umich.ms.datatypes.scancollection.impl

Class ScanCollectionDefault

java.lang.Object

umich.ms.datatypes.scancollection.impl.ScanCollectionDefault

All Implemented Interfaces:

Serializable, IScanCollection

public class ScanCollectionDefault
extends Object
implements IScanCollection

The default implementation of IScanCollection.

Author:

Dmitry Avtonomov

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected StorageStrategy	defaultStorageStrategy
protected ScanIndexRoot	index
protected boolean	isAutoloadSpectra
TreeMap<Integer,IntervalST<Double,TreeMap<Integer,IScan>>>	msLevel2rangeGroups
LCMSRunInfo	runInfo
protected LCMSDataSource<?>	source

Fields inherited from interface umich.ms.datatypes.scancollection.IScanCollection

DEFAULT_STORAGE_STRATEGY, MIN_GROUP_OVERLAP

Constructor Summary

Constructors

Constructor and Description
ScanCollectionDefault()
ScanCollectionDefault(boolean isAutoloadSpectra) With this constructor you can pre-configure the scan collection to automatically load spectra if they were not parsed in the first place.

Method Summary

Modifier and Type	Method and Description
IScan	addScan(IScan scan) Adds a new scan to this collection, maintains all the proper inside mappings.
IScan	createScanStub(int num) Creates a scan stub, using the right StorageStrategy.
LCMSDataSource<?>	getDataSource()
StorageStrategy	getDefaultStorageStrategy()
TreeMap<Integer,ScanIndex>	getMapMsLevel2index() Get a map which links MS Levels (starting from 1) to maps of (scanNum => scanObject).
TreeMap<Integer,IntervalST<Double,TreeMap<Integer,IScan>>>	getMapMsLevel2rangeGroups() Get a map, holding spectra groupped by precursor m/z isolation window.
TreeMap<Integer,IScan>	getMapNum2scan() Get a map which links actual scan numbers to instances of Scan objects.
TreeMap<Double,List<IScan>>	getMapRt2scan() Maps retention time (in minutes) to lists of Scan objects.
IScan	getNextScan(int scanNum) Gets the next scan in the collection (by number).
IScan	getNextScanAtMsLevel(int scanNum, int msLevel) Finds the next scan at the same MS level, as the scan with scanNum.
IScan	getNextScanAtSameMsLevel(IScan scan) Convenience method, calls getNextScanAtMsLevel(int, int) internally
TreeMap<Integer,IScan>	getNum2scan() Deprecated. This is just a side effect of encapsulating the old Maps into the new ScanIndex. Use getMapNum2scan() instead.
IScan	getPrevScan(int scanNum) Gets the previous scan in the collection (by number).
IScan	getPrevScanAtMsLevel(int scanNum, int msLevel) Finds the next scan at the same MS level, as the scan with scanNum.
IScan	getPrevScanAtSameMsLevel(IScan scan) Convenience method, calls getPrevScanAtMsLevel(int, int) internally
TreeMap<Double,List<IScan>>	getRt2scan() Deprecated. This is just a side effect of encapsulating the old Maps into the new ScanIndex. Use getMapRt2scan() instead.
Double	getRtMax() RT of the last scan in this scan collection.
Double	getRtMin() RT of the first scan.
LCMSRunInfo	getRunInfo()
IScan	getScanByNum(int scanNum) The name says it all.
IScan	getScanByNumClosest(int scanNum) Scan with the closest Number is returned.
IScan	getScanByNumLower(int scanNum) Scan with closest Number STRICTLY less than the provided one is returned.
IScan	getScanByNumUpper(int scanNum) Scan with the closest Number greater or equal to the provided one is returned.
int	getScanCount() Get the total number of scans in this ScansCollection.
Integer	getScanCountAtMsLevel(int msLevel) If the msLevel doesn't exist in this ScanCollectionDefault, returns null
TreeMap<Integer,NavigableMap<Integer,IScan>>	getScansByNumSpan(int numStart, int numEnd)
NavigableMap<Integer,IScan>	getScansByNumSpanAtMsLevel(int numStart, int numEnd, int msLevel) A view(not a copy!) of the original scan map, containing only scans from numStart to numEnd (inclusive).
List<IScan>	getScansByRt(double rt) Provided RT MUST be EXACT RT, existing in the map.
List<IScan>	getScansByRtClosest(double rt) Scans with the closest RT are returned.
List<IScan>	getScansByRtLower(double rt) Scan List with closest RT less or equal to the provided one are returned.
TreeMap<Integer,NavigableMap<Integer,IScan>>	getScansByRtSpan(double rtStart, double rtEnd) Returns a range of scans, whose RT is in the inclusive interval [rtStart; rtEnd].
NavigableMap<Integer,IScan>	getScansByRtSpanAtMsLevel(double rtStart, double rtEnd, int msLevel) Same as getScansByRtSpan(double, double), but only searches at one MS Level.
List<IScan>	getScansByRtUpper(double rt) Scan List with the closest RT greater or equal to the provided one are returned.
boolean	isAutoloadSpectra() Decides if spectra should be automatically loaded, when a spectrumRef is requested from a Scan, but there is no spectrumRef present.
void	isAutoloadSpectra(boolean newVal) Sets the new configuration for spectra autoloading.
boolean	isEmpty() Tells if the collection has at least one scan in it.
void	loadData(LCMSDataSubset subset) IMPLEMENTATIONS MUST BE SYNCHRONIZED Loads spectra for a subset of scans, or all of them, depending on the configuration.
void	loadData(LCMSDataSubset subset, StorageStrategy storageStrategy) IMPLEMENTATIONS MUST BE SYNCHRONIZED Loads spectra for a subset of scans, or all of them, depending on the configuration.
void	reset() Bring the collection back to initial empty state.
void	setDataSource(LCMSDataSource<?> source) Set the data source from which the collection will be filled.
void	setDefaultStorageStrategy(StorageStrategy storageStrategy)
void	setRunInfo(LCMSRunInfo runInfo)
void	setStorageStrategy(LCMSDataSubset subset, StorageStrategy storageStrategy)
void	setStorageStrategy(LCMSDataSubset subset, StorageStrategy strategyInSet, StorageStrategy strategyNotInSet)
void	unloadData(LCMSDataSubset subset) IMPLEMENTATIONS MUST BE SYNCHRONIZED Unloads SPECTRA from the underlying ScanCollection.
void	unloadData(LCMSDataSubset subset, Set<LCMSDataSubset> exlude) IMPLEMENTATIONS MUST BE SYNCHRONIZED Unloads SPECTRA from the underlying ScanCollection.

Methods inherited from class java.lang.Object

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

Field Detail

runInfo

public volatile LCMSRunInfo runInfo

msLevel2rangeGroups

public TreeMap<Integer,IntervalST<Double,TreeMap<Integer,IScan>>> msLevel2rangeGroups

index

protected volatile ScanIndexRoot index

defaultStorageStrategy

protected StorageStrategy defaultStorageStrategy

isAutoloadSpectra

protected boolean isAutoloadSpectra

source

protected LCMSDataSource<?> source

Constructor Detail

ScanCollectionDefault

public ScanCollectionDefault()

ScanCollectionDefault

public ScanCollectionDefault(boolean isAutoloadSpectra)

With this constructor you can pre-configure the scan collection to automatically load spectra if they were not parsed in the first place. Using this feature, you can parse only the structure of the file, and then safely access spectra from any scans. If the spectrum is not there (i.e. the reference to ISpectrum in an IScan returns null), then the spectrum should be automatically parsed from the file. This will be very slow, if you do it this was to access all MS1 spectra in a large run, for example.

Method Detail

isEmpty

public boolean isEmpty()

Description copied from interface: IScanCollection

Tells if the collection has at least one scan in it.

Specified by:

isEmpty in interface IScanCollection

getDefaultStorageStrategy

public StorageStrategy getDefaultStorageStrategy()

Specified by:

getDefaultStorageStrategy in interface IScanCollection

setDefaultStorageStrategy

public void setDefaultStorageStrategy(StorageStrategy storageStrategy)

Specified by:

setDefaultStorageStrategy in interface IScanCollection

isAutoloadSpectra

public boolean isAutoloadSpectra()

Description copied from interface: IScanCollection

Decides if spectra should be automatically loaded, when a spectrumRef is requested from a Scan, but there is no spectrumRef present.

Specified by:

isAutoloadSpectra in interface IScanCollection

isAutoloadSpectra

public void isAutoloadSpectra(boolean newVal)

Description copied from interface: IScanCollection

Sets the new configuration for spectra autoloading.

Specified by:

isAutoloadSpectra in interface IScanCollection

getDataSource

public LCMSDataSource<?> getDataSource()

Specified by:

getDataSource in interface IScanCollection

setDataSource

public void setDataSource(LCMSDataSource<?> source)

Description copied from interface: IScanCollection

Set the data source from which the collection will be filled.

Specified by:

setDataSource in interface IScanCollection

addScan

public IScan addScan(IScan scan)

Adds a new scan to this collection, maintains all the proper inside mappings. If a scan with the same scan number is already in the map it will be replaced and the old entry will be returned. If no replacement took place - null is returned.

Specified by:

addScan in interface IScanCollection

Parameters:

scan - scan to be added

Returns:

null if the scan was just added, or the old Scan, if it was replaced

getMapMsLevel2rangeGroups

public TreeMap<Integer,IntervalST<Double,TreeMap<Integer,IScan>>> getMapMsLevel2rangeGroups()

Get a map, holding spectra groupped by precursor m/z isolation window. MS1 spectra are groupped by their overall m/z range.

Specified by:

getMapMsLevel2rangeGroups in interface IScanCollection

Returns:

Interval search tree for every level, this is only created after a call to Object.finalize(). A call to Object.finalize() will be made for you automatically, if you load scans using an LCMSDataSubset with lo/hi scan nums as null.

getMapNum2scan

public TreeMap<Integer,IScan> getMapNum2scan()

Get a map which links actual scan numbers to instances of Scan objects.

Specified by:

getMapNum2scan in interface IScanCollection

Returns:

mapping from internal (1-based) scan numbers to scans

getMapMsLevel2index

public TreeMap<Integer,ScanIndex> getMapMsLevel2index()

Get a map which links MS Levels (starting from 1) to maps of (scanNum => scanObject).

Specified by:

getMapMsLevel2index in interface IScanCollection

Returns:

the mapping

getMapRt2scan

public TreeMap<Double,List<IScan>> getMapRt2scan()

Maps retention time (in minutes) to lists of Scan objects. Generally there will be just one Scan object in the list, but newer instruments, like Thermo Fusion should be able to measure several spectra simultaneously hence the use of List here for future-proofing.

Specified by:

getMapRt2scan in interface IScanCollection

Returns:

the mapping

getRunInfo

public LCMSRunInfo getRunInfo()

Specified by:

getRunInfo in interface IScanCollection

setRunInfo

public void setRunInfo(LCMSRunInfo runInfo)

Specified by:

setRunInfo in interface IScanCollection

getRtMax

public Double getRtMax()

RT of the last scan in this scan collection.

Specified by:

getRtMax in interface IScanCollection

getRtMin

public Double getRtMin()

RT of the first scan. Useful if a scan collection is a subset of the original run, in which case start RT might be e.g. 40min.

Specified by:

getRtMin in interface IScanCollection

getScanByNum

public IScan getScanByNum(int scanNum)

The name says it all.

Specified by:

getScanByNum in interface IScanCollection

Parameters:

scanNum - Scan number as it was in the original MS file

Returns:

Scan or null, if no such scan number exists in this ScanCollection

getScanByNumLower

public IScan getScanByNumLower(int scanNum)

Scan with closest Number STRICTLY less than the provided one is returned.

Specified by:

getScanByNumLower in interface IScanCollection

Parameters:

scanNum - scan number

Returns:

Scan or null, if the ScanCollection didn't have any scans with numbers <= than this one

getScanByNumUpper

public IScan getScanByNumUpper(int scanNum)

Scan with the closest Number greater or equal to the provided one is returned.

Specified by:

getScanByNumUpper in interface IScanCollection

Parameters:

scanNum - scan number

Returns:

Scan or null, if the ScanCollection didn't have any scans with numbers >= than this one

getScanByNumClosest

public IScan getScanByNumClosest(int scanNum)

Scan with the closest Number is returned.

Specified by:

getScanByNumClosest in interface IScanCollection

Parameters:

scanNum - scan number

Returns:

null might be returned in an extreme case when the scan collection is empty.

getScansByRt

public List<IScan> getScansByRt(double rt)

Provided RT MUST be EXACT RT, existing in the map.

Specified by:

getScansByRt in interface IScanCollection

Parameters:

rt - RT in minutes

Returns:

list of Scans or null if no such RT exists

getScansByRtLower

public List<IScan> getScansByRtLower(double rt)

Scan List with closest RT less or equal to the provided one are returned.

Specified by:

getScansByRtLower in interface IScanCollection

getScansByRtUpper

public List<IScan> getScansByRtUpper(double rt)

Scan List with the closest RT greater or equal to the provided one are returned.

Specified by:

getScansByRtUpper in interface IScanCollection

getScansByRtClosest

public List<IScan> getScansByRtClosest(double rt)

Scans with the closest RT are returned.

Specified by:

getScansByRtClosest in interface IScanCollection

Returns:

null if no scans were found at all, but this should only happen if your ScanCollection is empty.

getScansByNumSpanAtMsLevel

public NavigableMap<Integer,IScan> getScansByNumSpanAtMsLevel(int numStart,
                                                              int numEnd,
                                                              int msLevel)

A view(not a copy!) of the original scan map, containing only scans from numStart to numEnd (inclusive). Scan numbers don't need to be exact matches, scans from the closed interval [numStart; numEnd] are returned.

Specified by:

getScansByNumSpanAtMsLevel in interface IScanCollection

Returns:

A view or null if there were no scans at this ms level in [numStart; numEnd] interval

getScansByNumSpan

public TreeMap<Integer,NavigableMap<Integer,IScan>> getScansByNumSpan(int numStart,
                                                                      int numEnd)

Specified by:

getScansByNumSpan in interface IScanCollection

Parameters:

numStart - Starting scan number (inclusive)

numEnd - The last scan number in range (inclusive)

getScansByRtSpanAtMsLevel

public NavigableMap<Integer,IScan> getScansByRtSpanAtMsLevel(double rtStart,
                                                             double rtEnd,
                                                             int msLevel)

Same as getScansByRtSpan(double, double), but only searches at one MS Level. If it so happens, that the RTs are between just 2 consecutive scans, then null is returned. You get a view of the original scan map, not a copy!

Specified by:

getScansByRtSpanAtMsLevel in interface IScanCollection

Parameters:

rtStart - The beginning of RT window

rtEnd - The end of RT window

msLevel - MS Level at which to get scans

Returns:

null, if no scans were in this window.

getScansByRtSpan

public TreeMap<Integer,NavigableMap<Integer,IScan>> getScansByRtSpan(double rtStart,
                                                                     double rtEnd)

Returns a range of scans, whose RT is in the inclusive interval [rtStart; rtEnd]. That means, ceil RT match is used for rtStart and floor RT for rtEnd. If it so happens, that the RTs are between just 2 consecutive scans, then null is returned.

Specified by:

getScansByRtSpan in interface IScanCollection

Parameters:

rtStart - The beginning of RT window

rtEnd - The end of RT window

Returns:

null, if no scans were in this window

getScanCount

public int getScanCount()

Get the total number of scans in this ScansCollection.

Specified by:

getScanCount in interface IScanCollection

Returns:

number of scans

See Also:

getScanCountAtMsLevel(int)

getScanCountAtMsLevel

public Integer getScanCountAtMsLevel(int msLevel)

If the msLevel doesn't exist in this ScanCollectionDefault, returns null

Specified by:

getScanCountAtMsLevel in interface IScanCollection

Returns:

null, if msLevel doesn't exist. Actual number of scans otherwise.

getNextScan

public IScan getNextScan(int scanNum)

Description copied from interface: IScanCollection

Gets the next scan in the collection (by number).

Specified by:

getNextScan in interface IScanCollection

Returns:

null, if the provided scan number is the last number in the collection.

getNextScanAtMsLevel

public IScan getNextScanAtMsLevel(int scanNum,
                                  int msLevel)

Finds the next scan at the same MS level, as the scan with scanNum. If the scan number provided is not in the map, this method will find the next existing one.

Specified by:

getNextScanAtMsLevel in interface IScanCollection

Parameters:

scanNum - Scan number

msLevel - MS Level at which to search for that scan number. That MS level must be present in the collection, otherwise an NPE is thrown.

Returns:

either next Scan, or null, if there are no further scans at this level. If MS level is incorrect, also returns null.

getNextScanAtSameMsLevel

public IScan getNextScanAtSameMsLevel(IScan scan)

Convenience method, calls getNextScanAtMsLevel(int, int) internally

Specified by:

getNextScanAtSameMsLevel in interface IScanCollection

Parameters:

scan - an existing scan from THIS ScanCollection

getPrevScan

public IScan getPrevScan(int scanNum)

Description copied from interface: IScanCollection

Gets the previous scan in the collection (by number).

Specified by:

getPrevScan in interface IScanCollection

Returns:

null, if the provided scan number is the first number in the collection.

getPrevScanAtMsLevel

public IScan getPrevScanAtMsLevel(int scanNum,
                                  int msLevel)

Finds the next scan at the same MS level, as the scan with scanNum. If the scan number provided is not in the map, this method will find the next existing one.

Specified by:

getPrevScanAtMsLevel in interface IScanCollection

Parameters:

scanNum - Scan number

msLevel - MS Level at which to search for that scan number

Returns:

either next Scan, or null, if there are no further scans at this level. If MS level is incorrect, also returns null.

getPrevScanAtSameMsLevel

public IScan getPrevScanAtSameMsLevel(IScan scan)

Convenience method, calls getPrevScanAtMsLevel(int, int) internally

Specified by:

getPrevScanAtSameMsLevel in interface IScanCollection

setStorageStrategy

public void setStorageStrategy(LCMSDataSubset subset,
                               StorageStrategy storageStrategy)

Specified by:

setStorageStrategy in interface IScanCollection

setStorageStrategy

public void setStorageStrategy(LCMSDataSubset subset,
                               StorageStrategy strategyInSet,
                               StorageStrategy strategyNotInSet)

Specified by:

setStorageStrategy in interface IScanCollection

loadData

public void loadData(LCMSDataSubset subset)
              throws FileParsingException

Description copied from interface: IScanCollection

IMPLEMENTATIONS MUST BE SYNCHRONIZED Loads spectra for a subset of scans, or all of them, depending on the configuration. Uses the default storage strategy.

Specified by:

loadData in interface IScanCollection

Parameters:

subset - configuration, for which scans what data should be loaded. Can't be null. Scans in the range of scan numbers should be loaded, but spectra should be loaded only for the scans, specified by MS level and m/z ranges.

Throws:

FileParsingException

loadData

public void loadData(LCMSDataSubset subset,
                     StorageStrategy storageStrategy)
              throws FileParsingException

Description copied from interface: IScanCollection

IMPLEMENTATIONS MUST BE SYNCHRONIZED Loads spectra for a subset of scans, or all of them, depending on the configuration.

Specified by:

loadData in interface IScanCollection

Parameters:

subset - configuration, for which scans what data should be loaded. Can't be null. Scans in the range of scan numbers should be loaded, but spectra should be loaded only for the scans, specified by MS level and m/z ranges.

storageStrategy - spectral storage strategy, can be null, in which case the default storage strategy of the underlying ScanCollection should be used

Throws:

FileParsingException

unloadData

public void unloadData(LCMSDataSubset subset)

Description copied from interface: IScanCollection

IMPLEMENTATIONS MUST BE SYNCHRONIZED Unloads SPECTRA from the underlying ScanCollection. This method should be synchronized.

Specified by:

unloadData in interface IScanCollection

unloadData

public void unloadData(LCMSDataSubset subset,
                       Set<LCMSDataSubset> exlude)

Description copied from interface: IScanCollection

IMPLEMENTATIONS MUST BE SYNCHRONIZED Unloads SPECTRA from the underlying ScanCollection. This method should be synchronized.

Specified by:

unloadData in interface IScanCollection

Parameters:

subset - the subset to be unloaded

exlude - a set of LCMSDataSubsets to be excluded from the unloading operation

createScanStub

public IScan createScanStub(int num)

Description copied from interface: IScanCollection

Creates a scan stub, using the right StorageStrategy.

Specified by:

createScanStub in interface IScanCollection

Parameters:

num - scan number

getNum2scan

@Deprecated
public TreeMap<Integer,IScan> getNum2scan()

Deprecated. This is just a side effect of encapsulating the old Maps into the new ScanIndex. Use getMapNum2scan() instead.

Returns:

the num2scan

getRt2scan

@Deprecated
public TreeMap<Double,List<IScan>> getRt2scan()

Deprecated. This is just a side effect of encapsulating the old Maps into the new ScanIndex. Use getMapRt2scan() instead.

Returns:

the rt2scan

reset

public void reset()

Description copied from interface: IScanCollection

Bring the collection back to initial empty state. Users should be able to add scans to the collection afterwards as if they called the constructor again. The reason for having this method is re-use of the exact scan collection type in LCMSData (BatMass) after a request to release memory.

Specified by:

reset in interface IScanCollection