maltcms.datastructures.caches
Class SparseScanLineCache

java.lang.Object
  maltcms.datastructures.caches.SparseScanLineCache

All Implemented Interfaces:

cross.IConfigurable, Serializable, IScanLine

public class SparseScanLineCache
extends Object
implements IScanLine

This class is a dataholder for mass spectra. This class will cache all mass spectra which were read an hold a SoftReference to it. TODO: Change to AScanLineCache

Author:

Mathias Wilhelm(mwilhelm A T TechFak.Uni-Bielefeld.DE)

See Also:

Serialized Form

Method Summary

void	clear()
void	configure(org.apache.commons.configuration.Configuration cfg)
int	getBinsSize() Getter.
boolean	getCacheModulation() Getter.
int	getLastIndex() Getter.
Array	getMassSpectra(int x, int y) Getter for one mass spectra.
Array	getMassSpectra(Point p) This Method is a wrapper for getMassPectra(int, int).
int	getScanLineCount() Getter.
List<Array>	getScanlineMS(int x) Getter.
List<cross.datastructures.tuple.Tuple2D<Array,Array>>	getScanlineSparseMS(int x)
int	getScansPerModulation() Getter.
cross.datastructures.tuple.Tuple2D<Array,Array>	getSparseMassSpectra(int x, int y)
cross.datastructures.tuple.Tuple2D<Array,Array>	getSparseMassSpectra(Point p)
Point	mapIndex(int scanIndex) Map a global scan index to a Point of x,y coordinates.
int	mapPoint(int x, int y) Map two coordinates x,y to a global scan index.
int	mapPoint(Point p) Map a Point to a global scan index.
void	setBinSize(int size) Setter.
void	setCacheModulations(boolean cacheMod) Setter.
void	setLastIndex(int index) Setter.
void	showStat() Will view some statistical information about the cache usage.

Methods inherited from class java.lang.Object

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

Method Detail

configure

public void configure(org.apache.commons.configuration.Configuration cfg)

Specified by:

configure in interface cross.IConfigurable

getBinsSize

public int getBinsSize()

Getter.

Specified by:

getBinsSize in interface IScanLine

Returns:

bin size

getCacheModulation

public boolean getCacheModulation()

Getter.

Specified by:

getCacheModulation in interface IScanLine

Returns:

getLastIndex

public int getLastIndex()

Getter.

Specified by:

getLastIndex in interface IScanLine

Returns:

last index

getMassSpectra

public Array getMassSpectra(int x,
                            int y)

Getter for one mass spectra. If the requested mass spectra is out of bound, then this method will return null.

Specified by:

getMassSpectra in interface IScanLine

Parameters:

x - scanline number

y - mass spectra inside this scanline

Returns:

array representing one mass spectra

getMassSpectra

public Array getMassSpectra(Point p)

This Method is a wrapper for getMassPectra(int, int).

Specified by:

getMassSpectra in interface IScanLine

Parameters:

p - point of requested mass spectra

Returns:

mass spectra

getScanLineCount

public int getScanLineCount()

Getter.

Specified by:

getScanLineCount in interface IScanLine

Returns:

scan line count

getScanlineMS

public List<Array> getScanlineMS(int x)

Getter.

Specified by:

getScanlineMS in interface IScanLine

Parameters:

x - scan line number

Returns:

complete ms list of this scan line

getScansPerModulation

public int getScansPerModulation()

Getter.

Specified by:

getScansPerModulation in interface IScanLine

Returns:

scans per modulation

setBinSize

public void setBinSize(int size)

Setter.

Specified by:

setBinSize in interface IScanLine

Parameters:

size - bin size

setCacheModulations

public void setCacheModulations(boolean cacheMod)

Setter. Default value is true.

Specified by:

setCacheModulations in interface IScanLine

Parameters:

cacheMod - true if all modulations should be cached

setLastIndex

public void setLastIndex(int index)

Setter.

Specified by:

setLastIndex in interface IScanLine

Parameters:

index - last index

showStat

public void showStat()

Will view some statistical information about the cache usage.

Specified by:

showStat in interface IScanLine

getScanlineSparseMS

public List<cross.datastructures.tuple.Tuple2D<Array,Array>> getScanlineSparseMS(int x)

Specified by:

getScanlineSparseMS in interface IScanLine

getSparseMassSpectra

public cross.datastructures.tuple.Tuple2D<Array,Array> getSparseMassSpectra(int x,
                                                                            int y)

Specified by:

getSparseMassSpectra in interface IScanLine

getSparseMassSpectra

public cross.datastructures.tuple.Tuple2D<Array,Array> getSparseMassSpectra(Point p)

Specified by:

getSparseMassSpectra in interface IScanLine

mapIndex

public Point mapIndex(int scanIndex)

Description copied from interface: IScanLine

Map a global scan index to a Point of x,y coordinates.

Specified by:

mapIndex in interface IScanLine

Returns:

mapPoint

public int mapPoint(int x,
                    int y)

Description copied from interface: IScanLine

Map two coordinates x,y to a global scan index.

Specified by:

mapPoint in interface IScanLine

Returns:

mapPoint

public int mapPoint(Point p)

Description copied from interface: IScanLine

Map a Point to a global scan index.

Specified by:

mapPoint in interface IScanLine

Returns:

clear

public void clear()

Specified by:

clear in interface IScanLine