Package | Description |
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com.compomics.util.experiment.identification |
Experiment classes related to identifications.
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com.compomics.util.experiment.identification.identification_parameters |
Parameters settings for the spectrum identification algorithms.
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com.compomics.util.experiment.identification.identification_parameters.tool_specific |
Parameters settings for the search algorithms.
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com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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com.compomics.util.experiment.identification.spectrum_assumptions |
Implementations of the SpectrumIdentificationAssumption.
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com.compomics.util.experiment.massspectrometry |
Experiment classes related to spectra.
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Modifier and Type | Field and Description |
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protected Charge |
SpectrumIdentificationAssumption.identificationCharge
The charge used for identification.
|
Modifier and Type | Method and Description |
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Charge |
SpectrumIdentificationAssumption.getIdentificationCharge()
Returns the charge used for identification.
|
Modifier and Type | Method and Description |
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void |
SpectrumIdentificationAssumption.setIdentificationCharge(Charge identificationCharge)
Sets the identification charge.
|
Modifier and Type | Method and Description |
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Charge |
SearchParameters.getMaxChargeSearched()
Returns the maximal charge searched.
|
Charge |
SearchParameters.getMinChargeSearched()
Returns the minimal charge searched.
|
Modifier and Type | Method and Description |
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void |
SearchParameters.setMaxChargeSearched(Charge maxChargeSearched)
Sets the maximal charge searched.
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void |
SearchParameters.setMinChargeSearched(Charge minChargeSearched)
Sets the minimal charge searched.
|
Modifier and Type | Method and Description |
---|---|
Charge |
OmssaParameters.getMinimalChargeForMultipleChargedFragments()
Returns the minimal precursor charge to account for multiply charged
fragments in OMSSA.
|
Modifier and Type | Method and Description |
---|---|
void |
OmssaParameters.setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
Sets the minimal precursor charge to account for multiply charged
fragments in OMSSA.
|
Modifier and Type | Field and Description |
---|---|
Charge |
IonMatch.charge
The supposed charge of the ion.
|
Modifier and Type | Method and Description |
---|---|
static String |
IonMatch.getPeakAnnotation(boolean html,
Ion ion,
Charge charge)
Returns the annotation to use for a given ion and charge as a String.
|
static String |
IonMatch.getPeakAnnotation(Ion ion,
Charge charge)
Returns the annotation to use for a given ion and charge as a String.
|
Constructor and Description |
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IonMatch(Peak aPeak,
Ion anIon,
Charge aCharge)
Constructor for an ion peak.
|
Constructor and Description |
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PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
Charge identificationCharge,
double score)
Constructor for a peptide assumption.
|
PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
Charge identificationCharge,
double score,
String identificationFile)
Constructor for a peptide assumption.
|
TagAssumption(int advocate,
int rank,
Tag tag,
Charge identificationCharge,
double score)
Constructor.
|
Modifier and Type | Method and Description |
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ArrayList<Charge> |
Precursor.getPossibleCharges()
Getter for the possible charges.
|
Constructor and Description |
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Precursor(double rt,
double mz,
ArrayList<Charge> possibleCharges)
Constructor for the precursor.
|
Precursor(double mz,
double intensity,
ArrayList<Charge> possibleCharges,
double rtMin,
double rtMax)
Constructor with retention time window and no reference retention time.
|
Precursor(double rt,
double mz,
double intensity,
ArrayList<Charge> possibleCharges)
Constructor for the precursor.
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Precursor(double rt,
double mz,
double intensity,
ArrayList<Charge> possibleCharges,
double rtMin,
double rtMax)
Constructor with retention time window.
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