umich.ms.fileio.filetypes.thermo.raw

Class ThermoRawFile

java.lang.Object

umich.ms.util.file.AbstractFile

umich.ms.fileio.filetypes.AbstractLCMSDataSource<ThermoRawIndex>

umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile

All Implemented Interfaces:

Closeable, Serializable, AutoCloseable, LCMSDataSource<ThermoRawIndex>

public class ThermoRawFile
extends AbstractLCMSDataSource<ThermoRawIndex>

LC/MS data source for Thermo RAW files. Can only be used on Windows. Requires installation of MSFileReader library from Thermo, it can be downloaded here: https://thermo.flexnetoperations.com You will need to register there first. The latest version as of this writing (2016-04-25) was 3.1-SP2. Install it as Administrator, otherwise the service might not get registered. Created by Dmitry Avtonomov on 2016-04-25.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ThermoRawIndex	index
protected LCMSRunInfo	runInfo
protected umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5	xRawfile5

Fields inherited from class umich.ms.fileio.filetypes.AbstractLCMSDataSource

excludeEmptyScans, parsingTimeout, tasksPerCpuPerBatch

Fields inherited from class umich.ms.util.file.AbstractFile

BUF_SIZE, path

Constructor Summary

Constructors

Constructor and Description
ThermoRawFile(String path) Create a new source with autoload of spectra disabled.

Method Summary

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.

Methods inherited from class umich.ms.fileio.filetypes.AbstractLCMSDataSource

fetchRunInfo, getNumThreadsForParsing, getParsingTimeout, getRunInfo, getTasksPerCpuPerBatch, isExcludeEmptyScans, setExcludeEmptyScans, setNumThreadsForParsing, setParsingTimeout, setTasksPerCpuPerBatch

Methods inherited from class umich.ms.util.file.AbstractFile

close, getBufferedInputStream, getPath, getRandomAccessFile

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

index

protected ThermoRawIndex index

runInfo

protected LCMSRunInfo runInfo

xRawfile5

protected volatile umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5 xRawfile5

Constructor Detail

ThermoRawFile

public ThermoRawFile(String path)

Create a new source with autoload of spectra disabled.

Method Detail

isPlatformSupported

public static boolean isPlatformSupported()

Just checks if the OS is some flavor of windows.

isThermoLibInstalled

public 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.

isThermoSupportedHere

public 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

fetchXrawfile

protected umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5 fetchXrawfile()

getName

public String getName()

Description copied from interface: LCMSDataSource

Some identifier for the source, that can be used as its name.

releaseMemory

public void releaseMemory()

Description copied from interface: LCMSDataSource

The intent is to be able to free the memory, e.g. release references to ScanCollection, etc.

parseRunInfo

public LCMSRunInfo parseRunInfo()
                         throws FileParsingException

Throws:

FileParsingException

getIndex

public ThermoRawIndex getIndex()

Description copied from interface: LCMSDataSource

Gets the index without an attempt to parse it. Will only return a non null value if LCMSDataSource.fetchIndex() was called before.

fetchIndex

public ThermoRawIndex fetchIndex()
                          throws FileParsingException

Description copied from interface: LCMSDataSource

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.

Throws:

FileParsingException

parseIndex

public ThermoRawIndex parseIndex()
                          throws FileParsingException

Throws:

FileParsingException

parseSpectrum

public ISpectrum parseSpectrum(int num)
                        throws FileParsingException

Description copied from interface: LCMSDataSource

Parse a single spectrumRef from file on disk by it's number. Assuming every LCMS file interface must be able to do that.

Parameters:

num - scan number

Throws:

FileParsingException

parseScan

public IScan parseScan(int num,
                       boolean parseSpectrum)
                throws FileParsingException

Description copied from interface: LCMSDataSource

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.

Parameters:

num - scan number

parseSpectrum - if false, the spectrumRef should not be parsed. Can provide significant speed and memory benefits if you only need scan metadata

Returns:

the value should never be null, throw an exception if it could not be parsed

Throws:

FileParsingException

parse

public List<IScan> parse(LCMSDataSubset subset)
                  throws FileParsingException

Description copied from interface: LCMSDataSource

Parse a range of scan numbers. The storage strategy should always be StorageStrategy.STRONG, the receiver then can set it to whatever it needs.

Parameters:

subset - the region of LC/MS data to be parsed as scans

Returns:

ScanCollectionDefault of all scans from the file

Throws:

FileParsingException

parse

public List<IScan> parse(List<Integer> scanNums)
                  throws FileParsingException

Description copied from interface: LCMSDataSource

The storage strategy should always be StorageStrategy.STRONG, the receiver then can set it to whatever it needs.

Parameters:

scanNums - List of scan numbers to be parsed. All scan numbers MUST be present in the file.

Returns:

ScanCollection of requested scans. Unlike other parseIndexEntries...() methods, this one does not set up proper child/parent relations between spectra. However, PrecursorInfo for MSn spectra is still parsed, so you might get the correct precursorScanNum. This scan num might not be present in the returned scan collection. Moreover, even if the precursorScanNum is parsed, the pointer to parent scan in PrecursorInfo is not set (as no checks are made in this method).

Throws:

FileParsingException