public interface SpectrumProvider extends AutoCloseable
Modifier and Type | Method and 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 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.
|
Spectrum |
getSpectrum(String fileNameWithoutExtension,
String spectrumTitle)
Returns the spectrum with the given title in the given file.
|
String[] |
getSpectrumTitles(String fileNameWithoutExtension)
Returns the spectrum titles for the given mass spectrometry file name.
|
Spectrum getSpectrum(String fileNameWithoutExtension, String spectrumTitle)
fileNameWithoutExtension
- The name of the spectrum file without
file extension.spectrumTitle
- The title of the spectrum.Precursor getPrecursor(String fileNameWithoutExtension, String spectrumTitle)
fileNameWithoutExtension
- The name of the spectrum file without
file extension.spectrumTitle
- The title of the spectrum.double getPrecursorMz(String fileNameWithoutExtension, String spectrumTitle)
fileNameWithoutExtension
- The name of the spectrum file without
file extension.spectrumTitle
- The title of the spectrum.double getPrecursorRt(String fileNameWithoutExtension, String spectrumTitle)
fileNameWithoutExtension
- The name of the spectrum file without
file extension.spectrumTitle
- The title of the spectrum.double[][] getPeaks(String fileNameWithoutExtension, String spectrumTitle)
fileNameWithoutExtension
- The name of the spectrum file without
file extension.spectrumTitle
- The title of the spectrum.double getMinPrecMz(String fileNameWithoutExtension)
fileNameWithoutExtension
- The name of the spectrum file without
file extension.double getMaxPrecMz(String fileNameWithoutExtension)
fileNameWithoutExtension
- The name of the spectrum file without
file extension.double getMaxPrecInt(String fileNameWithoutExtension)
fileNameWithoutExtension
- The name of the spectrum file without
file extension.double getMaxPrecRT(String fileNameWithoutExtension)
fileNameWithoutExtension
- The name of the spectrum file without
file extension.double getMinPrecMz()
double getMaxPrecMz()
double getMaxPrecInt()
double getMaxPrecRT()
String[] getOrderedFileNamesWithoutExtensions()
String[] getSpectrumTitles(String fileNameWithoutExtension)
fileNameWithoutExtension
- The mass spectrometry file name without
file extension.HashMap<String,String> getFilePaths()
HashMap<String,String> getCmsFilePaths()
void close()
close
in interface AutoCloseable
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