public class PSModificationScores extends DbObject implements UrParameter
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,
int originalRepresentativeSite,
int newRepresentativeSite)
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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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 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, int originalRepresentativeSite, int newRepresentativeSite)
modName
- the name of the modification of interestoriginalRepresentativeSite
- the original representative sitenewRepresentativeSite
- the new representative sitepublic 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 (0 is first amino acid) //@TODO:
check that it is 0 and not 1public 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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