge, chargeStates, comprised, description, dist, intensityLeadingPeaks, intensityTrailingPeaks, intensityWindow, kl, mass, mModifiedAminoAcids, MZ_RANGE, mzPeak0, next, peaks, scanCount, scanFirst, scanLast, skippedPeaks, time, totalIntensity

Fields inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.Spectrum.Peak

background, excluded, intensity, median, mz, scan

Constructor Summary

FeatureAsMap()

Method Summary

void	clear()
boolean	containsKey(java.lang.Object o)
boolean	containsValue(java.lang.Object o)
java.util.Set	entrySet()
java.lang.Object	get(java.lang.Object propertyName)
boolean	isEmpty()
java.util.Set	keySet()
java.lang.Object	put(java.lang.Object propertyName, java.lang.Object propertyValue) A cover on setProperty().
void	putAll(java.util.Map namesAndValues)
java.lang.Object	remove(java.lang.Object propertyName)
int	size()
java.util.Collection	values()

Methods inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.Feature

addFeatureToRange, afterPopulate, calculateFeatureIntensityInRange, clone, ContainsPeak, determineExtraInformationTypes, equals, findOverlappingScanRange, getCharge, getChargeStates, getDescription, getDoubleProperty, getFeatureHeader, getFloatProperty, getIntProperty, getKl, getMass, getMZRange, getPeaks, getProperty, getProperty, getPropertyMap, getScanCount, getScanFirst, getScanLast, getStringProperty, getSumSquaresDist, getTime, getTotalIntensity, hashCode, hasProperty, isAccurateMZ, isFeatureInRange, isFeatureInRange, isPropertySet, setAccurateMZ, setCharge, setChargeStates, setDescription, setKl, setMass, setMz, setPeaks, setProperty, setScanCount, setScanFirst, setScanLast, setSumSquaresDist, setTime, setTotalIntensity, toString, toString, unsetProperty, updateMass, updateMz

Methods inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.Spectrum.Peak

getBackground, getIntensity, getMedian, getMz, getScan, setBackground, setIntensity, setMedian, setScan

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

equals, hashCode

Field Detail

_log

protected static org.apache.log4j.Logger _log

Constructor Detail

FeatureAsMap

public FeatureAsMap()

Method Detail

put

public java.lang.Object put(java.lang.Object propertyName,
                            java.lang.Object propertyValue)

A cover on setProperty(). But before calling setProperty(), it tries to determine if this property name is known and if the value is a String. If both of those are true, then, before calling setProperty, convert the property to the appropriate class.

Specified by:

put in interface java.util.Map

Parameters:

propertyName -

propertyValue -

Returns:

get

public java.lang.Object get(java.lang.Object propertyName)

Specified by:

get in interface java.util.Map

Overrides:

get in class Feature

putAll

public void putAll(java.util.Map namesAndValues)

Specified by:

putAll in interface java.util.Map

remove

public java.lang.Object remove(java.lang.Object propertyName)

Specified by:

remove in interface java.util.Map

clear

public void clear()

Specified by:

clear in interface java.util.Map

keySet

public java.util.Set keySet()

Specified by:

keySet in interface java.util.Map

values

public java.util.Collection values()

Specified by:

values in interface java.util.Map

entrySet

public java.util.Set entrySet()

Specified by:

entrySet in interface java.util.Map

size

public int size()

Specified by:

size in interface java.util.Map

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface java.util.Map

containsKey

public boolean containsKey(java.lang.Object o)

Specified by:

containsKey in interface java.util.Map

containsValue

public boolean containsValue(java.lang.Object o)

Specified by:

containsValue in interface java.util.Map