fr.profi.mzdb.model

Class SpectrumHeader

java.lang.Object

fr.profi.mzdb.util.misc.AbstractInMemoryIdGen

fr.profi.mzdb.db.model.AbstractTableModel

fr.profi.mzdb.model.SpectrumHeader

All Implemented Interfaces:

IParamContainer, ILcContext

public class SpectrumHeader
extends AbstractTableModel
implements ILcContext

The Class SpectrumHeader.

Author:

David Bouyssie

Field Summary

Fields

Modifier and Type	Field and Description
protected float	basePeakIntensity The base peak intensity.
protected double	basePeakMz The base peak mz.
protected int	bbFirstSpectrumId The bounding box first spectrum id.
protected int	cycle The cycle.
protected long	id The id.
protected int	initialId The initial id.
protected boolean	isHighResolution Is high resolution boolean.
protected int	msLevel The ms level.
protected int	peaksCount The peaks count.
protected Precursor	precursor The precursor: contains selected ions list
protected int	precursorCharge The precursor charge.
protected double	precursorMz The precursor mz.
static Comparator<SpectrumHeader>	rtComp The rt comp.
protected ScanList	scanList The spectrum list.
protected float	tic total ion chromatogram of the spectrum
protected float	time The time.

Fields inherited from class fr.profi.mzdb.db.model.AbstractTableModel

paramTree, TABLE_NAME

Constructor Summary

Constructors

Constructor and Description
SpectrumHeader(long id, int initialId, int cycle, float time, int msLevel, int peaksCount, boolean isHighResolution, float tic, double basePeakMz, float basePeakIntensity, double precursorMz, int precursorCharge, int firstBBSpectrumId) Instantiates a new spectrum header.

Method Summary

Modifier and Type	Method and Description
float	getBasePeakIntensity() Gets the base peak intensity.
double	getBasePeakMz() Gets the base peak mz.
int	getBBFirstSpectrumId()
int	getCycle() Gets the cycle.
float	getElutionTime() Gets the elution time.
long	getId() Gets the id.
int	getInitialId() Gets the initial id.
int	getMsLevel() Gets the ms level.
int	getPeaksCount() Gets the peaks count.
Precursor	getPrecursor()
int	getPrecursorCharge() Gets the precursor charge.
double	getPrecursorMz() Gets the precursor mz.
ScanList	getScanList()
long	getSpectrumId() Gets the spectrum id.
float	getTIC()
float	getTime() Gets the time.
boolean	isHighResolution() Checks if is high resolution.
void	loadParamTree(com.almworks.sqlite4java.SQLiteConnection mzDbConnection) Loads the param tree.
static void	loadParamTrees(SpectrumHeader[] spectrumHeaders, com.almworks.sqlite4java.SQLiteConnection mzDbConnection)
void	loadPrecursorList(com.almworks.sqlite4java.SQLiteConnection mzDbConnection)
void	loadScanList(com.almworks.sqlite4java.SQLiteConnection mzDbConnection)
void	setPrecursor(Precursor precursor)
void	setScanList(ScanList scanList)

Methods inherited from class fr.profi.mzdb.db.model.AbstractTableModel

getCVParams, getParamTree, getUserParam, getUserParams, getUserTexts, hasParamTree, setParamTree

Methods inherited from class fr.profi.mzdb.util.misc.AbstractInMemoryIdGen

generateNewId

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

id

protected final long id

The id.

initialId

protected final int initialId

The initial id.

cycle

protected final int cycle

The cycle.

time

protected final float time

The time.

msLevel

protected final int msLevel

The ms level.

peaksCount

protected final int peaksCount

The peaks count.

isHighResolution

protected final boolean isHighResolution

Is high resolution boolean.

tic

protected final float tic

total ion chromatogram of the spectrum

basePeakMz

protected final double basePeakMz

The base peak mz.

basePeakIntensity

protected final float basePeakIntensity

The base peak intensity.

precursorMz

protected final double precursorMz

The precursor mz.

precursorCharge

protected final int precursorCharge

The precursor charge.

bbFirstSpectrumId

protected final int bbFirstSpectrumId

The bounding box first spectrum id.

scanList

protected ScanList scanList

The spectrum list.

precursor

protected Precursor precursor

The precursor: contains selected ions list

rtComp

public static Comparator<SpectrumHeader> rtComp

The rt comp.

Constructor Detail

SpectrumHeader

public SpectrumHeader(long id,
                      int initialId,
                      int cycle,
                      float time,
                      int msLevel,
                      int peaksCount,
                      boolean isHighResolution,
                      float tic,
                      double basePeakMz,
                      float basePeakIntensity,
                      double precursorMz,
                      int precursorCharge,
                      int firstBBSpectrumId)

Instantiates a new spectrum header.

Parameters:

id - the id

initialId - the initial id

cycle - the cycle

time - the time

msLevel - the ms level

peaksCount - the peaks count

dataMode - the data mode

basePeakMz - the base peak mz

basePeakIntensity - the base peak intensity

precursorMz - the precursor mz

precursorCharge - the precursor charge

Method Detail

getId

public long getId()

Gets the id.

Overrides:

getId in class AbstractTableModel

Returns:

the id

getInitialId

public int getInitialId()

Gets the initial id.

Returns:

the initial id

getCycle

public int getCycle()

Gets the cycle.

Returns:

the cycle

getTime

public float getTime()

Gets the time.

Returns:

the time

getMsLevel

public int getMsLevel()

Gets the ms level.

Returns:

the ms level

getPeaksCount

public int getPeaksCount()

Gets the peaks count.

Returns:

the peaks count

isHighResolution

public boolean isHighResolution()

Checks if is high resolution.

Returns:

true, if is high resolution

getBasePeakMz

public double getBasePeakMz()

Gets the base peak mz.

Returns:

the base peak mz

getBasePeakIntensity

public float getBasePeakIntensity()

Gets the base peak intensity.

Returns:

the base peak intensity

getPrecursorMz

public double getPrecursorMz()

Gets the precursor mz.

Returns:

the precursor mz

getPrecursorCharge

public int getPrecursorCharge()

Gets the precursor charge.

Returns:

the precursor charge

getSpectrumId

public long getSpectrumId()

Description copied from interface: ILcContext

Gets the spectrum id.

Specified by:

getSpectrumId in interface ILcContext

Returns:

the spectrum id

getElutionTime

public float getElutionTime()

Description copied from interface: ILcContext

Gets the elution time.

Specified by:

getElutionTime in interface ILcContext

Returns:

the elution time

getBBFirstSpectrumId

public int getBBFirstSpectrumId()

getScanList

public ScanList getScanList()

setScanList

public void setScanList(ScanList scanList)

getPrecursor

public Precursor getPrecursor()

setPrecursor

public void setPrecursor(Precursor precursor)

getTIC

public float getTIC()

loadParamTrees

public static void loadParamTrees(SpectrumHeader[] spectrumHeaders,
                                  com.almworks.sqlite4java.SQLiteConnection mzDbConnection)

loadParamTree

public void loadParamTree(com.almworks.sqlite4java.SQLiteConnection mzDbConnection)
                   throws com.almworks.sqlite4java.SQLiteException

Description copied from class: AbstractTableModel

Loads the param tree.

Overrides:

loadParamTree in class AbstractTableModel

Throws:

com.almworks.sqlite4java.SQLiteException

loadScanList

public void loadScanList(com.almworks.sqlite4java.SQLiteConnection mzDbConnection)
                  throws com.almworks.sqlite4java.SQLiteException

Throws:

com.almworks.sqlite4java.SQLiteException

loadPrecursorList

public void loadPrecursorList(com.almworks.sqlite4java.SQLiteConnection mzDbConnection)
                       throws com.almworks.sqlite4java.SQLiteException

Throws:

com.almworks.sqlite4java.SQLiteException