public class ThermoRawFile extends AbstractLCMSDataSource<ThermoRawIndex>
| Modifier and Type | Field and Description |
|---|---|
protected ThermoRawIndex |
index |
protected LCMSRunInfo |
runInfo |
protected umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5 |
xRawfile5 |
excludeEmptyScans, parsingTimeout, tasksPerCpuPerBatchBUF_SIZE, path| Constructor and Description |
|---|
ThermoRawFile(String path)
Create a new source with autoload of spectra disabled.
|
| Modifier and Type | Method and Description |
|---|---|
ThermoRawIndex |
fetchIndex()
Returns the index, or parses it from the original file and caches for future reuse.
|
protected umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5 |
fetchXrawfile() |
ThermoRawIndex |
getIndex()
Gets the index without an attempt to parse it.
|
String |
getName()
Some identifier for the source, that can be used as its name.
|
static boolean |
isPlatformSupported()
Just checks if the OS is some flavor of windows.
|
static boolean |
isThermoLibInstalled()
Checks if the MSFileReader Type Library from Thermo is installed as a COM object.
|
static boolean |
isThermoSupportedHere()
Checks if the particular machine the code runs on can read Thermo RAW files.
|
List<IScan> |
parse(LCMSDataSubset subset)
Parse a range of scan numbers.
|
List<IScan> |
parse(List<Integer> scanNums)
The storage strategy should always be
StorageStrategy.STRONG,
the receiver then can set it to whatever it needs. |
ThermoRawIndex |
parseIndex() |
LCMSRunInfo |
parseRunInfo() |
IScan |
parseScan(int num,
boolean parseSpectrum)
Parse a single scan from file on disk by it's number.
|
ISpectrum |
parseSpectrum(int num)
Parse a single spectrumRef from file on disk by it's number.
|
void |
releaseMemory()
The intent is to be able to free the memory, e.g.
|
fetchRunInfo, getNumThreadsForParsing, getParsingTimeout, getRunInfo, getTasksPerCpuPerBatch, isExcludeEmptyScans, setExcludeEmptyScans, setNumThreadsForParsing, setParsingTimeout, setTasksPerCpuPerBatchclose, getBufferedInputStream, getPath, getRandomAccessFileprotected ThermoRawIndex index
protected LCMSRunInfo runInfo
protected volatile umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5 xRawfile5
public ThermoRawFile(String path)
path - public static boolean isPlatformSupported()
public static boolean isThermoLibInstalled()
protected umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5 fetchXrawfile()
public static boolean isThermoSupportedHere()
public String getName()
LCMSDataSourcepublic void releaseMemory()
LCMSDataSourcepublic LCMSRunInfo parseRunInfo() throws FileParsingException
FileParsingExceptionpublic ThermoRawIndex getIndex()
LCMSDataSourceLCMSDataSource.fetchIndex() was called before.public ThermoRawIndex fetchIndex() throws FileParsingException
LCMSDataSourceLCMSDataSource.parseIndex() instead.FileParsingExceptionpublic ThermoRawIndex parseIndex() throws FileParsingException
FileParsingExceptionpublic ISpectrum parseSpectrum(int num) throws FileParsingException
LCMSDataSourcenum - scan numberFileParsingExceptionpublic IScan parseScan(int num, boolean parseSpectrum) throws FileParsingException
LCMSDataSourceStorageStrategy.STRONG,
the receiver then can set it to whatever it needs.num - scan numberparseSpectrum - if false, the spectrumRef should not be parsed. Can provide significant speed and memory
benefits if you only need scan metadataFileParsingExceptionpublic List<IScan> parse(LCMSDataSubset subset) throws FileParsingException
LCMSDataSourceStorageStrategy.STRONG,
the receiver then can set it to whatever it needs.subset - the region of LC/MS data to be parsed as scansFileParsingExceptionpublic List<IScan> parse(List<Integer> scanNums) throws FileParsingException
LCMSDataSourceStorageStrategy.STRONG,
the receiver then can set it to whatever it needs.scanNums - List of scan numbers to be parsed. All scan numbers MUST be present in the file.FileParsingExceptionCopyright © 2017. All rights reserved.