Class MsFileHandler
java.lang.Object
com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler
- All Implemented Interfaces:
SpectrumProvider
,AutoCloseable
public class MsFileHandler extends Object implements SpectrumProvider
A spectrum provider for mass spectrometry files based on Compomics Mass
Spectrometry (cms) files.
- Author:
- Marc Vaudel, Harald Barsnes
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Constructor Summary
Constructors Constructor Description MsFileHandler()
Constructor. -
Method Summary
Modifier and Type Method Description void
close()
static String
getCmsFilePath(File msFile, File cmsFolder)
Returns the path of the cms file expected for the given mass spectrometry file and cms folder.HashMap<String,String>
getCmsFilePaths()
Returns the absolute path to the cms file indexed by ms file name without file extension.HashMap<String,String>
getFilePaths()
Returns the absolute path to the original mass spec file containing the spectra in a map indexed by file name without file extension.double
getMaxPrecInt()
Returns the maximum precursor intensity among all files.double
getMaxPrecInt(String fileNameWithoutExtension)
Returns the maximum precursor intensity in a given file.double
getMaxPrecMz()
Returns the maximum precursor m/z among all files.double
getMaxPrecMz(String fileNameWithoutExtension)
Returns the maximum precursor m/z in a given file.double
getMaxPrecRT()
Returns the maximum precursor RT among all files.double
getMaxPrecRT(String fileNameWithoutExtension)
Returns the maximum precursor RT in a given file.double
getMinPrecMz()
Returns the minimum precursor m/z among all files.double
getMinPrecMz(String fileNameWithoutExtension)
Returns the minimum precursor m/z in a given file.String[]
getOrderedFileNamesWithoutExtensions()
Returns the spectrum file names without file extensions.double[][]
getPeaks(String fileNameWithoutExtension, String spectrumTitle)
Returns the spectrum peaks.Precursor
getPrecursor(String fileNameWithoutExtension, String spectrumTitle)
Returns the precursor.double
getPrecursorMz(String fileNameWithoutExtension, String spectrumTitle)
Returns the measured precursor m/z.double
getPrecursorRt(String fileNameWithoutExtension, String spectrumTitle)
Returns the precursor RT window.CmsFileReader
getReader(String fileNameWithoutExtension)
Returns the cms file reader for the given ms file.Spectrum
getSpectrum(String fileNameWithoutExtension, String spectrumTitle)
Returns the spectrum with the given title in the given file.String[]
getSpectrumTitles(String fileName)
Returns the spectrum titles for the given mass spectrometry file name.void
register(File msFile, WaitingHandler waitingHandler)
Registers a mass spectrometry file and enables querying its spectra.If the file is not a cms file, a cms file will be created along with the ms file.void
register(File msFile, File cmsFolder, WaitingHandler waitingHandler)
Registers a mass spectrometry file and enables querying its spectra.If the file is not a cms file, a cms file will be created in the cms folder if not null, along the ms file otherwise.
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Constructor Details
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MsFileHandler
public MsFileHandler()Constructor.
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Method Details
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register
Registers a mass spectrometry file and enables querying its spectra.If the file is not a cms file, a cms file will be created along with the ms file.- Parameters:
msFile
- The mass spectrometry file to register.waitingHandler
- The waiting handler.- Throws:
IOException
- Exception thrown if an error occurs while reading or writing a file.
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register
public void register(File msFile, File cmsFolder, WaitingHandler waitingHandler) throws IOExceptionRegisters a mass spectrometry file and enables querying its spectra.If the file is not a cms file, a cms file will be created in the cms folder if not null, along the ms file otherwise.- Parameters:
msFile
- The mass spectrometry file to register.cmsFolder
- The folder where to save the cms files.waitingHandler
- The waiting handler.- Throws:
IOException
- Exception thrown if an error occurs while reading or writing a file.
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getCmsFilePath
Returns the path of the cms file expected for the given mass spectrometry file and cms folder.- Parameters:
msFile
- The mass spectrometry file.cmsFolder
- The folder where to save the cms files.- Returns:
- The path of the cms file.
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getReader
Returns the cms file reader for the given ms file. Null if not set.- Parameters:
fileNameWithoutExtension
- The name of the ms file without file extension.- Returns:
- The cms file reader.
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getSpectrum
Description copied from interface:SpectrumProvider
Returns the spectrum with the given title in the given file.- Specified by:
getSpectrum
in interfaceSpectrumProvider
- Parameters:
fileNameWithoutExtension
- The name of the spectrum file without file extension.spectrumTitle
- The title of the spectrum.- Returns:
- The spectrum with the given title in the given file.
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getPrecursor
Description copied from interface:SpectrumProvider
Returns the precursor. Null if none.- Specified by:
getPrecursor
in interfaceSpectrumProvider
- Parameters:
fileNameWithoutExtension
- The name of the spectrum file without file extension.spectrumTitle
- The title of the spectrum.- Returns:
- The precursor.
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getPrecursorMz
Description copied from interface:SpectrumProvider
Returns the measured precursor m/z. NaN if none.- Specified by:
getPrecursorMz
in interfaceSpectrumProvider
- Parameters:
fileNameWithoutExtension
- The name of the spectrum file without file extension.spectrumTitle
- The title of the spectrum.- Returns:
- The measured precursor m/z.
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getPrecursorRt
Description copied from interface:SpectrumProvider
Returns the precursor RT window. NaN if none.- Specified by:
getPrecursorRt
in interfaceSpectrumProvider
- Parameters:
fileNameWithoutExtension
- The name of the spectrum file without file extension.spectrumTitle
- The title of the spectrum.- Returns:
- The precursor RT.
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getPeaks
Description copied from interface:SpectrumProvider
Returns the spectrum peaks.- Specified by:
getPeaks
in interfaceSpectrumProvider
- Parameters:
fileNameWithoutExtension
- The name of the spectrum file without file extension.spectrumTitle
- The title of the spectrum.- Returns:
- The peaks.
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getMinPrecMz
Description copied from interface:SpectrumProvider
Returns the minimum precursor m/z in a given file.- Specified by:
getMinPrecMz
in interfaceSpectrumProvider
- Parameters:
fileNameWithoutExtension
- The name of the spectrum file without file extension.- Returns:
- The minimum precursor m/z in a given file.
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getMaxPrecMz
Description copied from interface:SpectrumProvider
Returns the maximum precursor m/z in a given file.- Specified by:
getMaxPrecMz
in interfaceSpectrumProvider
- Parameters:
fileNameWithoutExtension
- The name of the spectrum file without file extension.- Returns:
- The maximum precursor m/z in a given file.
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getMaxPrecInt
Description copied from interface:SpectrumProvider
Returns the maximum precursor intensity in a given file.- Specified by:
getMaxPrecInt
in interfaceSpectrumProvider
- Parameters:
fileNameWithoutExtension
- The name of the spectrum file without file extension.- Returns:
- The maximum precursor intensity in a given file.
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getMaxPrecRT
Description copied from interface:SpectrumProvider
Returns the maximum precursor RT in a given file.- Specified by:
getMaxPrecRT
in interfaceSpectrumProvider
- Parameters:
fileNameWithoutExtension
- The name of the spectrum file without file extension.- Returns:
- The maximum precursor RT in a given file.
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getMinPrecMz
public double getMinPrecMz()Description copied from interface:SpectrumProvider
Returns the minimum precursor m/z among all files.- Specified by:
getMinPrecMz
in interfaceSpectrumProvider
- Returns:
- The minimum precursor m/z among all files.
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getMaxPrecMz
public double getMaxPrecMz()Description copied from interface:SpectrumProvider
Returns the maximum precursor m/z among all files.- Specified by:
getMaxPrecMz
in interfaceSpectrumProvider
- Returns:
- The maximum precursor m/z among all files.
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getMaxPrecInt
public double getMaxPrecInt()Description copied from interface:SpectrumProvider
Returns the maximum precursor intensity among all files.- Specified by:
getMaxPrecInt
in interfaceSpectrumProvider
- Returns:
- The maximum precursor intensity among all files.
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getMaxPrecRT
public double getMaxPrecRT()Description copied from interface:SpectrumProvider
Returns the maximum precursor RT among all files.- Specified by:
getMaxPrecRT
in interfaceSpectrumProvider
- Returns:
- The maximum precursor RT among all files.
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getOrderedFileNamesWithoutExtensions
Description copied from interface:SpectrumProvider
Returns the spectrum file names without file extensions.- Specified by:
getOrderedFileNamesWithoutExtensions
in interfaceSpectrumProvider
- Returns:
- The spectrum file names without file extensions.
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getFilePaths
Description copied from interface:SpectrumProvider
Returns the absolute path to the original mass spec file containing the spectra in a map indexed by file name without file extension.- Specified by:
getFilePaths
in interfaceSpectrumProvider
- Returns:
- The absolute path to the original mass spec file containing the spectra in a map indexed by file name.
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getCmsFilePaths
Description copied from interface:SpectrumProvider
Returns the absolute path to the cms file indexed by ms file name without file extension. Null if none.- Specified by:
getCmsFilePaths
in interfaceSpectrumProvider
- Returns:
- The absolute path to the cms file indexed by ms file name.
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close
public void close()- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceSpectrumProvider
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getSpectrumTitles
Description copied from interface:SpectrumProvider
Returns the spectrum titles for the given mass spectrometry file name.- Specified by:
getSpectrumTitles
in interfaceSpectrumProvider
- Parameters:
fileName
- The mass spectrometry file name without file extension.- Returns:
- The spectrum titles as array.
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