org.proteios.core.data
Class HitData

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

All Implemented Interfaces:

IdentifiableData

public class HitData
extends BasicData

Represents information about a spot and it's identification.

Hibernate: class

table="`Hits`" lazy="true"

Field Summary

static int	MAX_EXTERNALID_LENGTH
static int	MAX_FRACTION_ID_LENGTH The maximum length of the fraction ID that can be stored in the database.
static int	MAX_SPECTRUMSTRINGID_LENGTH

Constructor Summary

HitData()

Method Summary

Integer	getCharge() The charge measured in Dalton.
Float	getCombinedFDR()
Float	getCoverage()
Float	getDeltaMassInDaltons() The delta mass of this item measured in Dalton.
String	getDescription() The description of a proteion or peptide that was identified.
Float	getExpectationValue()
Float	getExperimentalMassInDaltons() The experimental mass measured in Dalton.
String	getExternalId() For proteins/peptides this is the Accession number.
String	getExtraString() This field is used if the External id was to long.
FeatureData	getFeature() Best matching feature
HitData	getFirstInCombination()
String	getFractionId() A fraction id, e.g. a serial number like 01.
String	getGelExternalId()
FileData	getIdentificationResultFile() identificationResultFile origin reference.
String	getLocalSampleId() An analysis sample's external id
Integer	getMatchedPeaks()
Boolean	getMicroPlate()
Float	getMwInDaltons()
FileData	getPeakListFile() peakListFile origin reference.
Float	getPi()
String	getPlateId() A plates external id
Float	getPrecursorQuantity()
Boolean	getPrimaryCombined()
ProjectData	getProject() Project origin reference.
Boolean	getProtein()
Float	getRetentionTimeInMinutes()
Float	getRootMeanSquareError()
Float	getScore()
String	getScoreType()
Date	getSearchDate() Date when the identification search was performed
Integer	getSpectrumId() Spectrum identifier
String	getSpectrumStringId()
Integer	getSpotId()
Float	getSpotXPixel() X coordinate of gel spot
Float	getSpotYPixel() Y coordinate of gel spot
Double	getTotalIntensity() The total intensity of a spot
Integer	getTotalPeaks()
String	getWellPosition() A well position, e.g.
void	setCharge(Integer charge)
void	setCombinedFDR(Float combinedFDR)
void	setCoverage(Float coverage)
void	setDeltaMassInDaltons(Float deltaMass)
void	setDescription(String description)
void	setExpectationValue(Float eValue)
void	setExperimentalMassInDaltons(Float experimentalMass)
void	setExternalId(String externalId)
void	setExtraString(String extraString)
void	setFeature(FeatureData feature)
void	setFirstInCombination(HitData firstInCombination)
void	setFractionId(String fractionId)
void	setGelExternalId(String gelExternalId)
void	setIdentificationResultFile(FileData identificationResultFile)
void	setLocalSampleId(String localSampleId)
void	setMatchedPeaks(Integer matchedPeaks)
void	setMicroPlate(Boolean microPlate)
void	setMwInDaltons(Float mw)
void	setPeakListFile(FileData peakListFile)
void	setPi(Float pi)
void	setPlateId(String plateId)
void	setPrecursorQuantity(Float precursorQuantity)
void	setPrimaryCombined(Boolean primaryCombined)
void	setProject(ProjectData project)
void	setProtein(Boolean protein)
void	setRetentionTimeInMinutes(Float retentionTimeInMinutes)
void	setRootMeanSquareError(Float RMSError)
void	setScore(Float score)
void	setScoreType(String scoreType)
void	setSearchDate(Date searchDate)
void	setSpectrumId(Integer spectrumId)
void	setSpectrumStringId(String spectrumStringId)
void	setSpotId(Integer spotId)
void	setSpotXPixel(Float spotXPixel)
void	setSpotYPixel(Float spotYPixel)
void	setTotalIntensity(Double totalIntensity)
void	setTotalPeaks(Integer totalPeaks)
void	setWellPosition(String wellPosition)

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_FRACTION_ID_LENGTH

public static final int MAX_FRACTION_ID_LENGTH

The maximum length of the fraction ID that can be stored in the database.

See Also:

setFractionId(String), Constant Field Values

MAX_EXTERNALID_LENGTH

public static final int MAX_EXTERNALID_LENGTH

See Also:

Constant Field Values

MAX_SPECTRUMSTRINGID_LENGTH

public static final int MAX_SPECTRUMSTRINGID_LENGTH

See Also:

Constant Field Values

Constructor Detail

HitData

public HitData()

Method Detail

getGelExternalId

public String getGelExternalId()

Hibernate: property

column="`gelExternalId`" length="32" type="string" not-null="false" index="gelExtId_idx"

setGelExternalId

public void setGelExternalId(String gelExternalId)

getSpotId

public Integer getSpotId()

Hibernate: property

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

setSpotId

public void setSpotId(Integer spotId)

getSpectrumId

public Integer getSpectrumId()

Spectrum identifier

Hibernate: property

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

setSpectrumId

public void setSpectrumId(Integer spectrumId)

getDeltaMassInDaltons

public Float getDeltaMassInDaltons()

The delta mass of this item measured in Dalton.

Hibernate: property

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

setDeltaMassInDaltons

public void setDeltaMassInDaltons(Float deltaMass)

getPlateId

public String getPlateId()

A plates external id

Hibernate: property

column="`plateId`" length="32" type="string" not-null="false"

setPlateId

public void setPlateId(String plateId)

getWellPosition

public String getWellPosition()

A well position, e.g. A1. Constrained to 8 characters.

Hibernate: property

column="`wellPosition`" length="8" type="string" not-null="false"

setWellPosition

public void setWellPosition(String wellPosition)

getLocalSampleId

public String getLocalSampleId()

An analysis sample's external id

Hibernate: property

column="`localSampleId`" length="32" type="string" not-null="false"

setLocalSampleId

public void setLocalSampleId(String localSampleId)

getFractionId

public String getFractionId()

A fraction id, e.g. a serial number like 01. Constrained to 8 characters.

Hibernate: property

column="`fractionId`" length="8" type="string" not-null="false"

setFractionId

public void setFractionId(String fractionId)

getMicroPlate

public Boolean getMicroPlate()

Hibernate: property

column="`microPlate`" type="boolean" not-null="false"

setMicroPlate

public void setMicroPlate(Boolean microPlate)

getSearchDate

public Date getSearchDate()

Date when the identification search was performed

Hibernate: property

column="`searchDate`" type="timestamp" not-null="false"

setSearchDate

public void setSearchDate(Date searchDate)

getExpectationValue

public Float getExpectationValue()

Hibernate: property

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

setExpectationValue

public void setExpectationValue(Float eValue)

getScore

public Float getScore()

Hibernate: property

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

setScore

public void setScore(Float score)

getScoreType

public String getScoreType()

Hibernate: property

column="`scoreType`" length="32" type="string" not-null="false"

setScoreType

public void setScoreType(String scoreType)

getProtein

public Boolean getProtein()

Hibernate: property

column="`protein`" type="boolean" not-null="false"

setProtein

public void setProtein(Boolean protein)

getExternalId

public String getExternalId()

For proteins/peptides this is the Accession number.

Hibernate: property

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

setExternalId

public void setExternalId(String externalId)

getExtraString

public String getExtraString()

This field is used if the External id was to long.

Hibernate: property

column="`extraString`" length="2500" type="string" not-null="false"

setExtraString

public void setExtraString(String extraString)

getDescription

public String getDescription()

The description of a proteion or peptide that was identified.

Hibernate: property

column="`description`" type="text" not-null="false"

setDescription

public void setDescription(String description)

getCoverage

public Float getCoverage()

Hibernate: property

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

setCoverage

public void setCoverage(Float coverage)

getMwInDaltons

public Float getMwInDaltons()

Hibernate: property

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

setMwInDaltons

public void setMwInDaltons(Float mw)

getPi

public Float getPi()

Hibernate: property

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

setPi

public void setPi(Float pi)

getMatchedPeaks

public Integer getMatchedPeaks()

Hibernate: property

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

setMatchedPeaks

public void setMatchedPeaks(Integer matchedPeaks)

getTotalPeaks

public Integer getTotalPeaks()

Hibernate: property

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

setTotalPeaks

public void setTotalPeaks(Integer totalPeaks)

getRootMeanSquareError

public Float getRootMeanSquareError()

Hibernate: property

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

setRootMeanSquareError

public void setRootMeanSquareError(Float RMSError)

getTotalIntensity

public Double getTotalIntensity()

The total intensity of a spot

Hibernate: property

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

setTotalIntensity

public void setTotalIntensity(Double totalIntensity)

getExperimentalMassInDaltons

public Float getExperimentalMassInDaltons()

The experimental mass measured in Dalton.

Hibernate: property

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

setExperimentalMassInDaltons

public void setExperimentalMassInDaltons(Float experimentalMass)

getCharge

public Integer getCharge()

The charge measured in Dalton.

Hibernate: property

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

setCharge

public void setCharge(Integer charge)

getProject

public ProjectData getProject()

Project origin reference.

Hibernate: many-to-one

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

setProject

public void setProject(ProjectData project)

getPeakListFile

public FileData getPeakListFile()

peakListFile origin reference.

Hibernate: many-to-one

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

setPeakListFile

public void setPeakListFile(FileData peakListFile)

getIdentificationResultFile

public FileData getIdentificationResultFile()

identificationResultFile origin reference.

Hibernate: many-to-one

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

setIdentificationResultFile

public void setIdentificationResultFile(FileData identificationResultFile)

getSpotXPixel

public Float getSpotXPixel()

X coordinate of gel spot

Returns:

Returns the spotXPixel.

Hibernate: property

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

setSpotXPixel

public void setSpotXPixel(Float spotXPixel)

Parameters:

spotXPixel - The spotXPixel to set.

getSpotYPixel

public Float getSpotYPixel()

Y coordinate of gel spot

Returns:

Returns the spotYPixel.

Hibernate: property

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

setSpotYPixel

public void setSpotYPixel(Float spotYPixel)

Parameters:

spotYPixel - The spotYPixel to set.

getCombinedFDR

public Float getCombinedFDR()

Returns:

Returns the combinedFDR.

Hibernate: property

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

setCombinedFDR

public void setCombinedFDR(Float combinedFDR)

Parameters:

combinedFDR - The combinedFDR to set.

getPrimaryCombined

public Boolean getPrimaryCombined()

Returns:

Returns tru if this is the primary entry in a combined search.

Hibernate: property

column="`primaryCombined`" type="boolean" not-null="false"

setPrimaryCombined

public void setPrimaryCombined(Boolean primaryCombined)

Parameters:

primaryCombined - The primaryCombined to set.

getFirstInCombination

public HitData getFirstInCombination()

Returns:

Returns the firstInCombination.

Hibernate: many-to-one

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

setFirstInCombination

public void setFirstInCombination(HitData firstInCombination)

Parameters:

firstInCombination - The firstInCombination to set.

getSpectrumStringId

public String getSpectrumStringId()

Returns:

Returns the spectrumStringId.

Hibernate: property

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

setSpectrumStringId

public void setSpectrumStringId(String spectrumStringId)

Parameters:

spectrumStringId - The spectrumStringId to set.

getRetentionTimeInMinutes

public Float getRetentionTimeInMinutes()

Returns:

Returns the retentionTimeInMinutes.

Hibernate: property

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

setRetentionTimeInMinutes

public void setRetentionTimeInMinutes(Float retentionTimeInMinutes)

Parameters:

retentionTimeInMinutes - The retentionTimeInMinutes to set.

getPrecursorQuantity

public Float getPrecursorQuantity()

Returns:

Returns the precursorQuantity.

Hibernate: property

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

setPrecursorQuantity

public void setPrecursorQuantity(Float precursorQuantity)

Parameters:

precursorQuantity - The precursorQuantity to set.

getFeature

public FeatureData getFeature()

Best matching feature

Hibernate: many-to-one

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

setFeature

public void setFeature(FeatureData feature)