public class IntermediateStructureCreator extends Object
Constructor and Description |
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IntermediateStructureCreator(int threads) |
Modifier and Type | Method and Description |
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protected void |
addCluster(Collection<IntermediateGroup> cluster)
Adds the given cluster information into the intermediate structure.
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IntermediatePeptide |
addPeptide(IntermediatePeptide peptide)
adds the given peptide to the peptides map
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void |
addPeptideToProteinConnection(Comparable peptideID,
String proteinAccession)
Connects the peptide with the protein.
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IntermediateProtein |
addProtein(IntermediateProtein protein)
adds the given protein to the proteins map
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void |
addProteinInformation(String proteinAccession,
IntermediateProtein newProtein)
potentially adds further information to a protein, coming from e.g.
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IntermediateStructure |
buildIntermediateStructure()
After the peptide and dbSeqeunce data is loaded, this method creates
the intermediate structure.
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protected Map<Comparable,Set<String>> |
getNextCluster()
Returns the next cluster in the clustered mapping of peptides to
proteins.
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int |
getNrPeptides() |
int |
getNrProteins() |
int |
getNrSpectrumIdentifications() |
IntermediatePeptide |
getPeptide(Comparable pepId)
getter for the peptide from the map with the given ID
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IntermediateProtein |
getProtein(Comparable proteinID)
getter for the protein from the map with the given ID
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boolean |
peptidesContains(Comparable peptideID)
returns true, if the peptides map already contains a peptide with the
given ID
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boolean |
proteinsContains(String accession)
returns true, if the proteins map already contains a protein with the
given accessions
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public boolean peptidesContains(Comparable peptideID)
peptideID
- public IntermediatePeptide addPeptide(IntermediatePeptide peptide)
peptide
- public IntermediatePeptide getPeptide(Comparable pepId)
pepId
- public boolean proteinsContains(String accession)
proteinID
- public IntermediateProtein addProtein(IntermediateProtein protein)
protein
- public void addProteinInformation(String proteinAccession, IntermediateProtein newProtein)
proteinAccession
- the accession of the protein, which should get
new informationnewProtein
- the protein, which may contain additional informationpublic IntermediateProtein getProtein(Comparable proteinID)
proteinID
- public void addPeptideToProteinConnection(Comparable peptideID, String proteinAccession)
peptideID
- proteinID
- public int getNrPeptides()
public int getNrProteins()
public int getNrSpectrumIdentifications()
public IntermediateStructure buildIntermediateStructure()
protected Map<Comparable,Set<String>> getNextCluster()
protected void addCluster(Collection<IntermediateGroup> cluster)
cluster
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