Package | Description |
---|---|
com.compomics.util.experiment.identification.psm_scoring.psm_scores |
Main PTM scoring classes.
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com.compomics.util.experiment.io.massspectrometry |
Reading and indexing of mgf files.
|
com.compomics.util.experiment.massspectrometry |
Experiment classes related to spectra.
|
com.compomics.util.experiment.massspectrometry.indexes |
Classes related to the indexing of spectra.
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Modifier and Type | Method and Description |
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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.
|
Modifier and Type | Method and Description |
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static Precursor |
MspReader.getPrecursor(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
Long index,
String fileName)
Returns the next precursor starting from the given index.
|
static Precursor |
MgfReader.getPrecursor(uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile,
Long index,
String fileName)
Returns the next precursor starting from the given index.
|
Modifier and Type | Method and Description |
---|---|
Precursor |
MSnSpectrum.getPrecursor()
Returns the precursor.
|
Precursor |
SpectrumFactory.getPrecursor(String spectrumKey)
Returns the precursor of the desired spectrum.
|
Precursor |
SpectrumFactory.getPrecursor(String spectrumKey,
boolean save)
Returns the precursor of the desired spectrum.
|
Precursor |
SpectrumFactory.getPrecursor(String fileName,
String spectrumTitle)
Returns the precursor of the desired spectrum.
|
Precursor |
SpectrumFactory.getPrecursor(String fileName,
String spectrumTitle,
boolean save)
Returns the precursor of the desired spectrum.
|
Precursor |
Precursor.getRecalibratedPrecursor(double mzCorrection,
double rtCorrection)
Returns a recalibrated precursor.
|
Modifier and Type | Method and Description |
---|---|
HashMap<String,Precursor> |
SpectrumFactory.getPrecursorMap(String fileName)
Returns a map containing all the precursors of a gven file indexed by spectrum title.
|
Modifier and Type | Method and Description |
---|---|
void |
MSnSpectrum.setPrecursor(Precursor precursor)
Set the precursor.
|
Constructor and Description |
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MSnSpectrum(int level,
Precursor precursor,
String spectrumTitle,
HashMap<Double,Peak> peakMap,
String fileName)
Constructor for the spectrum.
|
MSnSpectrum(int level,
Precursor precursor,
String spectrumTitle,
HashMap<Double,Peak> peakMap,
String fileName,
double scanStartTime)
Constructor for the spectrum.
|
MSnSpectrum(int level,
Precursor precursor,
String spectrumTitle,
String fileName)
Minimal constructor for the spectrum.
|
Modifier and Type | Field and Description |
---|---|
Precursor |
PrecursorMap.PrecursorWithTitle.precursor
The precursor
|
Constructor and Description |
---|
PrecursorWithTitle(Precursor precursor,
String spectrumTitle)
Constructor.
|
Constructor and Description |
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PrecursorMap(HashMap<String,Precursor> precursors,
double precursorTolerance,
boolean ppm)
Builds a precursor map.
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