public class ModificationScoring extends ExperimentObject
Modifier and Type | Field and Description |
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static int |
CONFIDENT
Index for a confident assignment.
|
static int |
DOUBTFUL
Index for a doubtful assignment.
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static int |
NOT_FOUND
Index indicating that the modification was not found.
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static int |
RANDOM
Index for a random location choice.
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static String |
SEPARATOR
The separator used to separate locations in the modification location
key.
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static int |
VERY_CONFIDENT
Index for a very confident assignment.
|
NO_KEY
Constructor and Description |
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ModificationScoring()
Default constructor Constructor.
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ModificationScoring(String ptmName)
Constructor.
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Modifier and Type | Method and Description |
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void |
addAll(ModificationScoring anotherScore)
Adds all scores from another score if better.
|
Set<Integer> |
getAllPtmLocations()
Returns the sites of all localized PTMs.
|
static String |
getConfidenceLevel(int index)
Convenience method returning the given confidence level as a string.
|
ArrayList<Integer> |
getConfidentPtmLocations()
Returns the confidently and very confidently localized PTMs.
|
double |
getDeltaScore(int site)
Returns the delta score at a given site.
|
Set<Integer> |
getDSites()
Returns a set of sites where a D-score is available
|
int |
getLocalizationConfidence(int site)
Returns the confidence of the PTM localization.
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int |
getMinimalLocalizationConfidence()
Returns the minimal confidence among the PTM sites of this scoring.
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String |
getName()
Returns the name of the inspected protein.
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ArrayList<Integer> |
getOrderedDSites()
Returns an ordered list of sites where the D-score was used.
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ArrayList<Integer> |
getOrderedProbabilisticSites()
Returns an ordered list of sites where the probabilistic score was used.
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ArrayList<Integer> |
getOrderedPtmLocations()
Returns sites of all localized PTMs ordered increasingly.
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static String[] |
getPossibleConfidenceLevels()
Convenience method returning all confidence levels as string.
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double |
getProbabilisticScore(int site)
Returns the probabilistic score at a given site.
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Set<Integer> |
getProbabilisticSites()
Returns a set of sites where a probabilistic score is available
|
HashMap<Integer,Integer> |
getPtmLocationAtAA()
Returns the map of the localization.
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ArrayList<Integer> |
getPtmLocations(int confidenceLevel)
Returns the PTM locations at a given confidence level (see static
fields).
|
Set<Integer> |
getScoredSites()
Returns a set of sites where a score is available.
|
ArrayList<Integer> |
getSecondaryPtmLocations()
Returns the not found, randomly or doubtfully localized PTMs.
|
void |
setDeltaScore(int site,
double score)
Sets the delta score at a given site.
|
void |
setProbabilisticScore(int site,
double score)
Sets the probabilistic score at a given site.
|
void |
setSiteConfidence(int site,
int confidenceLevel)
Sets the confidence level of a modification site.
|
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final int NOT_FOUND
public static final int RANDOM
public static final int DOUBTFUL
public static final int CONFIDENT
public static final int VERY_CONFIDENT
public static final String SEPARATOR
public ModificationScoring()
public ModificationScoring(String ptmName)
ptmName
- the name of the PTM of interest.public String getName()
public Set<Integer> getScoredSites()
public void setDeltaScore(int site, double score)
site
- the modification sitescore
- the delta scorepublic double getDeltaScore(int site)
site
- the site of interestpublic void setProbabilisticScore(int site, double score)
site
- the modification sitescore
- the delta scorepublic double getProbabilisticScore(int site)
site
- the site of interestpublic Set<Integer> getProbabilisticSites()
public ArrayList<Integer> getOrderedProbabilisticSites()
public Set<Integer> getDSites()
public ArrayList<Integer> getOrderedDSites()
public void addAll(ModificationScoring anotherScore)
anotherScore
- another scorepublic void setSiteConfidence(int site, int confidenceLevel)
site
- the modification siteconfidenceLevel
- the confidence levelpublic HashMap<Integer,Integer> getPtmLocationAtAA()
public Set<Integer> getAllPtmLocations()
public ArrayList<Integer> getOrderedPtmLocations()
public int getLocalizationConfidence(int site)
site
- the modification sitepublic int getMinimalLocalizationConfidence()
public ArrayList<Integer> getConfidentPtmLocations()
public ArrayList<Integer> getSecondaryPtmLocations()
public ArrayList<Integer> getPtmLocations(int confidenceLevel)
confidenceLevel
- the confidence levelpublic static String[] getPossibleConfidenceLevels()
public static String getConfidenceLevel(int index)
index
- the confidence levelCopyright © 2021. All rights reserved.