Uses of Class
com.compomics.util.experiment.mass_spectrometry.spectra.Precursor

Packages that use Precursor

Package	Description
com.compomics.util.experiment.identification.psm_scoring.psm_scores	Main PTM scoring classes.
com.compomics.util.experiment.io.mass_spectrometry	Classes for the handling of mass spectrometry files.
com.compomics.util.experiment.io.mass_spectrometry.cms	Classes for the handling of Compomics mass spectrometry (cms) files.
com.compomics.util.experiment.io.mass_spectrometry.mgf	Classes for the handling of mgf files.
com.compomics.util.experiment.mass_spectrometry	Experiment classes related to mass spectrometry.
com.compomics.util.experiment.mass_spectrometry.indexes	Classes related to the indexing of spectra.
com.compomics.util.experiment.mass_spectrometry.spectra	Experiment classes related to spectra.

Uses of Precursor in com.compomics.util.experiment.identification.psm_scoring.psm_scores

Methods in com.compomics.util.experiment.identification.psm_scoring.psm_scores with parameters of type Precursor

Modifier and Type	Method	Description
double	PrecursorAccuracy.getScore(Peptide peptide, int identificationCharge, Precursor precursor, boolean ppm, int minIsotope, int maxIsotope)	Scores the match between the given peptide and spectrum using the precursor m/z accuracy.

Uses of Precursor in com.compomics.util.experiment.io.mass_spectrometry

Methods in com.compomics.util.experiment.io.mass_spectrometry that return Precursor

Modifier and Type	Method	Description
Precursor	MsFileHandler.getPrecursor(String fileNameWithoutExtension, String spectrumTitle)

Uses of Precursor in com.compomics.util.experiment.io.mass_spectrometry.cms

Methods in com.compomics.util.experiment.io.mass_spectrometry.cms that return Precursor

Modifier and Type	Method	Description
Precursor	CmsFileReader.getPrecursor(String spectrumTitle)	Returns the precursor of the spectrum with the given title.
Precursor	CmsFileReader.getPrecursor(String fileName, String spectrumTitle)

Uses of Precursor in com.compomics.util.experiment.io.mass_spectrometry.mgf

Methods in com.compomics.util.experiment.io.mass_spectrometry.mgf that return Precursor

Modifier and Type	Method	Description
static Precursor	IndexedMgfReader.getPrecursor(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile, long index, String fileName)	Returns the next precursor starting from the given index.

Uses of Precursor in com.compomics.util.experiment.mass_spectrometry

Methods in com.compomics.util.experiment.mass_spectrometry that return Precursor

Modifier and Type	Method	Description
Precursor	SpectrumProvider.getPrecursor(String fileNameWithoutExtension, String spectrumTitle)	Returns the precursor.

Uses of Precursor in com.compomics.util.experiment.mass_spectrometry.indexes

Fields in com.compomics.util.experiment.mass_spectrometry.indexes declared as Precursor

Modifier and Type	Field	Description
final Precursor	PrecursorMap.PrecursorWithTitle.precursor	The precursor

Constructors in com.compomics.util.experiment.mass_spectrometry.indexes with parameters of type Precursor

Modifier	Constructor	Description
	PrecursorWithTitle(Precursor precursor, String spectrumTitle)	Constructor.

Constructor parameters in com.compomics.util.experiment.mass_spectrometry.indexes with type arguments of type Precursor

Modifier	Constructor	Description
	PrecursorMap(HashMap<String,Precursor> precursors, double precursorTolerance, boolean ppm)	Builds a precursor map.

Uses of Precursor in com.compomics.util.experiment.mass_spectrometry.spectra

Fields in com.compomics.util.experiment.mass_spectrometry.spectra declared as Precursor

Modifier and Type	Field	Description
Precursor	Spectrum.precursor	The precursor if any.

Methods in com.compomics.util.experiment.mass_spectrometry.spectra that return Precursor

Modifier and Type	Method	Description
Precursor	Spectrum.getPrecursor()	Returns the precursor.
static Precursor	RecalibrationUtils.getRecalibratedPrecursor(Precursor precursor, double mzCorrection, double rtCorrection)	Returns a recalibrated precursor.

Methods in com.compomics.util.experiment.mass_spectrometry.spectra with parameters of type Precursor

Modifier and Type	Method	Description
static Precursor	RecalibrationUtils.getRecalibratedPrecursor(Precursor precursor, double mzCorrection, double rtCorrection)	Returns a recalibrated precursor.
boolean	Precursor.isSameAs(Precursor otherPrecursor)	Returns a boolean indicating whether the precursor is identical to the other precursor.

Constructors in com.compomics.util.experiment.mass_spectrometry.spectra with parameters of type Precursor

Modifier	Constructor	Description
	Spectrum(Precursor precursor, double[] mz, double[] intensities, int spectrumLevel)	Constructor.Note: throughout the code, it is assumed that the m/z array is sorted by ascending m/z.