org.proteios.core
Class Hit

java.lang.Object
  org.proteios.core.BasicItem<HitData>
      org.proteios.core.Hit

All Implemented Interfaces:

AccessControlled, Identifiable

public class Hit
extends BasicItem<HitData>

Author:

gregory

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

Method Summary

Integer	getCharge()
Float	getCombinedFDR()
Float	getCoverage()
Float	getDeltaMassInDaltons()
String	getDescription()
Float	getExpectationValue()
Float	getExperimentalMassInDaltons()
String	getExternalId() For proteins this is the accession number.
Feature	getFeature() Best matching feature, source for precursor quantity
Hit	getFirstInCombination()
String	getFractionId()
String	getGelExternalId()
File	getIdentificationResultFile()
String	getLocalSampleId()
Integer	getMatchedPeaks()
Float	getMwInDaltons()
File	getPeakListFile()
Float	getPi()
String	getPlateId()
Float	getPrecursorQuantity()
Boolean	getPrimaryCombined()
ProjectData	getProject()
static ItemQuery<Hit>	getQuery()
static ItemQuery<Hit>	getQuery(Project project)
Float	getRetentionTimeInMinutes()
Float	getRootMeanSquareError()
Float	getScore()
String	getScoreType()
Date	getSearchDate()
Integer	getSpectrumId()
String	getSpectrumStringId()
Integer	getSpotId()
Float	getSpotXPixel() X coordinate of gel spot
Float	getSpotYPixel() Y coordinate of gel spot
List<Hit>	getSubHitsInCombination() This function will return a list of combined hits that have this hit as their primary hit.
Double	getTotalIntensity()
Integer	getTotalPeaks()
Item	getType() Get the type of item represented by the object.
static List<Integer>	getUniqueCharges(Project project, DbControl dc)
static List<String>	getUniqueExternalIds(Project project, DbControl dc)
static List<String>	getUniqueFractionIds(Project project, DbControl dc)
static List<String>	getUniqueGelIds(Project project, DbControl dc)
static List<String>	getUniqueLocalSampleIds(Project project, DbControl dc)
static List<String>	getUniquePeptideSequences(Project project, DbControl dc)
static List<String>	getUniquePlateIds(Project project, DbControl dc)
static List<String>	getUniqueScoreTypes(Project project, DbControl dc)
String	getWellPosition()
Boolean	isMicroPlate()
Boolean	isProtein()
boolean	isUsed() Check if this item is used by some other item.
void	setCharge(Integer charge)
void	setCombinedFDR(Float combinedFDR)
void	setCoverage(Float coverage)
void	setDeltaMassInDaltons(Float arg0)
void	setDescription(String description)
void	setExpectationValue(Float eValue)
void	setExperimentalMassInDaltons(Float experimentalMass)
void	setExternalId(String externalId)
void	setFeature(Feature feature) Best matching feature, source for precursor quantity
void	setFirstInCombination(Hit firstInCombination)
void	setFractionId(String fractionId)
void	setGelExternalId(String gelExternalId)
void	setIdentificationResultFile(File identificationResultFile)
void	setLocalSampleId(String localSampleId)
void	setMatchedPeaks(Integer matchedPeaks)
void	setMicroPlate(Boolean microPlate)
void	setMwInDaltons(Float mw)
void	setPeakListFile(File peakListFile)
void	setPi(Float pi)
void	setPlateId(String plateId)
void	setPrecursorQuantity(Float precursorQuantity)
void	setPrimaryCombined(Boolean primaryCombined)
void	setProject(Project project)
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 arg0)
void	setSpectrumStringId(String spectrumStringId) Set the spectrumStringId for this SearchResult item.
void	setSpotId(Integer spotId)
void	setSpotXPixel(Float spotXPixel) X coordinate of gel spot
void	setSpotYPixel(Float spotYPixel) Y coordinate of gel spot
void	setTotalIntensity(Double totalIntensity)
void	setTotalPeaks(Integer totalPeaks)
void	setWellPosition(String wellPosition)

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

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

Method Detail

getUniqueScoreTypes

public static List<String> getUniqueScoreTypes(Project project,
                                               DbControl dc)

getUniquePlateIds

public static List<String> getUniquePlateIds(Project project,
                                             DbControl dc)

getUniqueGelIds

public static List<String> getUniqueGelIds(Project project,
                                           DbControl dc)

getUniqueLocalSampleIds

public static List<String> getUniqueLocalSampleIds(Project project,
                                                   DbControl dc)

getUniqueFractionIds

public static List<String> getUniqueFractionIds(Project project,
                                                DbControl dc)

getUniquePeptideSequences

public static List<String> getUniquePeptideSequences(Project project,
                                                     DbControl dc)

getUniqueCharges

public static List<Integer> getUniqueCharges(Project project,
                                             DbControl dc)

getUniqueExternalIds

public static List<String> getUniqueExternalIds(Project project,
                                                DbControl dc)

getGelExternalId

public String getGelExternalId()

isMicroPlate

public Boolean isMicroPlate()

setGelExternalId

public void setGelExternalId(String gelExternalId)

setMicroPlate

public void setMicroPlate(Boolean microPlate)

getIdentificationResultFile

public File getIdentificationResultFile()

getPeakListFile

public File getPeakListFile()

setIdentificationResultFile

public void setIdentificationResultFile(File identificationResultFile)

setPeakListFile

public void setPeakListFile(File peakListFile)

getRootMeanSquareError

public Float getRootMeanSquareError()

getTotalIntensity

public Double getTotalIntensity()

setRootMeanSquareError

public void setRootMeanSquareError(Float RMSError)

setTotalIntensity

public void setTotalIntensity(Double totalIntensity)

getPlateId

public String getPlateId()

getWellPosition

public String getWellPosition()

setPlateId

public void setPlateId(String plateId)

setProject

public void setProject(ProjectData project)

setWellPosition

public void setWellPosition(String wellPosition)

getLocalSampleId

public String getLocalSampleId()

setLocalSampleId

public void setLocalSampleId(String localSampleId)

getFractionId

public String getFractionId()

setFractionId

public void setFractionId(String fractionId)

getQuery

public static ItemQuery<Hit> getQuery()

getQuery

public static ItemQuery<Hit> getQuery(Project project)

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<HitData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException

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

getCharge

public Integer getCharge()

getCoverage

public Float getCoverage()

getDescription

public String getDescription()

getExpectationValue

public Float getExpectationValue()

getExperimentalMassInDaltons

public Float getExperimentalMassInDaltons()

getExternalId

public String getExternalId()

For proteins this is the accession number. For peptides this is a comma spearated list of accession numbers.

Returns:

the External id string. Long external ids will be placed in the extraString field instead. If this field is not null it is returned instead of the content of the External ID.

getMatchedPeaks

public Integer getMatchedPeaks()

getMwInDaltons

public Float getMwInDaltons()

getPi

public Float getPi()

getProject

public ProjectData getProject()

getScore

public Float getScore()

getScoreType

public String getScoreType()

getSearchDate

public Date getSearchDate()

getSpotId

public Integer getSpotId()

getTotalPeaks

public Integer getTotalPeaks()

isProtein

public Boolean isProtein()

setCharge

public void setCharge(Integer charge)

setCoverage

public void setCoverage(Float coverage)

setDescription

public void setDescription(String description)

setExpectationValue

public void setExpectationValue(Float eValue)

setExperimentalMassInDaltons

public void setExperimentalMassInDaltons(Float experimentalMass)

setExternalId

public void setExternalId(String externalId)

setMatchedPeaks

public void setMatchedPeaks(Integer matchedPeaks)

setMwInDaltons

public void setMwInDaltons(Float mw)

setPi

public void setPi(Float pi)

setProject

public void setProject(Project project)

setProtein

public void setProtein(Boolean protein)

setScore

public void setScore(Float score)

setScoreType

public void setScoreType(String scoreType)

setSearchDate

public void setSearchDate(Date searchDate)

setSpotId

public void setSpotId(Integer spotId)

setTotalPeaks

public void setTotalPeaks(Integer totalPeaks)

getDeltaMassInDaltons

public Float getDeltaMassInDaltons()

getSpectrumId

public Integer getSpectrumId()

setDeltaMassInDaltons

public void setDeltaMassInDaltons(Float arg0)

setSpectrumId

public void setSpectrumId(Integer arg0)

getSpotXPixel

public Float getSpotXPixel()

X coordinate of gel spot

Returns:

Returns the spotXPixel.

setSpotXPixel

public void setSpotXPixel(Float spotXPixel)

X coordinate of gel spot

Parameters:

spotXPixel - The spotXPixel to set.

getSpotYPixel

public Float getSpotYPixel()

Y coordinate of gel spot

Returns:

Returns the spotYPixel.

Hibernate: property

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

setSpotYPixel

public void setSpotYPixel(Float spotYPixel)

Y coordinate of gel spot

Parameters:

spotYPixel - The spotYPixel to set.

getCombinedFDR

public Float getCombinedFDR()

Returns:

Returns the combinedFDR.

setCombinedFDR

public void setCombinedFDR(Float combinedFDR)

Parameters:

combinedFDR - The combinedFDR to set.

getPrimaryCombined

public Boolean getPrimaryCombined()

Returns:

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

setPrimaryCombined

public void setPrimaryCombined(Boolean primaryCombined)

Parameters:

primaryCombined - The primaryCombined to set.

getFirstInCombination

public Hit getFirstInCombination()

Returns:

Returns the first hit in the combination, for a combined hit.

setFirstInCombination

public void setFirstInCombination(Hit firstInCombination)

Parameters:

firstInCombination - The first hit in the combination to set, for a combined hit.

getSubHitsInCombination

public List<Hit> getSubHitsInCombination()

This function will return a list of combined hits that have this hit as their primary hit.

Returns:

the sub hits in the combination

getSpectrumStringId

public String getSpectrumStringId()

Returns:

Returns the spectrumStringId.

setSpectrumStringId

public void setSpectrumStringId(String spectrumStringId)
                         throws InvalidDataException

Set the spectrumStringId for this SearchResult item. The value may be null but must not be longer than the value specified by the

Parameters:

spectrumStringId - The spectrumStringId to set.

Throws:

InvalidDataException - If the spectrumStringId is longer than MAX_SPECTRUMSTRINGID_LENGTH

getRetentionTimeInMinutes

public Float getRetentionTimeInMinutes()

Returns:

Returns the retentionTimeInMinutes.

setRetentionTimeInMinutes

public void setRetentionTimeInMinutes(Float retentionTimeInMinutes)

Parameters:

retentionTimeInMinutes - The retentionTimeInMinutes to set.

getPrecursorQuantity

public Float getPrecursorQuantity()

Returns:

Returns the precursorQuantity.

setPrecursorQuantity

public void setPrecursorQuantity(Float precursorQuantity)

Parameters:

precursorQuantity - The precursorQuantity to set.

getFeature

public Feature getFeature()

Best matching feature, source for precursor quantity

setFeature

public void setFeature(Feature feature)

Best matching feature, source for precursor quantity