Package | Description |
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com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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com.compomics.util.experiment.identification.spectrum_assumptions |
Implementations of the SpectrumIdentificationAssumption.
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Modifier and Type | Method and Description |
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TagAssumption |
SpectrumMatch.getBestTagAssumption()
Getter for the best tag assumption.
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Modifier and Type | Method and Description |
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java.util.stream.Stream<TagAssumption> |
SpectrumMatch.getAllTagAssumptions()
Returns a stream of all tag assumptions
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TreeMap<Double,ArrayList<TagAssumption>> |
SpectrumMatch.getAllTagAssumptions(int advocateId)
Returns all tag assumptions for the specified search engine indexed by
their score.
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HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> |
SpectrumMatch.getTagAssumptionsMap()
Returns the tag assumptions map: advocate id > score > list of
assumptions.
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Modifier and Type | Method and Description |
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void |
SpectrumMatch.addTagAssumption(int advocateId,
TagAssumption tagAssumption)
Add a hit.
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void |
SpectrumMatch.removeTagAssumption(TagAssumption tagAssumption)
Removes an assumption from the mapping.
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void |
SpectrumMatch.setBestTagAssumption(TagAssumption bestTagAssumption)
Setter for the best tag assumption.
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Modifier and Type | Method and Description |
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void |
SpectrumMatch.setTagAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> tagAssumptionsMap)
Sets the tag assumption map.
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Modifier and Type | Method and Description |
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TagAssumption |
TagAssumption.reverse(boolean yIon)
Returns a new TagAssumption instance where the tag is a reversed version
of this tag.
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Modifier and Type | Method and Description |
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ArrayList<TagAssumption> |
TagAssumption.getPossibleTags(boolean forwardIon,
int minCharge,
int maxCharge,
int maxIsotope)
Computes the possible tag assumptions which can be obtained from this one
by accounting for other charges and isotopes.
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