public class IntermediatePeptide extends Object
Constructor and Description |
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IntermediatePeptide(String sequence)
Basic constructor, only initializes the sequence
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Modifier and Type | Method and Description |
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boolean |
addPeptideSpectrumMatch(IntermediatePeptideSpectrumMatch spectrumIdentification)
Adds the given spectrumIdentification to the peptide's PSMs
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static String |
computeID(String sequence)
Returns the ID computed by the given arguments.
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boolean |
equals(Object obj) |
void |
filterPSMs(List<AbstractFilter> filters)
Filters the PSMs using the given filters.
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List<IntermediatePeptideSpectrumMatch> |
getAllPeptideSpectrumMatches()
Getter for the PSMs, also the ones, which do not pass the filters.
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Set<IntermediateProtein> |
getAllProteins()
Returns all proteins (if the group is assigned)
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IntermediateGroup |
getGroup()
returns the group of this peptide
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Comparable |
getID()
Returns an identifier for the peptide
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Integer |
getNumberOfPeptideSpectrumMatches()
Getter for the number of PSMs.
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List<IntermediatePeptideSpectrumMatch> |
getPeptideSpectrumMatches()
Getter for the PSMs.
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ScoringItemType |
getPSMsScoringType(IntermediatePeptideSpectrumMatch psm)
Returns the
ScoringItemType of the PSM |
Set<IntermediatePeptideSpectrumMatch> |
getPSMsWithScoringType(ScoringItemType type)
Returns the PSMs with the given
ScoringItemType , which also pass
any filterings. |
Double |
getScore()
Getter for the peptide score.
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String |
getSequence()
Getter for the sequence.
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int |
hashCode() |
void |
removeAllScoringInformation()
Removes all information about which PSMs were used for scoring.
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void |
setGroup(IntermediateGroup group)
sets the group of this peptide
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void |
setPSMsScoringType(IntermediatePeptideSpectrumMatch psm,
ScoringItemType type)
Sets the scoring type of the stated PSM to the given
ScoringItemType . |
void |
setScore(Double score)
Sets the score of the peptide.
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public IntermediatePeptide(String sequence)
sequence
- public Comparable getID()
public static String computeID(String sequence)
This is for probable future integration of modifications
sequence
- public String getSequence()
public void setGroup(IntermediateGroup group)
group
- public IntermediateGroup getGroup()
public boolean addPeptideSpectrumMatch(IntermediatePeptideSpectrumMatch spectrumIdentification)
Is the PSM is added, it is also added to the filter passing PSMs.
spectrum
- public List<IntermediatePeptideSpectrumMatch> getPeptideSpectrumMatches()
If a passing set is created (i.e. data is filtered), only the passing PSMs are returned.
public Integer getNumberOfPeptideSpectrumMatches()
If a passing set is created (i.e. data is filtered), only the passing PSMs are returned.
public List<IntermediatePeptideSpectrumMatch> getAllPeptideSpectrumMatches()
public Set<IntermediateProtein> getAllProteins()
public void filterPSMs(List<AbstractFilter> filters)
filters
- public Double getScore()
public void setScore(Double score)
score
- public void setPSMsScoringType(IntermediatePeptideSpectrumMatch psm, ScoringItemType type)
ScoringItemType
.psmID
- public ScoringItemType getPSMsScoringType(IntermediatePeptideSpectrumMatch psm)
ScoringItemType
of the PSMpsmID
- public void removeAllScoringInformation()
public Set<IntermediatePeptideSpectrumMatch> getPSMsWithScoringType(ScoringItemType type)
ScoringItemType
, which also pass
any filterings.Copyright © 2015. All Rights Reserved.