public class PSParameter extends DbObject 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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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.
|
double |
getConfidence()
Returns the confidence.
|
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.
|
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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Integer |
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.
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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.
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void |
setPrecursorIntensityPerFraction(HashMap<String,ArrayList<Double>> precursorIntensityPerFraction)
Get the precursor intensity in the given fraction.
|
void |
setPrecursorIntensitySummedPerFraction(HashMap<String,Double> precursorIntensitySummedPerFraction)
Sets the summed precursor intensity per fraction map.
|
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).
|
getFirstLevel, getId, setFirstLevel, setId
jdoZooEvict, jdoZooGetBackup, jdoZooGetClassDef, jdoZooGetContext, jdoZooGetNode, jdoZooGetOid, jdoZooGetTimestamp, jdoZooHasState, jdoZooInit, jdoZooIsDeleted, jdoZooIsDetached, jdoZooIsDirty, jdoZooIsNew, jdoZooIsPersistent, jdoZooIsStateHollow, jdoZooIsTransactional, jdoZooMarkClean, jdoZooMarkDeleted, jdoZooMarkDetached, jdoZooMarkDirty, jdoZooMarkHollow, jdoZooMarkTransient, jdoZooSetOid, jdoZooSetTimestamp, toString, zooActivateRead, zooActivateWrite, zooActivateWrite
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 Integer 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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