Class CmsFileReader
java.lang.Object
com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader
- All Implemented Interfaces:
SpectrumProvider
,AutoCloseable
public class CmsFileReader extends Object implements SpectrumProvider
Reader for Compomics Mass Spectrometry (cms) files.
- Author:
- Marc Vaudel, Harald Barsnes
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Field Summary
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Constructor Summary
Constructors Constructor Description CmsFileReader(File file, WaitingHandler waitingHandler)
Constructor allocating for single thread usage. -
Method Summary
Modifier and Type Method Description void
close()
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 fileName)
Returns the maximum precursor intensity in a given file.double
getMaxPrecMz()
Returns the maximum precursor m/z among all files.double
getMaxPrecMz(String fileName)
Returns the maximum precursor m/z in a given file.double
getMaxPrecRT()
Returns the maximum precursor RT among all files.double
getMaxPrecRT(String fileName)
Returns the maximum precursor RT in a given file.double
getMinPrecMz()
Returns the minimum precursor m/z among all files.double
getMinPrecMz(String fileName)
Returns the minimum precursor m/z in a given file.String[]
getOrderedFileNamesWithoutExtensions()
Returns the spectrum file names without file extensions.double[][]
getPeaks(String spectrumTitle)
Returns the peaks of the spectrum with the given title.double[][]
getPeaks(String fileName, String spectrumTitle)
Returns the spectrum peaks.Precursor
getPrecursor(String spectrumTitle)
Returns the precursor of the spectrum with the given title.Precursor
getPrecursor(String fileName, String spectrumTitle)
Returns the precursor.double
getPrecursorMz(String spectrumTitle)
Returns the m/z of the precursor of the spectrum with the given title.double
getPrecursorMz(String fileName, String spectrumTitle)
Returns the measured precursor m/z.double
getPrecursorRt(String spectrumTitle)
Returns the RT of the precursor of the spectrum with the given title.double
getPrecursorRt(String fileName, String spectrumTitle)
Returns the precursor RT window.Spectrum
getSpectrum(String spectrumTitle)
Returns the spectrum with the given title.Spectrum
getSpectrum(String fileName, 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.static byte[]
uncompress(byte[] compressedByteArray, int uncompressedLength)
Uncompresses the given byte array.
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Field Details
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titles
The titles of the spectra.
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Constructor Details
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CmsFileReader
public CmsFileReader(File file, WaitingHandler waitingHandler) throws FileNotFoundException, IOExceptionConstructor allocating for single thread usage.- Parameters:
file
- the file to readwaitingHandler
- the waiting handler- Throws:
FileNotFoundException
- thrown if the file was not foundIOException
- thrown if an error occurred while attempting to read the file
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Method Details
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getSpectrum
Returns the spectrum with the given title.- Parameters:
spectrumTitle
- title of the spectrum- Returns:
- the spectrum
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getPrecursor
Returns the precursor of the spectrum with the given title.- Parameters:
spectrumTitle
- title of the spectrum- Returns:
- the precursor of the spectrum
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getPrecursorMz
Returns the m/z of the precursor of the spectrum with the given title.- Parameters:
spectrumTitle
- the title of the spectrum- Returns:
- the precursor m/z of the spectrum
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getPrecursorRt
Returns the RT of the precursor of the spectrum with the given title.- Parameters:
spectrumTitle
- the title of the spectrum- Returns:
- the precursor RT of the spectrum
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getPeaks
Returns the peaks of the spectrum with the given title.- Parameters:
spectrumTitle
- the title of the spectrum- Returns:
- the peaks of the spectrum
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uncompress
public static byte[] uncompress(byte[] compressedByteArray, int uncompressedLength)Uncompresses the given byte array.- Parameters:
compressedByteArray
- the compressed byte arrayuncompressedLength
- the uncompressed length- Returns:
- the uncompressed array
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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:
fileName
- 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:
fileName
- 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:
fileName
- 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:
fileName
- 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:
fileName
- 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:
fileName
- 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:
fileName
- 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:
fileName
- 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:
fileName
- 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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