Package com.compomics.util.experiment.identification.peptide_shaker

Class ModificationScoring

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring
All Implemented Interfaces:
Serializable
public class ModificationScoring extends ExperimentObject
This class contains stores the modification localization scores.
Author:
Marc Vaudel
See Also:

  • Field Details

    • NOT_FOUND

      public static final int NOT_FOUND
      Index indicating that the modification was not found.
      See Also:

    • RANDOM

      public static final int RANDOM
      Index for a random location choice.
      See Also:

    • DOUBTFUL

      public static final int DOUBTFUL
      Index for a doubtful assignment.
      See Also:

    • CONFIDENT

      public static final int CONFIDENT
      Index for a confident assignment.
      See Also:

    • VERY_CONFIDENT

      public static final int VERY_CONFIDENT
      Index for a very confident assignment.
      See Also:

    • SEPARATOR

      public static final String SEPARATOR
      The separator used to separate locations in the modification location key.
      See Also:

  • Constructor Details

    • ModificationScoring

      public ModificationScoring()
      Default constructor Constructor.

    • ModificationScoring

      public ModificationScoring(String ptmName)
      Constructor.
      Parameters:
      ptmName - the name of the PTM of interest.

  • Method Details

    • getName

      public String getName()
      Returns the name of the inspected protein.
      Returns:
      the name of the inspected protein

    • getScoredSites

      public Set<Integer> getScoredSites()
      Returns a set of sites where a score is available.
      Returns:
      a set of sites where a score is available

    • setDeltaScore

      public void setDeltaScore(int site, double score)
      Sets the delta score at a given site. First amino acid is 1.
      Parameters:
      site - the modification site
      score - the delta score

    • getDeltaScore

      public double getDeltaScore(int site)
      Returns the delta score at a given site. First amino acid is 1.
      Parameters:
      site - the site of interest
      Returns:
      the attached delta score. 0 if not found.

    • setProbabilisticScore

      public void setProbabilisticScore(int site, double score)
      Sets the probabilistic score at a given site. First amino acid is 1.
      Parameters:
      site - the modification site
      score - the delta score

    • getProbabilisticScore

      public double getProbabilisticScore(int site)
      Returns the probabilistic score at a given site. First amino acid is 1.
      Parameters:
      site - the site of interest
      Returns:
      the attached probabilistic score. 0 if not found.

    • getProbabilisticSites

      public Set<Integer> getProbabilisticSites()
      Returns a set of sites where a probabilistic score is available
      Returns:
      a set of sites where a probabilistic score is available

    • getOrderedProbabilisticSites

      public ArrayList<Integer> getOrderedProbabilisticSites()
      Returns an ordered list of sites where the probabilistic score was used. Sites are ordered by decreasing score. In order to reduce systematic error, if sites score equally their order is random.
      Returns:
      a list of sites where the probabilistic score was used

    • getDSites

      public Set<Integer> getDSites()
      Returns a set of sites where a D-score is available
      Returns:
      a set of sites where a D-score is available

    • getOrderedDSites

      public ArrayList<Integer> getOrderedDSites()
      Returns an ordered list of sites where the D-score was used. Sites are ordered by decreasing score. In order to reduce systematic error, if sites score equally their order is random.
      Returns:
      a list of sites where the D-score was used

    • addAll

      public void addAll(ModificationScoring anotherScore)
      Adds all scores from another score if better.
      Parameters:
      anotherScore - another score

    • setSiteConfidence

      public void setSiteConfidence(int site, int confidenceLevel)
      Sets the confidence level of a modification site. 1 is the first amino acid.
      Parameters:
      site - the modification site
      confidenceLevel - the confidence level

    • getPtmLocationAtAA

      public HashMap<Integer,Integer> getPtmLocationAtAA()
      Returns the map of the localization. site > confidence level.
      Returns:
      the map of the localization

    • getAllPtmLocations

      public Set<Integer> getAllPtmLocations()
      Returns the sites of all localized PTMs.
      Returns:
      the sites of all localized PTMs

    • getOrderedPtmLocations

      public ArrayList<Integer> getOrderedPtmLocations()
      Returns sites of all localized PTMs ordered increasingly.
      Returns:
      sites of all localized PTMs ordered increasingly

    • getLocalizationConfidence

      public int getLocalizationConfidence(int site)
      Returns the confidence of the PTM localization.
      Parameters:
      site - the modification site
      Returns:
      the confidence of the localization as indexed by the static fields

    • getMinimalLocalizationConfidence

      public int getMinimalLocalizationConfidence()
      Returns the minimal confidence among the PTM sites of this scoring.
      Returns:
      the minimal confidence among the PTM sites of this scoring

    • getConfidentPtmLocations

      public ArrayList<Integer> getConfidentPtmLocations()
      Returns the confidently and very confidently localized PTMs.
      Returns:
      the confidently and very confidently localized PTMs

    • getSecondaryPtmLocations

      public ArrayList<Integer> getSecondaryPtmLocations()
      Returns the not found, randomly or doubtfully localized PTMs.
      Returns:
      the not found, randomly or doubtfully localized PTMs

    • getPtmLocations

      public ArrayList<Integer> getPtmLocations(int confidenceLevel)
      Returns the PTM locations at a given confidence level (see static fields).
      Parameters:
      confidenceLevel - the confidence level
      Returns:
      the PTM locations at the given confidence level

    • getPossibleConfidenceLevels

      public static String[] getPossibleConfidenceLevels()
      Convenience method returning all confidence levels as string.
      Returns:
      an array with all confidence levels as string

    • getConfidenceLevel

      public static String getConfidenceLevel(int index)
      Convenience method returning the given confidence level as a string.
      Parameters:
      index - the confidence level
      Returns:
      the corresponding string