org.proteios.core
Class Feature

java.lang.Object
  org.proteios.core.BasicItem<FeatureData>
      org.proteios.core.Feature

All Implemented Interfaces:

AccessControlled, Identifiable

public class Feature
extends BasicItem<FeatureData>

Represents information about features from an LC-MS run, as picked by a feature extraction algorithm.

Field Summary

static int	MAX_PEPTIDESEQUENCE_LENGTH
static Item	TYPE

Method Summary

void	addHit(Hit hit) Add a Hit
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()
File	getFeatureFile() feature file.
Set<Hit>	getHits()
Float	getIntegratedIntensity()
Double	getMassToChargeRatio()
File	getMsFile() mzML / mzXML file.
String	getPeptideSequence()
ProjectData	getProject() The project.
Float	getSignalToNoiseRatio()
Float	getStartRetentionTimeInMinutes()
Item	getType() Get the type of item represented by the object.
static List<File>	getUniqueMsFiles(Project project, DbControl dc)
boolean	isUsed() Check if this item is used by some other item.
void	setApexIntensity(Float apexIntensity)
void	setApexRetentionTimeInMinutes(Float apexRetentionTimeInMinutes)
void	setChargeState(Integer chargeState)
void	setClusterId(Long clusterId) Features that have been matched between files should be assigned the same cluster id.
void	setEndRetentionTimeInMinutes(Float endRetentionTimeInMinutes)
void	setFeatureExternalId(Integer featureExternalId)
void	setFeatureFile(File featureFile)
void	setHits(Set<Hit> hits) Set the Hit hits set.
void	setIntegratedIntensity(Float integratedIntensity)
void	setMassToChargeRatio(Double massToChargeRatio)
void	setMsFile(File msFile)
void	setPeptideSequence(String peptideSequence)
void	setProject(Project project)
void	setSignalToNoiseRatio(Float signalToNoiseRatio)
void	setStartRetentionTimeInMinutes(Float startRetentionTimeInMinutes)

Methods inherited from class org.proteios.core.BasicItem

checkPermission, equals, getDbControl, getId, getPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, toString

Methods inherited from class java.lang.Object

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

Field Detail

TYPE

public static final Item TYPE

MAX_PEPTIDESEQUENCE_LENGTH

public static final int MAX_PEPTIDESEQUENCE_LENGTH

See Also:

Constant Field Values

Method Detail

getUniqueMsFiles

public static List<File> getUniqueMsFiles(Project project,
                                          DbControl dc)

getType

public Item getType()

Description copied from interface: Identifiable

Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.

Returns:

A value indicating the type of item

isUsed

public boolean isUsed()
               throws BaseException

Description copied from class: BasicItem

Check if this item is used by some other item. With used we mean that another item is linking to this item in way that prevents this item from beeing deleted. Ie. if we tried to delete an item that is used, we would get a foreign key violation error from the database.

Specified by:

isUsed in class BasicItem<FeatureData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

getFeatureFile

public File getFeatureFile()

feature file.

setFeatureFile

public void setFeatureFile(File featureFile)

getMsFile

public File getMsFile()

mzML / mzXML file.

setMsFile

public void setMsFile(File msFile)

getProject

public ProjectData getProject()

The project.

Returns:

project

setProject

public void setProject(Project project)

getApexIntensity

public Float getApexIntensity()

Returns:

Returns the apexIntensity.

setApexIntensity

public void setApexIntensity(Float apexIntensity)

Parameters:

apexIntensity - The apexIntensity to set.

getApexRetentionTimeInMinutes

public Float getApexRetentionTimeInMinutes()

Returns:

Returns the apexRetentionTimeInMinutes.

setApexRetentionTimeInMinutes

public void setApexRetentionTimeInMinutes(Float apexRetentionTimeInMinutes)

Parameters:

apexRetentionTimeInMinutes - The apexRetentionTimeInMinutes to set.

getChargeState

public Integer getChargeState()

Returns:

Returns the chargeState.

setChargeState

public void setChargeState(Integer chargeState)

Parameters:

chargeState - The chargeState to set.

getMassToChargeRatio

public Double getMassToChargeRatio()

Returns:

Returns the massToChargeRatio.

setMassToChargeRatio

public void setMassToChargeRatio(Double massToChargeRatio)

Parameters:

massToChargeRatio - The massToChargeRatio to set.

getStartRetentionTimeInMinutes

public Float getStartRetentionTimeInMinutes()

Returns:

Returns the startRetentionTimeInMinutes.

setStartRetentionTimeInMinutes

public void setStartRetentionTimeInMinutes(Float startRetentionTimeInMinutes)

Parameters:

startRetentionTimeInMinutes - The startRetentionTimeInMinutes to set.

getEndRetentionTimeInMinutes

public Float getEndRetentionTimeInMinutes()

Returns:

Returns the endRetentionTimeInMinutes.

setEndRetentionTimeInMinutes

public void setEndRetentionTimeInMinutes(Float endRetentionTimeInMinutes)

Parameters:

endRetentionTimeInMinutes - The endRetentionTimeInMinutes to set.

getIntegratedIntensity

public Float getIntegratedIntensity()

Returns:

Returns the integratedIntensity.

setIntegratedIntensity

public void setIntegratedIntensity(Float integratedIntensity)

Parameters:

integratedIntensity - The integratedIntensity to set.

getSignalToNoiseRatio

public Float getSignalToNoiseRatio()

Returns:

Returns the signalToNoiseRatio.

setSignalToNoiseRatio

public void setSignalToNoiseRatio(Float signalToNoiseRatio)

Parameters:

signalToNoiseRatio - The signalToNoiseRatio to set.

getPeptideSequence

public String getPeptideSequence()

Returns:

Returns the most probable peptide sequence.

setPeptideSequence

public void setPeptideSequence(String peptideSequence)
                        throws StringTooLongException

Parameters:

peptideSequence - The peptideSequence to set.

Throws:

StringTooLongException

getFeatureExternalId

public Integer getFeatureExternalId()

Returns:

Returns the featureExternalId.

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.

setClusterId

public void setClusterId(Long clusterId)

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.

Parameters:

clusterId - The clusterId to set.

getHits

public Set<Hit> getHits()
                 throws ItemNotFoundException,
                        BaseException

Returns:

Returns the Hits associated with this feature.

Throws:

ItemNotFoundException

BaseException

setHits

public void setHits(Set<Hit> hits)

Set the Hit hits set.

Parameters:

hits - The new Set item.

addHit

public void addHit(Hit hit)

Add a Hit

Parameters:

hit - The Search Database to add to the Set