public class SpectrumMatch extends IdentificationMatch
IdentificationMatch.MatchType
NO_KEY
Constructor and Description |
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SpectrumMatch()
Constructor for the spectrum match.
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SpectrumMatch(String spectrumFile,
String spectrumTitle)
Constructor for the spectrum match.
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Modifier and Type | Method and Description |
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void |
addPeptideAssumption(int advocateId,
PeptideAssumption peptideAssumption)
Add a hit.
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void |
addTagAssumption(int advocateId,
TagAssumption tagAssumption)
Add a hit.
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HashSet<Integer> |
getAdvocates()
Returns the advocates supporting hits for this spectrum.
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java.util.stream.Stream<PeptideAssumption> |
getAllPeptideAssumptions()
Returns a stream of all peptide assumptions
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TreeMap<Double,ArrayList<PeptideAssumption>> |
getAllPeptideAssumptions(int advocateId)
Returns all peptide assumptions for the specified search engine indexed
by their score.
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java.util.stream.Stream<TagAssumption> |
getAllTagAssumptions()
Returns a stream of all tag assumptions
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TreeMap<Double,ArrayList<TagAssumption>> |
getAllTagAssumptions(int advocateId)
Returns all tag assumptions for the specified search engine indexed by
their score.
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PeptideAssumption |
getBestPeptideAssumption()
Getter for the best peptide assumption.
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TagAssumption |
getBestTagAssumption()
Getter for the best tag assumption.
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long |
getKey()
Returns the key of a match.
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static long |
getKey(String spectrumFile,
String spectrumTitle)
Returns a key to use for the spectrum match based on the file where the
spectrum was found and its title.
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HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> |
getPeptideAssumptionsMap()
Returns the peptide assumptions map: advocate id > score > list of
assumptions.
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String |
getSpectrumFile()
Returns the name of the file where this spectrum was found.
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String |
getSpectrumTitle()
Returns the title of the spectrum.
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HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> |
getTagAssumptionsMap()
Returns the tag assumptions map: advocate id > score > list of
assumptions.
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IdentificationMatch.MatchType |
getType()
Returns the type of match.
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boolean |
hasPeptideAssumption()
Indicates whether the spectrum match contains a peptide assumption.
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boolean |
hasPeptideAssumption(int advocateId)
Indicates whether the spectrum match contains a peptide assumption for
the given advocate (see the Advocate class).
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boolean |
hasTagAssumption()
Indicates whether the spectrum match contains a tag assumption.
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boolean |
hasTagAssumption(int advocateId)
Indicates whether the spectrum match contains a tag assumption for the
given advocate (see the Advocate class).
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void |
removePeptideAssumption(PeptideAssumption peptideAssumption)
Removes an assumption from the mapping.
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void |
removeTagAssumption(TagAssumption tagAssumption)
Removes an assumption from the mapping.
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void |
setBestPeptideAssumption(PeptideAssumption bestPeptideAssumption)
Setter for the best peptide assumption.
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void |
setBestTagAssumption(TagAssumption bestTagAssumption)
Setter for the best tag assumption.
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void |
setPeptideAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> peptideAssumptionsMap)
Sets the peptide assumption map.
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void |
setSpectrumFile(String spectrumFile)
Sets the spectrum file name.
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void |
setSpectrumTitle(String spectrumTitle)
Sets the spectrum title.
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void |
setTagAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> tagAssumptionsMap)
Sets the tag assumption map.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public void setPeptideAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> peptideAssumptionsMap)
peptideAssumptionsMap
- the peptide assumption mappublic void setTagAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> tagAssumptionsMap)
tagAssumptionsMap
- the tag assumption mappublic static long getKey(String spectrumFile, String spectrumTitle)
spectrumFile
- The name of the file containing the spectrum.spectrumTitle
- The title of the spectrum.public PeptideAssumption getBestPeptideAssumption()
public void setBestPeptideAssumption(PeptideAssumption bestPeptideAssumption)
bestPeptideAssumption
- the best peptide assumption for the spectrumpublic TagAssumption getBestTagAssumption()
public void setBestTagAssumption(TagAssumption bestTagAssumption)
bestTagAssumption
- the best tag assumption for the spectrumpublic String getSpectrumFile()
public void setSpectrumFile(String spectrumFile)
spectrumFile
- The spectrum file name.public String getSpectrumTitle()
public void setSpectrumTitle(String spectrumTitle)
spectrumTitle
- The spectrum title.public long getKey()
IdentificationMatch
getKey
in class IdentificationMatch
public HashSet<Integer> getAdvocates()
public TreeMap<Double,ArrayList<PeptideAssumption>> getAllPeptideAssumptions(int advocateId)
advocateId
- the desired advocate IDpublic TreeMap<Double,ArrayList<TagAssumption>> getAllTagAssumptions(int advocateId)
advocateId
- the desired advocate IDpublic java.util.stream.Stream<PeptideAssumption> getAllPeptideAssumptions()
public java.util.stream.Stream<TagAssumption> getAllTagAssumptions()
public HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> getPeptideAssumptionsMap()
public HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> getTagAssumptionsMap()
public void addPeptideAssumption(int advocateId, PeptideAssumption peptideAssumption)
advocateId
- the index of the advocate of the new hitpeptideAssumption
- the new identification assumptionpublic void addTagAssumption(int advocateId, TagAssumption tagAssumption)
advocateId
- the index of the advocate of the new hittagAssumption
- the new identification assumptionpublic IdentificationMatch.MatchType getType()
IdentificationMatch
getType
in class IdentificationMatch
public void removePeptideAssumption(PeptideAssumption peptideAssumption)
peptideAssumption
- the peptide assumption to removepublic void removeTagAssumption(TagAssumption tagAssumption)
tagAssumption
- the tag assumption to removepublic boolean hasPeptideAssumption()
public boolean hasTagAssumption()
public boolean hasPeptideAssumption(int advocateId)
advocateId
- The index of the advocatepublic boolean hasTagAssumption(int advocateId)
advocateId
- The index of the advocateCopyright © 2021. All rights reserved.