public class InferenceProteinGroup extends Object
Constructor and Description |
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InferenceProteinGroup(String id,
boolean considerModifications)
Basic constructor
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Modifier and Type | Method and Description |
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IntermediatePeptide |
addPeptide(IntermediatePeptide peptide)
Adds one IntermediatePeptide to the map of peptides
|
boolean |
addPeptides(Collection<IntermediatePeptide> peptides)
Adds a collection of IntermediatePeptides to the map of peptides
|
boolean |
addProtein(IntermediateProtein protein)
Adds one protein to the set of proteins
|
boolean |
addSubgroup(InferenceProteinGroup proteinGroup)
Adds a protein group to the subGroups of this group
|
boolean |
equals(Object obj) |
String |
getID() |
Set<IntermediatePeptide> |
getPeptides()
Returns the set of IntermediatePeptides
|
ScoringItemType |
getPeptidesScoringType(IntermediatePeptide peptide)
Returns the
ScoringItemType of the peptide |
Set<IntermediatePeptide> |
getPeptidesWithScoringType(ScoringItemType type)
Returns the peptides with the given
ScoringItemType |
Set<IntermediateProtein> |
getProteins()
Returns the set of proteins
|
Double |
getScore()
Getter for the protein score.
|
Set<InferenceProteinGroup> |
getSubGroups()
Returns the set of sub-groups
|
int |
hashCode() |
void |
removeAllScoringInformation()
Removes all information about which peptides were used for scoring.
|
void |
setPeptidesScoringType(IntermediatePeptide peptide,
ScoringItemType type)
Sets the scoring type of the stated peptide to the given
ScoringItemType . |
void |
setScore(Double score)
Sets the score of the protein.
|
public InferenceProteinGroup(String id, boolean considerModifications)
sequence
- public String getID()
public boolean addProtein(IntermediateProtein protein)
protein
- public Set<IntermediateProtein> getProteins()
public IntermediatePeptide addPeptide(IntermediatePeptide peptide)
specID
- public boolean addPeptides(Collection<IntermediatePeptide> peptides)
specID
- public Set<IntermediatePeptide> getPeptides()
public Double getScore()
public void setScore(Double score)
score
- public boolean addSubgroup(InferenceProteinGroup proteinGroup)
proteinGroup
- public Set<InferenceProteinGroup> getSubGroups()
public void setPeptidesScoringType(IntermediatePeptide peptide, ScoringItemType type)
ScoringItemType
.psmID
- public ScoringItemType getPeptidesScoringType(IntermediatePeptide peptide)
ScoringItemType
of the peptidepsmID
- public void removeAllScoringInformation()
public Set<IntermediatePeptide> getPeptidesWithScoringType(ScoringItemType type)
ScoringItemType
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