org.proteios.core.data
Class FeatureData

java.lang.Object
  org.proteios.core.data.BasicData
      org.proteios.core.data.FeatureData

All Implemented Interfaces:

IdentifiableData

public class FeatureData
extends BasicData

Represents information about features from an LC-MS run.

Hibernate: class

table="`Features`" lazy="true"

Field Summary

static int

MAX_PEPTIDESEQUENCE_LENGTH

Constructor Summary

FeatureData()

Method Summary

Float	getApexIntensity()
Float	getApexRetentionTimeInMinutes()
Integer	getChargeState()
Long	getClusterId() Features that have been matched between files should be assigned the same cluster id.
Float	getEndRetentionTimeInMinutes()
Integer	getFeatureExternalId()
FileData	getFeatureFile() feature file.
Set<HitData>	getHits() Get the Hits matched to this feature.
Float	getIntegratedIntensity()
Double	getMassToChargeRatio()
FileData	getMsFile() mzML / mzXML file.
String	getPeptideSequence()
ProjectData	getProject() Project origin reference.
Float	getSignalToNoiseRatio()
Float	getStartRetentionTimeInMinutes()
void	setApexIntensity(Float apexIntensity)
void	setApexRetentionTimeInMinutes(Float apexRetentionTimeInMinutes)
void	setChargeState(Integer chargeState)
void	setClusterId(Long clusterId)
void	setEndRetentionTimeInMinutes(Float endRetentionTimeInMinutes)
void	setFeatureExternalId(Integer featureExternalId)
void	setFeatureFile(FileData featureFile)
void	setHits(Set<HitData> hits) Set the Hits
void	setIntegratedIntensity(Float integratedIntensity)
void	setMassToChargeRatio(Double massToChargeRatio)
void	setMsFile(FileData msFile)
void	setPeptideSequence(String peptideSequence)
void	setProject(ProjectData project)
void	setSignalToNoiseRatio(Float signalToNoiseRatio)
void	setStartRetentionTimeInMinutes(Float startRetentionTimeInMinutes)

Methods inherited from class org.proteios.core.data.BasicData

equals, getId, getVersion, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

MAX_PEPTIDESEQUENCE_LENGTH

public static final int MAX_PEPTIDESEQUENCE_LENGTH

See Also:

Constant Field Values

Constructor Detail

FeatureData

public FeatureData()

Method Detail

getFeatureFile

public FileData getFeatureFile()

feature file.

Hibernate: many-to-one

column="`featureFile`" not-null="false"

setFeatureFile

public void setFeatureFile(FileData featureFile)

getMsFile

public FileData getMsFile()

mzML / mzXML file.

Hibernate: many-to-one

column="`msFile`" not-null="false"

setMsFile

public void setMsFile(FileData msFile)

getProject

public ProjectData getProject()

Project origin reference.

Hibernate: many-to-one

column="`project`" not-null="true" update="false"

setProject

public void setProject(ProjectData project)

getApexIntensity

public Float getApexIntensity()

Returns:

Returns the apexIntensity.

Hibernate: property

column="`apexIntensity`" type="float" not-null="false"

setApexIntensity

public void setApexIntensity(Float apexIntensity)

Parameters:

apexIntensity - The apexIntensity to set.

getApexRetentionTimeInMinutes

public Float getApexRetentionTimeInMinutes()

Returns:

Returns the apexRetentionTimeInMinutes.

Hibernate: property

column="`apexRetentionTimeInMinutes`" type="float" not-null="false"

setApexRetentionTimeInMinutes

public void setApexRetentionTimeInMinutes(Float apexRetentionTimeInMinutes)

Parameters:

apexRetentionTimeInMinutes - The apexRetentionTimeInMinutes to set.

getChargeState

public Integer getChargeState()

Returns:

Returns the chargeState.

Hibernate: property

column="`chargeState`" type="int" not-null="false"

setChargeState

public void setChargeState(Integer chargeState)

Parameters:

chargeState - The chargeState to set.

getMassToChargeRatio

public Double getMassToChargeRatio()

Returns:

Returns the massToChargeRatio.

Hibernate: property

column="`mz`" type="double" not-null="false"

setMassToChargeRatio

public void setMassToChargeRatio(Double massToChargeRatio)

Parameters:

massToChargeRatio - The massToChargeRatio to set.

getStartRetentionTimeInMinutes

public Float getStartRetentionTimeInMinutes()

Returns:

Returns the startRetentionTimeInMinutes.

Hibernate: property

column="`startRetentionTimeInMinutes`" type="float" not-null="false"

setStartRetentionTimeInMinutes

public void setStartRetentionTimeInMinutes(Float startRetentionTimeInMinutes)

Parameters:

startRetentionTimeInMinutes - The startRetentionTimeInMinutes to set.

getEndRetentionTimeInMinutes

public Float getEndRetentionTimeInMinutes()

Returns:

Returns the endRetentionTimeInMinutes.

Hibernate: property

column="`endRetentionTimeInMinutes`" type="float" not-null="false"

setEndRetentionTimeInMinutes

public void setEndRetentionTimeInMinutes(Float endRetentionTimeInMinutes)

Parameters:

endRetentionTimeInMinutes - The endRetentionTimeInMinutes to set.

getIntegratedIntensity

public Float getIntegratedIntensity()

Returns:

Returns the integratedIntensity.

Hibernate: property

column="`integratedIntensity`" type="float" not-null="false"

setIntegratedIntensity

public void setIntegratedIntensity(Float integratedIntensity)

Parameters:

integratedIntensity - The integratedIntensity to set.

getSignalToNoiseRatio

public Float getSignalToNoiseRatio()

Returns:

Returns the signalToNoiseRatio.

Hibernate: property

column="`signalToNoiseRatio`" type="float" not-null="false"

setSignalToNoiseRatio

public void setSignalToNoiseRatio(Float signalToNoiseRatio)

Parameters:

signalToNoiseRatio - The signalToNoiseRatio to set.

getPeptideSequence

public String getPeptideSequence()

Returns:

Returns the peptideSequence.

Hibernate: property

column="`peptideSequence`" type="string" length="255" not-null="false"

setPeptideSequence

public void setPeptideSequence(String peptideSequence)

Parameters:

peptideSequence - The peptideSequence to set.

getHits

public Set<HitData> getHits()

Get the Hits matched to this feature. Note that the there is no cascading for delete

Returns:

The HitData set of hits

Hibernate: set

table="`Hits`" cascade="none" lazy="true" inverse="true"

Hibernate: collection-key

column="`feature`"

Hibernate: collection-one-to-many

class="org.proteios.core.data.HitData" not-null="false"

setHits

public void setHits(Set<HitData> hits)

Set the Hits

getFeatureExternalId

public Integer getFeatureExternalId()

Returns:

Returns the featureExternalId.

Hibernate: property

column="`featureExternalId`" type="int" not-null="false"

setFeatureExternalId

public void setFeatureExternalId(Integer featureExternalId)

Parameters:

featureExternalId - The featureExternalId to set.

getClusterId

public Long getClusterId()

Features that have been matched between files should be assigned the same cluster id. All features with the same cluster id in the database should represent the same peptide.

Returns:

Returns the clusterId.

Hibernate: property

column="`clusterId`" type="long" not-null="false"

setClusterId

public void setClusterId(Long clusterId)

Parameters:

clusterlId - The featureExternalId to set.