public class PSParameter extends ExperimentObject implements UrParameter
Modifier and Type | Field and Description |
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static PSParameter |
dummy
An empty parameter used for instantiation.
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static int |
NOT_GROUP
Static index for a protein inference group: 0 - not a protein group or
unique peptide of single protein group.
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static int |
RELATED
Static index for a protein group: 1 - related proteins or peptide from
related protein groups (not necessarily unique to the group).
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static int |
RELATED_AND_UNRELATED
Static index for a protein group: 2 - related and a unrelated proteins or
peptide shared by related and unrelated proteins (not necessarily unique
to the group).
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static int |
UNRELATED
Static index for a protein group: 3 - unrelated proteins proteins or
peptide shared by unrelated proteins.
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NO_KEY
Constructor and Description |
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PSParameter()
Constructor.
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Modifier and Type | Method and Description |
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void |
createIntermediateScoreMap()
Instantiates the intermediate scores map if null.
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Double |
getAlgorithmDeltaPEP()
Returns the difference in identification algorithm level PEP with the
next best peptide assumption with sequence difference for the given
search engine.
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double |
getConfidence()
Returns the confidence.
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double |
getDeltaPEP()
Returns the difference in identification algorithm level PEP with the
next best peptide assumption with sequence difference across all search
engines.
|
Double |
getFractionConfidence(String fraction)
Returns the fraction confidence.
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HashMap<String,Double> |
getFractionPEP()
Returns the fraction pep map.
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Double |
getFractionPEP(String fraction)
Returns the fraction pep.
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Set<String> |
getFractions()
Return the fractions where this match was found.
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HashMap<String,Double> |
getFractionScore()
Return the fractions where this match was found.
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Double |
getFractionScore(String fraction)
Returns the fraction score.
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int |
getFractionValidatedPeptides(String fraction)
Get the number of validated peptides in the given fraction.
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Integer |
getFractionValidatedSpectra(String fraction)
Get the number of validated spectra in the given fraction.
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boolean |
getHidden()
Returns whether a match is hidden or not.
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Double |
getIntermediateScore(int scoreId)
Returns the desired intermediate score.
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HashMap<Integer,Double> |
getIntermediateScores()
Returns the intermediate scores map.
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boolean |
getManualValidation()
Indicates whether the match validation was manually inspected.
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MatchValidationLevel |
getMatchValidationLevel()
Returns the validation level of the match.
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long |
getParameterKey()
This method returns the key of the parameter.
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HashMap<String,Double> |
getPrecursorIntensityAveragePerFraction()
Returns the fraction precursor intensity average map.
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Double |
getPrecursorIntensityAveragePerFraction(String fraction)
Get the average precursor intensity in the given fraction.
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HashMap<String,ArrayList<Double>> |
getPrecursorIntensityPerFraction()
Returns the precursor intensity per fraction map.
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ArrayList<Double> |
getPrecursorIntensityPerFraction(String fraction)
Get the precursor intensity in the given fraction.
|
HashMap<String,Double> |
getPrecursorIntensitySummedPerFraction()
Returns the fraction summed intensity map.
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Double |
getPrecursorIntensitySummedPerFraction(String fraction)
Get the summed precursor intensity in the given fraction.
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double |
getProbability()
Returns the match probability.
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String |
getProteinInferenceClassAsString()
Returns the protein inference class as a string for the given
integer-based class
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static String |
getProteinInferenceClassAsString(int matchClass)
Returns the protein inference class as a string for the given
integer-based class.
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int |
getProteinInferenceGroupClass()
Returns the protein inference class of the protein match.
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Set<String> |
getQcCriteria()
Returns the list of QC checks made for this match.
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HashMap<String,Boolean> |
getQcFilters()
Returns the qc filters map.
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double |
getScore()
Returns the score.
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boolean |
getStarred()
Returns whether a match is starred or not.
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double |
getTransformedScore()
Returns the log transformed score.
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HashMap<String,Integer> |
getValidatedPeptidesPerFraction()
Returns the number of validated peptides per fraction.
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HashMap<String,Integer> |
getValidatedSpectraPerFraction()
Returns the number of validated spectra per fraction.
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boolean |
hasQcFilters()
Indicates whether QC filters were implemented for this match.
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Boolean |
isQcPassed(String criterion)
Indicates whether the given QC check was passed.
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void |
resetQcResults()
Resets the results of the QC filters.
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void |
setAlgorithmDeltaPEP(double deltaPEP)
Sets the difference in identification algorithm level PEP with the next
best peptide assumption with sequence difference for the given search
engine.
|
void |
setDeltaPEP(double deltaPEP)
Sets the difference in identification algorithm level PEP with the next
best peptide assumption with sequence difference across all search
engines.
|
void |
setFractionPEP(HashMap<String,Double> fractionPEP) |
void |
setFractionPEP(String fraction,
Double confidence)
Sets the fraction confidence.
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void |
setFractionScore(HashMap<String,Double> fractionScore)
Sets the fraction score map.
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void |
setFractionScore(String fraction,
double confidence)
Sets the fraction confidence.
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void |
setGroupClass(int groupClass) |
void |
setHidden(boolean hidden)
Hide/Unhide a match.
|
void |
setIntermediateScore(Integer scoreId,
Double score)
Adds an intermediate score.
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void |
setIntermediateScores(HashMap<Integer,Double> intermediateScores) |
void |
setManualValidation(boolean manualValidation)
Sets whether the match validation was manually inspected.
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void |
setMatchValidationLevel(MatchValidationLevel matchValidationLevel)
Sets the validation level of the match.
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void |
setPrecursorIntensityAveragePerFraction(HashMap<String,Double> precursorIntensityAveragePerFraction)
Sets the precursor intensity per fraction map.
|
void |
setPrecursorIntensityPerFraction(HashMap<String,ArrayList<Double>> precursorIntensityPerFraction)
Get the precursor intensity in the given fraction.
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void |
setPrecursorIntensitySummedPerFraction(HashMap<String,Double> precursorIntensitySummedPerFraction)
Sets the summed precursor intensity per fraction map.
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void |
setProbability(double probability)
Set the probability.
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void |
setProteinInferenceClass(int groupClass)
Sets the protein group class.
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void |
setQcFilters(HashMap<String,Boolean> qcFilters)
Sets the qc filters.
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void |
setQcResult(String criterion,
boolean validated)
Sets whether the match passed a quality control check.
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void |
setScore(double score)
Set the peptide score.
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void |
setStarred(boolean starred)
Star/Unstar a match.
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void |
setValidatedPeptidesPerFraction(HashMap<String,Integer> validatedPeptidesPerFraction)
Get the number of validated peptides in the given fraction.
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void |
setValidatedSpectraPepFraction(HashMap<String,Integer> validatedSpectraPerFraction)
Get the number of validated spectra in the given fraction.
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static double |
transformScore(double rawScore)
Returns a score from a raw score where the score = -10*log(rawScore).
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final int NOT_GROUP
public static final int RELATED
public static final int RELATED_AND_UNRELATED
public static final int UNRELATED
public static final PSParameter dummy
public double getProbability()
public void setProbability(double probability)
probability
- the new peptide posterior error probabilitypublic void setGroupClass(int groupClass)
public double getScore()
public double getTransformedScore()
public void setScore(double score)
score
- the scorepublic double getConfidence()
public Double getAlgorithmDeltaPEP()
public void setAlgorithmDeltaPEP(double deltaPEP)
deltaPEP
- the difference in identification algorithm level PEP with
the next best peptide assumption with sequence difference for the given
search enginepublic double getDeltaPEP()
public void setDeltaPEP(double deltaPEP)
deltaPEP
- the difference in identification algorithm level PEP with
the next best peptide assumption with sequence difference across all
search enginespublic void setQcFilters(HashMap<String,Boolean> qcFilters)
qcFilters
- the qc filterspublic MatchValidationLevel getMatchValidationLevel()
public void setMatchValidationLevel(MatchValidationLevel matchValidationLevel)
matchValidationLevel
- the validation level of the matchpublic void setHidden(boolean hidden)
hidden
- boolean indicating whether the match should be hiddenpublic boolean getHidden()
public void setStarred(boolean starred)
starred
- boolean indicating whether the match should be starredpublic boolean getStarred()
public int getProteinInferenceGroupClass()
public String getProteinInferenceClassAsString()
public static String getProteinInferenceClassAsString(int matchClass)
matchClass
- the protein inference class as integer (see static
fields)public void setProteinInferenceClass(int groupClass)
groupClass
- the protein group classpublic HashMap<String,Integer> getValidatedPeptidesPerFraction()
public HashMap<String,Integer> getValidatedSpectraPerFraction()
public void setFractionScore(String fraction, double confidence)
fraction
- the fractionconfidence
- the confidencepublic void setFractionScore(HashMap<String,Double> fractionScore)
fractionScore
- the fraction score mappublic Double getFractionScore(String fraction)
fraction
- the fractionpublic Set<String> getFractions()
public HashMap<String,Double> getFractionScore()
public void setFractionPEP(String fraction, Double confidence)
fraction
- the fractionconfidence
- the confidencepublic Double getFractionPEP(String fraction)
fraction
- the fractionpublic HashMap<String,Double> getFractionPEP()
public Double getFractionConfidence(String fraction)
fraction
- the fractionpublic int getFractionValidatedPeptides(String fraction)
fraction
- the fractionpublic void setValidatedPeptidesPerFraction(HashMap<String,Integer> validatedPeptidesPerFraction)
validatedPeptidesPerFraction
- the validated peptides per fraction
mappublic Integer getFractionValidatedSpectra(String fraction)
fraction
- the fractionpublic void setValidatedSpectraPepFraction(HashMap<String,Integer> validatedSpectraPerFraction)
validatedSpectraPerFraction
- the validated spectra per fraction mappublic ArrayList<Double> getPrecursorIntensityPerFraction(String fraction)
fraction
- the fractionpublic HashMap<String,ArrayList<Double>> getPrecursorIntensityPerFraction()
public void setPrecursorIntensityAveragePerFraction(HashMap<String,Double> precursorIntensityAveragePerFraction)
precursorIntensityAveragePerFraction
- the precursor intensity per
fraction mappublic void setPrecursorIntensitySummedPerFraction(HashMap<String,Double> precursorIntensitySummedPerFraction)
precursorIntensitySummedPerFraction
- the summed precursor intensity
per fraction mappublic void setPrecursorIntensityPerFraction(HashMap<String,ArrayList<Double>> precursorIntensityPerFraction)
precursorIntensityPerFraction
- the precursor intensities per
fraction mappublic Double getPrecursorIntensityAveragePerFraction(String fraction)
fraction
- the fractionpublic HashMap<String,Double> getPrecursorIntensityAveragePerFraction()
public Double getPrecursorIntensitySummedPerFraction(String fraction)
fraction
- the fractionpublic HashMap<String,Double> getPrecursorIntensitySummedPerFraction()
public boolean getManualValidation()
public void setManualValidation(boolean manualValidation)
manualValidation
- a boolean indicating whether the match validation
was manually inspectedpublic void setQcResult(String criterion, boolean validated)
criterion
- the QC criterionvalidated
- boolean indicating whether the test was passedpublic Boolean isQcPassed(String criterion)
criterion
- the QC criterionpublic Set<String> getQcCriteria()
public HashMap<String,Boolean> getQcFilters()
public void resetQcResults()
public boolean hasQcFilters()
public void setIntermediateScore(Integer scoreId, Double score)
scoreId
- the index of the scorescore
- the value of the scorepublic void createIntermediateScoreMap()
public Double getIntermediateScore(int scoreId)
scoreId
- the index of the scorepublic HashMap<Integer,Double> getIntermediateScores()
public static double transformScore(double rawScore)
rawScore
- the raw scorepublic long getParameterKey()
UrParameter
getParameterKey
in interface UrParameter
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