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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
Precursor |
MsFileHandler.getPrecursor(String fileNameWithoutExtension,
String spectrumTitle) |
Modifier and Type | Method and Description |
---|---|
Precursor |
CmsFileReader.getPrecursor(String spectrumTitle)
Returns the precursor of the spectrum with the given title.
|
Precursor |
CmsFileReader.getPrecursor(String fileName,
String spectrumTitle) |
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
Precursor |
SpectrumProvider.getPrecursor(String fileNameWithoutExtension,
String spectrumTitle)
Returns the precursor.
|
Modifier and Type | Field and Description |
---|---|
Precursor |
PrecursorMap.PrecursorWithTitle.precursor
The precursor
|
Constructor and Description |
---|
PrecursorWithTitle(Precursor precursor,
String spectrumTitle)
Constructor.
|
Constructor and Description |
---|
PrecursorMap(HashMap<String,Precursor> precursors,
double precursorTolerance,
boolean ppm)
Builds a precursor map.
|
Modifier and Type | Field and Description |
---|---|
Precursor |
Spectrum.precursor
The precursor if any.
|
Modifier and Type | Method and Description |
---|---|
Precursor |
Spectrum.getPrecursor()
Returns the precursor.
|
static Precursor |
RecalibrationUtils.getRecalibratedPrecursor(Precursor precursor,
double mzCorrection,
double rtCorrection)
Returns a recalibrated precursor.
|
Modifier and Type | Method and 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.
|
Constructor and Description |
---|
Spectrum(Precursor precursor,
double[] mz,
double[] intensities)
Constructor.
|
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