| Modifier and Type | Field and Description |
|---|---|
static LCMSDataSubset |
LCMSDataSubset.MS1_WITH_SPECTRA
Sets up the parsing parameters to parse all scans, but spectra only for MS1 scans.
|
static LCMSDataSubset |
LCMSDataSubset.MS2_WITH_SPECTRA
Sets up the parsing parameters to parse all scans, but spectra only for MS2 scans.
|
static LCMSDataSubset |
LCMSDataSubset.STRUCTURE_ONLY
Sets up the parsing parameters to parse only scans for the whole run, no spectra.
|
static LCMSDataSubset |
LCMSDataSubset.WHOLE_RUN
Sets up the parsing parameters to parse all the scans and spectra in a run.
|
| Modifier and Type | Method and Description |
|---|---|
LCMSDataSubset |
LCMSDataSubset.merge(LCMSDataSubset other)
Doesn't modify original values, always returns a new one.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
LCMSDataSubset.contains(LCMSDataSubset other)
Checks if data ranges described by this subset fully contain ranges
specified in another set.
|
boolean |
LCMSData.isLoaded(LCMSDataSubset subset)
Checks among the loaded by all users if this particular subset has already
been loaded by someone else.
|
void |
LCMSData.load(LCMSDataSubset subset)
Will load scan meta-info and spectra for the specified subset.
|
void |
LCMSData.load(LCMSDataSubset subset,
Object user)
Will load scan meta-info and spectra for the specified subset.
|
LCMSDataSubset |
LCMSDataSubset.merge(LCMSDataSubset other)
Doesn't modify original values, always returns a new one.
|
void |
LCMSData.unload(LCMSDataSubset subset)
Unloads spectra matched by this subset.
|
void |
LCMSData.unload(LCMSDataSubset subset,
Object user,
Set<LCMSDataSubset> exclude)
Unloads spectra matched by this subset.
|
| Modifier and Type | Method and Description |
|---|---|
void |
LCMSData.unload(LCMSDataSubset subset,
Object user,
Set<LCMSDataSubset> exclude)
Unloads spectra matched by this subset.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IScanCollection.loadData(LCMSDataSubset subset)
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Loads spectra for a subset of scans, or all of them, depending on the configuration.
|
void |
IScanCollection.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 |
IScanCollection.setStorageStrategy(LCMSDataSubset subset,
StorageStrategy storageStrategy) |
void |
IScanCollection.setStorageStrategy(LCMSDataSubset subset,
StorageStrategy strategyInSet,
StorageStrategy strategyNotInSet) |
void |
IScanCollection.unloadData(LCMSDataSubset subset)
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Unloads SPECTRA from the underlying ScanCollection.
|
void |
IScanCollection.unloadData(LCMSDataSubset subset,
Set<LCMSDataSubset> exlude)
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Unloads SPECTRA from the underlying ScanCollection.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IScanCollection.unloadData(LCMSDataSubset subset,
Set<LCMSDataSubset> exlude)
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Unloads SPECTRA from the underlying ScanCollection.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ScanCollectionDefault.loadData(LCMSDataSubset subset) |
void |
ScanCollectionDefault.loadData(LCMSDataSubset subset,
StorageStrategy storageStrategy) |
void |
ScanCollectionDefault.setStorageStrategy(LCMSDataSubset subset,
StorageStrategy storageStrategy) |
void |
ScanCollectionDefault.setStorageStrategy(LCMSDataSubset subset,
StorageStrategy strategyInSet,
StorageStrategy strategyNotInSet) |
void |
ScanCollectionDefault.unloadData(LCMSDataSubset subset) |
void |
ScanCollectionDefault.unloadData(LCMSDataSubset subset,
Set<LCMSDataSubset> exlude) |
| Modifier and Type | Method and Description |
|---|---|
void |
ScanCollectionDefault.unloadData(LCMSDataSubset subset,
Set<LCMSDataSubset> exlude) |
| Modifier and Type | Method and Description |
|---|---|
IScan |
SequentialScanReader.next(LCMSDataSubset subset,
boolean removeNonMatching)
Gets the next scan.
|
List<IScan> |
LCMSDataSource.parse(LCMSDataSubset subset)
Parse a range of scan numbers.
|
| Modifier and Type | Method and Description |
|---|---|
MZMLMultiSpectraParser |
MZMLFile.getSpectraParser(InputStream inputStream,
LCMSDataSubset subset,
org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool,
Integer numSpectra) |
| Constructor and Description |
|---|
MZMLMultiSpectraParser(InputStream is,
LCMSDataSubset subset,
MZMLFile source) |
| Modifier and Type | Method and Description |
|---|---|
MZXMLMultiSpectraParser |
MZXMLFile.getSpectraParser(InputStream inputStream,
LCMSDataSubset subset,
org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool,
Integer numSpectra) |
| Modifier and Type | Method and Description |
|---|---|
List<IScan> |
ThermoRawFile.parse(LCMSDataSubset subset) |
| Modifier and Type | Field and Description |
|---|---|
protected LCMSDataSubset |
MultiSpectraParser.subset |
| Modifier and Type | Method and Description |
|---|---|
abstract MultiSpectraParser |
AbstractXMLBasedDataSource.getSpectraParser(InputStream inputStream,
LCMSDataSubset subset,
org.apache.commons.pool2.ObjectPool<javolution.xml.internal.stream.XMLStreamReaderImpl> readerPool,
Integer numSpectra)
File type specific parser.
|
List<IScan> |
AbstractXMLBasedDataSource.parse(LCMSDataSubset subset) |
protected ArrayList<Future<List<IScan>>> |
AbstractXMLBasedDataSource.submitParseTasks(LCMSDataSubset subset,
LCMSRunInfo info,
int numWorkers,
ExecutorService exec,
byte[] readBuf1,
ArrayList<OffsetLength> readTasks,
int[] workerScanCounts,
boolean areScansContinuous) |
| Constructor and Description |
|---|
MultiSpectraParser(InputStream is,
LCMSDataSubset subset) |
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