| 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.
|
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.
|
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. |
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.
|
| 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 | Method and Description |
|---|---|
List<IScan> |
MZXMLMultiSpectraParser.call() |
| 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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