org.proteios.core.data
Class PeakListData

java.lang.Object
  org.proteios.core.data.BasicData
      org.proteios.core.data.OwnedData
          org.proteios.core.data.SharedData
              org.proteios.core.data.CommonData
                  org.proteios.core.data.AnnotatedData
                      org.proteios.core.data.PeakListData

All Implemented Interfaces:

AnnotatableData, BatchableData, IdentifiableData, NameableData, OwnableData, RemovableData, ShareableData

public class PeakListData
extends AnnotatedData
implements BatchableData

This represents a peaklist which is a starting point of a peak.

Version:

2.0

Author:

Olle

See Also:

PeakList, PeakLists overview

Last modified

$Date: 2006-06-01 14:31:54Z $

Hibernate: class

table="`PeakLists`" lazy="true"

Hibernate: subclass

discriminator-value="1"

Field Summary

static int	MAX_COMBINATIONMETHOD_LENGTH
static int	MAX_DESCRIPTION_LENGTH

Fields inherited from interface org.proteios.core.data.NameableData

MAX_NAME_LENGTH

Constructor Summary

PeakListData()

Method Summary

List<AcquisitionData>	getAcquisitionList() Get the acquisitionList.
Float	getBasePeakIntensity() Get the base peak intensity.
String	getCombinationMethod() Get the combinationMethod
String	getDescription() Get the description
int	getMsLevel() Get the msLevel value
Float	getMzRangeStart() Get the start of the mzRange.
Float	getMzRangeStop() Get the stop of the mzRange.
PeakListSetData	getPeakListSet() Get the PeakListSetData this peakList is created from.
Set<PeakData>	getPeaks() Get the peaks.
List<PrecursorData>	getPrecursorList() Get the precursorList.
int	getSpectrumId() Get the spectrumId value Note: No underscore is used in the database column name, i.e.
InstrumentConfigurationData	getSpectrumInstrument() Get the spectrumInstrument
Float	getTimeInMinutes() Get the time in minutes.
Float	getTotalIntensity() Get the total peak intensity.
boolean	isIntensityDoublePrecision() Get the doublePrecision flag
boolean	isMonoisotopic() Get the monoisotopic flag
boolean	isMzDoublePrecision() Get the doublePrecision flag
void	setAcquisitionList(List<AcquisitionData> acquisitionList) Set the acquisitionList
void	setBasePeakIntensity(Float basePeakIntensity) Set the base peak intensity.
void	setCombinationMethod(String combinationMethod) Set the combinationMethod
void	setDescription(String description) Set the description
void	setIntensityDoublePrecision(boolean doublePrecision) Set the intensityDoublePrecision flag
void	setMonoisotopic(boolean monoisotopic) Set the monoisotopic flag
void	setMsLevel(int msLevel) Set the msLevel
void	setMzDoublePrecision(boolean doublePrecision) Set the mzDoublePrecision flag
void	setMzRangeStart(Float mzRangeStart) Set the start of the mzRange
void	setMzRangeStop(Float mzRangeStop) Set the stop of the mzRange
void	setPeakListSet(PeakListSetData peakListSet) Set the PeakListSetData this peakList is created from.
void	setPeaks(Set<PeakData> peakSet) Set the peaks
void	setPrecursorList(List<PrecursorData> precursorList) Set the precursorList
void	setSpectrumId(int spectrumId) Set the spectrumId
void	setSpectrumInstrument(InstrumentConfigurationData spectrumInstrument) Set the spectrumInstrument
void	setTimeInMinutes(Float timeInMinutes) Set the time in minutes
void	setTotalIntensity(Float totalIntensity) Set the total peak intensity.

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

getAnnotationSet, setAnnotationSet

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

getName, isRemoved, setName, setRemoved

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

getItemKey, getProjectKey, setItemKey, setProjectKey

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

getOwner, setOwner

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

Methods inherited from interface org.proteios.core.data.IdentifiableData

getId, getVersion

Methods inherited from interface org.proteios.core.data.OwnableData

getOwner, setOwner

Field Detail

MAX_COMBINATIONMETHOD_LENGTH

public static final int MAX_COMBINATIONMETHOD_LENGTH

See Also:

Constant Field Values

MAX_DESCRIPTION_LENGTH

public static final int MAX_DESCRIPTION_LENGTH

See Also:

Constant Field Values

Constructor Detail

PeakListData

public PeakListData()

Method Detail

getPeakListSet

public PeakListSetData getPeakListSet()

Get the PeakListSetData this peakList is created from.

Returns:

The PeakListSetData item or null if not known

Hibernate: many-to-one

column="`peakListSetId`" not-null="false" outer-join="false"

setPeakListSet

public void setPeakListSet(PeakListSetData peakListSet)

Set the PeakListSetData this peakList is created from.

Parameters:

peakListSet - The creator peakListSet

getCombinationMethod

public String getCombinationMethod()

Get the combinationMethod

Returns:

the combinationMethod string

Hibernate: property

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

setCombinationMethod

public void setCombinationMethod(String combinationMethod)

Set the combinationMethod

Parameters:

combinationMethod - The combinationMethod string

getDescription

public String getDescription()

Get the description

Specified by:

getDescription in interface NameableData

Overrides:

getDescription in class CommonData

Returns:

the description string

Hibernate: property

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

setDescription

public void setDescription(String description)

Set the description

Specified by:

setDescription in interface NameableData

Overrides:

setDescription in class CommonData

Parameters:

description - The description string

isMzDoublePrecision

public boolean isMzDoublePrecision()

Get the doublePrecision flag

Returns:

the mzDoublePrecision flag

Hibernate: property

column="`mz_double_precision`" type="boolean" not-null="true"

setMzDoublePrecision

public void setMzDoublePrecision(boolean doublePrecision)

Set the mzDoublePrecision flag

Parameters:

doublePrecision - The mzDoublePrecision flag

isIntensityDoublePrecision

public boolean isIntensityDoublePrecision()

Get the doublePrecision flag

Returns:

the mzDoublePrecision flag

Hibernate: property

column="`int_double_precision`" type="boolean" not-null="true"

setIntensityDoublePrecision

public void setIntensityDoublePrecision(boolean doublePrecision)

Set the intensityDoublePrecision flag

Parameters:

doublePrecision - The intensityDoublePrecision flag

isMonoisotopic

public boolean isMonoisotopic()

Get the monoisotopic flag

Returns:

the monoisotopic flag

Hibernate: property

column="`monoisotopic`" type="boolean" not-null="true"

setMonoisotopic

public void setMonoisotopic(boolean monoisotopic)

Set the monoisotopic flag

Parameters:

monoisotopic - The monoisotopic flag

getMsLevel

public int getMsLevel()

Get the msLevel value

Returns:

the msLevel value

Hibernate: property

column="`mslevel`" type="int" not-null="true"

setMsLevel

public void setMsLevel(int msLevel)

Set the msLevel

Parameters:

msLevel - The msLevel value

getTotalIntensity

public Float getTotalIntensity()

Get the total peak intensity.

Returns:

the totalIntensity value

Hibernate: property

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

setTotalIntensity

public void setTotalIntensity(Float totalIntensity)

Set the total peak intensity.

Parameters:

totalIntensity - The total intensity value

getBasePeakIntensity

public Float getBasePeakIntensity()

Get the base peak intensity.

Returns:

the basePeakIntensity value

Hibernate: property

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

setBasePeakIntensity

public void setBasePeakIntensity(Float basePeakIntensity)

Set the base peak intensity.

Parameters:

basePeakIntensity - The base peak intensity value

getMzRangeStart

public Float getMzRangeStart()

Get the start of the mzRange.

Returns:

the mzRangeStart value

Hibernate: property

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

setMzRangeStart

public void setMzRangeStart(Float mzRangeStart)

Set the start of the mzRange

Parameters:

mzRangeStart - The msRangeStart value

getMzRangeStop

public Float getMzRangeStop()

Get the stop of the mzRange.

Returns:

the mzRangeStop value

Hibernate: property

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

setMzRangeStop

public void setMzRangeStop(Float mzRangeStop)

Set the stop of the mzRange

Parameters:

mzRangeStop - The msRangeStop value

getSpectrumId

public int getSpectrumId()

Get the spectrumId value Note: No underscore is used in the database column name, i.e. "spectrumid" instead of "spectrum_id", as the "id" is part of the name, and doesn't indicate a database index.

Returns:

the spectrumId value

Hibernate: property

column="`spectrumid`" type="int" not-null="true"

setSpectrumId

public void setSpectrumId(int spectrumId)

Set the spectrumId

Parameters:

spectrumId - The spectrumId value

getSpectrumInstrument

public InstrumentConfigurationData getSpectrumInstrument()

Get the spectrumInstrument

Returns:

The InstrumentConfigurationData spectrumInstrument

Hibernate: many-to-one

column="`spectrumInstrument_id`" cascade="all" not-null="false" outer-join="false"

setSpectrumInstrument

public void setSpectrumInstrument(InstrumentConfigurationData spectrumInstrument)

Set the spectrumInstrument

Parameters:

spectrumInstrument - The InstrumentConfigurationData spectrumInstrument

getTimeInMinutes

public Float getTimeInMinutes()

Get the time in minutes.

Returns:

the timeInMinutes value

Hibernate: property

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

setTimeInMinutes

public void setTimeInMinutes(Float timeInMinutes)

Set the time in minutes

Parameters:

timeInMinutes - The timeInMinutes value

getAcquisitionList

public List<AcquisitionData> getAcquisitionList()

Get the acquisitionList.

Returns:

The AcquisitionData acquisitionList

See Also:

AcquisitionData.getPeakList()

Hibernate: list

table="`Acquisitions`" cascade="delete" lazy="true"

Hibernate: collection-key

column="`peakListId`"

Hibernate: collection-index

column="`list_index`"

Hibernate: collection-one-to-many

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

setAcquisitionList

public void setAcquisitionList(List<AcquisitionData> acquisitionList)

Set the acquisitionList

Parameters:

acquisitionList - The AcquisitionData acquisitionList

getPrecursorList

public List<PrecursorData> getPrecursorList()

Get the precursorList.

Returns:

The PrecursorData precursorList

See Also:

PrecursorData.getPeakList()

Hibernate: list

table="`Precursors`" cascade="delete" lazy="true"

Hibernate: collection-key

column="`peakListId`"

Hibernate: collection-index

column="`list_index`"

Hibernate: collection-one-to-many

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

setPrecursorList

public void setPrecursorList(List<PrecursorData> precursorList)

Set the precursorList

Parameters:

precursorList - The PrecursorData precursorList

getPeaks

public Set<PeakData> getPeaks()

Get the peaks.

Returns:

The PeakData peakSet

Hibernate: set

table="`Peaks`" cascade="delete" lazy="true" inverse="true"

Hibernate: collection-key

column="`peakListId`"

Hibernate: collection-one-to-many

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

setPeaks

public void setPeaks(Set<PeakData> peakSet)

Set the peaks

Parameters:

peakSet - The PeakData peakSet