| Modifier and Type | Method and Description |
|---|---|
boolean |
LCMSDataSubset.isInSubset(IScan scan)
In some cases we don't have the lower/upper mz window (for MS1 this
requires either this data to be in scan meta info, or the
spectrumRef to be parsed).
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractScan
The most general representation of a Scan.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ScanDefault
All the constructors produce Scans that have
StorageStrategy set to
StorageStrategy.STRONG, it's up to the client to reset this to anything else. |
| Modifier and Type | Field and Description |
|---|---|
protected TreeMap<Integer,IScan> |
ScanIndex.num2scan |
protected TreeMap<Double,List<IScan>> |
ScanIndex.rt2scan |
| Modifier and Type | Method and Description |
|---|---|
IScan |
ScanIndexRoot.add(IScan scan) |
IScan |
ScanIndex.add(IScan scan)
Adds a scan to the index.
|
IScan |
IScanCollection.addScan(IScan scan)
Adds a new scan to this collection, maintains all the proper inside mappings.
|
IScan |
IScanCollection.createScanStub(int num)
Creates a scan stub, using the right
StorageStrategy. |
IScan |
IScanCollection.getNextScan(int scanNum)
Gets the next scan in the collection (by number).
|
IScan |
IScanCollection.getNextScanAtMsLevel(int scanNum,
int msLevel)
Finds the next scan at the same MS level, as the scan with scanNum.
|
IScan |
IScanCollection.getNextScanAtSameMsLevel(IScan scan)
Convenience method, calls
IScanCollection.getNextScanAtMsLevel(int, int) internally |
IScan |
IScanCollection.getPrevScan(int scanNum)
Gets the previous scan in the collection (by number).
|
IScan |
IScanCollection.getPrevScanAtMsLevel(int scanNum,
int msLevel)
Finds the next scan at the same MS level, as the scan with scanNum.
|
IScan |
IScanCollection.getPrevScanAtSameMsLevel(IScan scan)
Convenience method, calls
IScanCollection.getPrevScanAtMsLevel(int, int) internally |
IScan |
IScanCollection.getScanByNum(int scanNum)
The name says it all.
|
IScan |
IScanCollection.getScanByNumClosest(int scanNum)
Scan with the closest Number is returned.
|
IScan |
IScanCollection.getScanByNumLower(int scanNum)
Scan with closest Number less or equal to the provided one is returned.
|
IScan |
IScanCollection.getScanByNumUpper(int scanNum)
Scan with the closest Number greater or equal to the provided one is returned.
|
| Modifier and Type | Method and Description |
|---|---|
TreeMap<Integer,IntervalST<Double,TreeMap<Integer,IScan>>> |
IScanCollection.getMapMsLevel2rangeGroups()
Get a map, holding spectra groupped by precursor m/z isolation window.
MS1 spectra are groupped by their overall m/z range. |
TreeMap<Integer,IScan> |
IScanCollection.getMapNum2scan()
Get a map which links actual scan numbers to instances of Scan objects
|
TreeMap<Double,List<IScan>> |
IScanCollection.getMapRt2scan()
Maps retention time (in minutes) to lists of Scan objects.
|
TreeMap<Integer,IScan> |
ScanIndex.getNum2scan() |
TreeMap<Double,List<IScan>> |
ScanIndex.getRt2scan() |
TreeMap<Integer,NavigableMap<Integer,IScan>> |
IScanCollection.getScansByNumSpan(int numStart,
int numEnd) |
NavigableMap<Integer,IScan> |
IScanCollection.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> |
IScanCollection.getScansByRt(double rt)
Provided RT MUST be EXACT RT, existing in the map.
|
List<IScan> |
IScanCollection.getScansByRtClosest(double rt)
Scans with the closest RT are returned.
|
List<IScan> |
IScanCollection.getScansByRtLower(double rt)
Scan List with closest RT less or equal to the provided one are returned.
|
TreeMap<Integer,NavigableMap<Integer,IScan>> |
IScanCollection.getScansByRtSpan(double rtStart,
double rtEnd)
Returns a range of scans, whose RT is in the inclusive interval [rtStart; rtEnd].
|
NavigableMap<Integer,IScan> |
IScanCollection.getScansByRtSpanAtMsLevel(double rtStart,
double rtEnd,
int msLevel)
Same as
IScanCollection.getScansByRtSpan(double, double), but only searches at one MS Level |
List<IScan> |
IScanCollection.getScansByRtUpper(double rt)
Scan List with the closest RT greater or equal to the provided one are returned.
|
| Modifier and Type | Method and Description |
|---|---|
IScan |
ScanIndexRoot.add(IScan scan) |
IScan |
ScanIndex.add(IScan scan)
Adds a scan to the index.
|
IScan |
IScanCollection.addScan(IScan scan)
Adds a new scan to this collection, maintains all the proper inside mappings.
|
IScan |
IScanCollection.getNextScanAtSameMsLevel(IScan scan)
Convenience method, calls
IScanCollection.getNextScanAtMsLevel(int, int) internally |
IScan |
IScanCollection.getPrevScanAtSameMsLevel(IScan scan)
Convenience method, calls
IScanCollection.getPrevScanAtMsLevel(int, int) internally |
| Modifier and Type | Field and Description |
|---|---|
TreeMap<Integer,IntervalST<Double,TreeMap<Integer,IScan>>> |
ScanCollectionDefault.msLevel2rangeGroups |
| Modifier and Type | Method and Description |
|---|---|
IScan |
ScanCollectionDefault.addScan(IScan scan)
Adds a new scan to this collection, maintains all the proper inside mappings.
|
IScan |
ScanCollectionDefault.createScanStub(int num) |
IScan |
ScanCollectionDefault.getNextScan(int scanNum) |
IScan |
ScanCollectionDefault.getNextScanAtMsLevel(int scanNum,
int msLevel)
Finds the next scan at the same MS level, as the scan with scanNum.
|
IScan |
ScanCollectionDefault.getNextScanAtSameMsLevel(IScan scan)
Convenience method, calls
ScanCollectionDefault.getNextScanAtMsLevel(int, int) internally |
IScan |
ScanCollectionDefault.getPrevScan(int scanNum) |
IScan |
ScanCollectionDefault.getPrevScanAtMsLevel(int scanNum,
int msLevel)
Finds the next scan at the same MS level, as the scan with scanNum.
|
IScan |
ScanCollectionDefault.getPrevScanAtSameMsLevel(IScan scan)
Convenience method, calls
ScanCollectionDefault.getPrevScanAtMsLevel(int, int) internally |
IScan |
ScanCollectionDefault.getScanByNum(int scanNum)
The name says it all.
|
IScan |
ScanCollectionDefault.getScanByNumClosest(int scanNum)
Scan with the closest Number is returned.
|
IScan |
ScanCollectionDefault.getScanByNumLower(int scanNum)
Scan with closest Number STRICTLY less than the provided one is returned.
|
IScan |
ScanCollectionDefault.getScanByNumUpper(int scanNum)
Scan with the closest Number greater or equal to the provided one is returned.
|
| Modifier and Type | Method and Description |
|---|---|
TreeMap<Integer,IntervalST<Double,TreeMap<Integer,IScan>>> |
ScanCollectionDefault.getMapMsLevel2rangeGroups()
Get a map, holding spectra groupped by precursor m/z isolation window.
MS1 spectra are groupped by their overall m/z range. |
TreeMap<Integer,IScan> |
ScanCollectionDefault.getMapNum2scan()
Get a map which links actual scan numbers to instances of Scan objects.
|
TreeMap<Double,List<IScan>> |
ScanCollectionDefault.getMapRt2scan()
Maps retention time (in minutes) to lists of Scan objects.
|
TreeMap<Integer,IScan> |
ScanCollectionDefault.getNum2scan()
Deprecated.
This is just a side effect of encapsulating the old Maps into
the new ScanIndex. Use
ScanCollectionDefault.getMapNum2scan() instead. |
TreeMap<Double,List<IScan>> |
ScanCollectionDefault.getRt2scan()
Deprecated.
This is just a side effect of encapsulating the old Maps into
the new ScanIndex. Use
ScanCollectionDefault.getMapRt2scan() instead. |
TreeMap<Integer,NavigableMap<Integer,IScan>> |
ScanCollectionDefault.getScansByNumSpan(int numStart,
int numEnd) |
NavigableMap<Integer,IScan> |
ScanCollectionDefault.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> |
ScanCollectionDefault.getScansByRt(double rt)
Provided RT MUST be EXACT RT, existing in the map.
|
List<IScan> |
ScanCollectionDefault.getScansByRtClosest(double rt)
Scans with the closest RT are returned.
|
List<IScan> |
ScanCollectionDefault.getScansByRtLower(double rt)
Scan List with closest RT less or equal to the provided one are returned.
|
TreeMap<Integer,NavigableMap<Integer,IScan>> |
ScanCollectionDefault.getScansByRtSpan(double rtStart,
double rtEnd)
Returns a range of scans, whose RT is in the inclusive interval [rtStart; rtEnd].
|
NavigableMap<Integer,IScan> |
ScanCollectionDefault.getScansByRtSpanAtMsLevel(double rtStart,
double rtEnd,
int msLevel)
Same as
ScanCollectionDefault.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! |
List<IScan> |
ScanCollectionDefault.getScansByRtUpper(double rt)
Scan List with the closest RT greater or equal to the provided one are returned.
|
| Modifier and Type | Method and Description |
|---|---|
IScan |
ScanCollectionDefault.addScan(IScan scan)
Adds a new scan to this collection, maintains all the proper inside mappings.
|
IScan |
ScanCollectionDefault.getNextScanAtSameMsLevel(IScan scan)
Convenience method, calls
ScanCollectionDefault.getNextScanAtMsLevel(int, int) internally |
IScan |
ScanCollectionDefault.getPrevScanAtSameMsLevel(IScan scan)
Convenience method, calls
ScanCollectionDefault.getPrevScanAtMsLevel(int, int) internally |
| Modifier and Type | Method and Description |
|---|---|
IScan |
SequentialScanReader.next(LCMSDataSubset subset,
boolean removeNonMatching)
Gets the next scan.
|
IScan |
LCMSDataSource.parseScan(int num,
boolean parseSpectrum)
Parse a single scan from file on disk by it's number.
Assuming every LCMS file interface must be able to do that. The storage strategy should always be StorageStrategy.STRONG,
the receiver then can set it to whatever it needs. |
| Modifier and Type | Method and Description |
|---|---|
List<IScan> |
LCMSDataSource.parse(LCMSDataSubset subset)
Parse a range of scan numbers.
|
List<IScan> |
LCMSDataSource.parse(List<Integer> scanNums)
The storage strategy should always be
StorageStrategy.STRONG,
the receiver then can set it to whatever it needs. |
| Modifier and Type | Field and Description |
|---|---|
protected ArrayList<IScan> |
MZMLMultiSpectraParser.parsedScans |
| Modifier and Type | Method and Description |
|---|---|
List<IScan> |
MZMLMultiSpectraParser.call() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
MZMLMultiSpectraParser.doesNeedSpectrumParsing(IScan scan) |
| Modifier and Type | Field and Description |
|---|---|
protected ArrayList<IScan> |
MZXMLMultiSpectraParser.parsedScans |
| Modifier and Type | Method and Description |
|---|---|
List<IScan> |
MZXMLMultiSpectraParser.call() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
MZXMLMultiSpectraParser.doesNeedSpectrumParsing(IScan scan) |
| Modifier and Type | Method and Description |
|---|---|
IScan |
ThermoRawFile.parseScan(int num,
boolean parseSpectrum) |
| Modifier and Type | Method and Description |
|---|---|
List<IScan> |
ThermoRawFile.parse(LCMSDataSubset subset) |
List<IScan> |
ThermoRawFile.parse(List<Integer> scanNums) |
| Modifier and Type | Method and Description |
|---|---|
IScan |
AbstractXMLBasedDataSource.parseScan(int num,
boolean parseSpectrum) |
| Modifier and Type | Method and Description |
|---|---|
List<IScan> |
AbstractXMLBasedDataSource.parse(LCMSDataSubset subset) |
List<IScan> |
AbstractXMLBasedDataSource.parse(List<Integer> scanNums)
Deprecated.
this method has not been updated to the new parsing version
|
protected ArrayList<Future<List<IScan>>> |
AbstractXMLBasedDataSource.submitParseTasks(LCMSDataSubset subset,
LCMSRunInfo info,
int numWorkers,
ExecutorService exec,
byte[] readBuf1,
ArrayList<OffsetLength> readTasks,
int[] workerScanCounts,
boolean areScansContinuous) |
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