umich.ms.datatypes

Class LCMSData

java.lang.Object

umich.ms.datatypes.LCMSData

All Implemented Interfaces:

Serializable

public class LCMSData
extends Object
implements Serializable

A wrapper uniting a data source and a scan collection.

Author:

Dmitry Avtonomov

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	LCMSData.User This is a PhantomRef for the object, that requests loading of data, so we could track it being garbage collected.

Field Summary

Fields

Modifier and Type	Field and Description
protected static com.google.common.base.FinalizableReferenceQueue	FRQ
protected boolean	isReleasingMemory
protected IScanCollection	scans
protected LCMSDataSource<?>	source

Constructor Summary

Constructors

Constructor and Description
LCMSData(LCMSDataSource<?> source) Will create LCMSData backed up by ScanCollectionDefault with spectra auto-loading turned off.
LCMSData(LCMSDataSource<?> source, IScanCollection scans) You can pass you IScanCollection implementation, but you likely won't want to do that.

Method Summary

Modifier and Type	Method and Description
IScanCollection	getScans()
LCMSDataSource<?>	getSource()
boolean	isLoaded(LCMSDataSubset subset) Checks among the loaded by all users if this particular subset has already been loaded by someone else.
void	load(LCMSDataSubset subset) Will load scan meta-info and spectra for the specified subset.
void	load(LCMSDataSubset subset, Object user) Will load scan meta-info and spectra for the specified subset.
void	releaseMemory() Releases all memory by calling LCMSDataSource.releaseMemory() and IScanCollection.reset().
void	unload(LCMSDataSubset subset) Unloads spectra matched by this subset.
void	unload(LCMSDataSubset subset, Object user, Set<LCMSDataSubset> exclude) Unloads spectra matched by this subset.

Methods inherited from class java.lang.Object

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

Field Detail

FRQ

protected static final transient com.google.common.base.FinalizableReferenceQueue FRQ

source

protected LCMSDataSource<?> source

scans

protected IScanCollection scans

isReleasingMemory

protected volatile boolean isReleasingMemory

Constructor Detail

LCMSData

public LCMSData(LCMSDataSource<?> source)

Will create LCMSData backed up by ScanCollectionDefault with spectra auto-loading turned off.

LCMSData

public LCMSData(LCMSDataSource<?> source,
                IScanCollection scans)

You can pass you IScanCollection implementation, but you likely won't want to do that.

Method Detail

getSource

public LCMSDataSource<?> getSource()

getScans

public IScanCollection getScans()

isLoaded

public boolean isLoaded(LCMSDataSubset subset)

Checks among the loaded by all users if this particular subset has already been loaded by someone else. Note that if for scan collection you've set a StorageStrategy other than StorageStrategy.STRONG, this check won't guarantee anything other than the scan meta info was loaded. Spectra might have been garbage collected. You can remedy this by setting IScanCollection.isAutoloadSpectra(boolean) true, in which case spectra will be automatically loaded, whenever spectrum references are null.

load

public void load(LCMSDataSubset subset)
          throws FileParsingException

Will load scan meta-info and spectra for the specified subset. Will also keep track of loaded subsets. If a subset is loaded, then it is considered to be in use by some component until it doesn't explicitly call unload(umich.ms.datatypes.LCMSDataSubset).

Throws:

FileParsingException

load

public void load(LCMSDataSubset subset,
                 Object user)
          throws FileParsingException

Will load scan meta-info and spectra for the specified subset. Will also keep track of loaded subsets. If a subset is loaded, then it is considered to be in use by some component until it doesn't explicitly call unload(umich.ms.datatypes.LCMSDataSubset).

Parameters:

user - identify yourself somehow, other components might be using this LCMSData as well, so if you don't provide that identifier, there is no way to tell, for example, when unloading a subset if it's in use by you or someone else. So some other component, might call unload() and without the identifier your spectra will be lost.

Throws:

FileParsingException

unload

public void unload(LCMSDataSubset subset)

Unloads spectra matched by this subset.

unload

public void unload(LCMSDataSubset subset,
                   Object user,
                   Set<LCMSDataSubset> exclude)

Unloads spectra matched by this subset.

Parameters:

subset - to be unloaded

user - the user, that has had this subset loaded. If other users have parts of this subset loaded, those parts won't be unloaded.

exclude - can be null. If specified, data from these subsets won't be excluded.

releaseMemory

public void releaseMemory()

Releases all memory by calling LCMSDataSource.releaseMemory() and IScanCollection.reset(). Effectively, you get this object to the same state as it was after calling the constructor, however any ScanCollection configurations are preserved (e.g. spectra auto-loading) setting. IMPORTANT: will clear the registry of loaded subsets without warning! It's up to you to make sure you don't call this method while some component is still using the data.