public class PSModificationScores extends ExperimentObject implements UrParameter
Modifier and Type | Field and Description |
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static PSModificationScores |
dummy
Dummy scores.
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NO_KEY
Constructor and Description |
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PSModificationScores()
Constructor.
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Modifier and Type | Method and Description |
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void |
addAmbiguousModificationSites(int representativeSite,
HashMap<Integer,HashSet<String>> possibleModifications)
Adds a group of modifications to the mapping of ambiguous sites.
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void |
addConfidentModificationSite(String modName,
int modificationSite)
Adds a confident modification site.
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void |
addModificationScoring(String modName,
ModificationScoring modificationScoring)
Adds a scoring result for the modification of interest.
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void |
changeRepresentativeSite(String modName,
String originalModName,
int originalRepresentativeSite,
int newRepresentativeSite,
int nMod,
ModificationProvider modificationProvider)
Changes the representative site for a given ambiguously localized
modification in all maps.
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boolean |
containsModification(String modName)
Indicates whether a modification has been already scored.
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TreeSet<String> |
getAmbiguouslyLocalizedModifications()
Returns a list of modifications presenting at least an ambiguous site.
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HashMap<Integer,HashSet<String>> |
getAmbiguousModificationsAtRepresentativeSite(int representativeSite)
Returns the ambiguous modification assignments registered at the given
representative site in a map: secondary site > modifications.
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HashMap<Integer,HashSet<Integer>> |
getAmbiguousModificationsSites(String modName)
Returns the ambiguous modification sites registered for the given
modification.
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TreeSet<String> |
getConfidentlyLocalizedModifications()
Returns a list of modifications presenting at least a confident site.
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HashSet<String> |
getConfidentModificationsAt(int site)
Returns the main potential modifications at the given amino acid index.
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TreeSet<Integer> |
getConfidentSites()
Returns a list of all confident modification sites.
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HashSet<Integer> |
getConfidentSitesForModification(String modName)
Returns the confident sites for the given modification.
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HashSet<String> |
getModificationsAtRepresentativeSite(int site)
Returns the modifications which have a representative ambiguous site at
the given site.
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ModificationScoring |
getModificationScoring(String modName)
Returns the modification scoring for the desired modification (null if
none found).
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long |
getParameterKey()
This method returns the key of the parameter.
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TreeSet<Integer> |
getRepresentativeSites()
Returns a list of all representative sites of ambiguously localized
modifications.
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Set<String> |
getScoredModifications()
Returns a list of scored modifications.
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boolean |
isConfidentModificationSite(int site,
String modificationName)
Indicates whether a site is already registered as confident modification
site.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final PSModificationScores dummy
public void addModificationScoring(String modName, ModificationScoring modificationScoring)
modName
- the modification of interestmodificationScoring
- the corresponding scoringpublic ModificationScoring getModificationScoring(String modName)
modName
- the modification of interestpublic boolean containsModification(String modName)
modName
- the modification of interestpublic Set<String> getScoredModifications()
public void addConfidentModificationSite(String modName, int modificationSite)
modName
- the modification namemodificationSite
- the modification sitepublic void addAmbiguousModificationSites(int representativeSite, HashMap<Integer,HashSet<String>> possibleModifications)
representativeSite
- the representative site of this modification
grouppossibleModifications
- the possible modifications in a map: site
> modification namepublic void changeRepresentativeSite(String modName, String originalModName, int originalRepresentativeSite, int newRepresentativeSite, int nMod, ModificationProvider modificationProvider)
modName
- The name of the modification at the new site.originalModName
- The name of the modification at the original site.originalRepresentativeSite
- The original representative site.newRepresentativeSite
- The new representative site.nMod
- The occurrence of modifications of the exact same mass in
this peptide.modificationProvider
- The modification provider to use.public boolean isConfidentModificationSite(int site, String modificationName)
site
- the site of interestmodificationName
- the name of the modificationpublic HashSet<String> getConfidentModificationsAt(int site)
site
- the index in the sequence (1 is first amino acid)public HashSet<String> getModificationsAtRepresentativeSite(int site)
site
- the index in the sequence (0 is first amino acid)public HashSet<Integer> getConfidentSitesForModification(String modName)
modName
- the name of the modification of interestpublic HashMap<Integer,HashSet<String>> getAmbiguousModificationsAtRepresentativeSite(int representativeSite)
representativeSite
- the representative site of interestpublic HashMap<Integer,HashSet<Integer>> getAmbiguousModificationsSites(String modName)
modName
- the name of the modification of interestpublic TreeSet<Integer> getConfidentSites()
public TreeSet<Integer> getRepresentativeSites()
public TreeSet<String> getConfidentlyLocalizedModifications()
public TreeSet<String> getAmbiguouslyLocalizedModifications()
public long getParameterKey()
UrParameter
getParameterKey
in interface UrParameter
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