public class ThermoRawFile extends AbstractLCMSDataSource<ThermoRawIndex>
| Modifier and Type | Field and Description |
|---|---|
protected ThermoRawIndex |
index |
protected LCMSRunInfo |
runInfo |
protected 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.
If you don't want the index to be cached, you can call LCMSDataSource.parseIndex() instead. |
protected 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.
We're using the latest IXrawfile5 interface, so if the machine has an older version of the library, which does not provide IXrawfile5, this method returns false. |
static boolean |
isThermoSupportedHere()
Checks if the particular machine the code runs on can read Thermo RAW files.
That is: The OS is Windows Thermo MSFileReader is installed |
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.
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. |
ISpectrum |
parseSpectrum(int num)
Parse a single spectrumRef from file on disk by it's number.
Assuming every LCMS file interface must be able to do that. |
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 IXRawfile5 xRawfile5
public ThermoRawFile(String path)
path - public static boolean isPlatformSupported()
public static boolean isThermoLibInstalled()
protected 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.