public class PeptideProteinMapping extends Object
Modifier and Type | Field and Description |
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int |
fmIndexPosition
The position in the FM index.
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Constructor and Description |
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PeptideProteinMapping()
Empty default constructor.
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PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index)
Constructor.
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PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index,
ModificationMatch[] modificationMatches)
Constructor.
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PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index,
ModificationMatch[] modificationMatches,
PeptideVariantMatches peptideVariantMatches)
Constructor.
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Modifier and Type | Method and Description |
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int |
getIndex()
Returns the index on the protein.
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static HashMap<String,HashMap<String,int[]>> |
getPeptideProteinIndexesMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
Returns a map made from the given mappings containing the indexes of the
peptides in the protein sequences indexed by peptide sequence and protein
accession.
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static HashMap<String,HashSet<String>> |
getPeptideProteinMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
Returns a map made from the given mappings containing protein accessions
for every peptide sequence.
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static Collection<Peptide> |
getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings,
SequenceMatchingParameters sequenceMatchingPreferences)
Aggregates the given mapping into a list of peptides.
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String |
getPeptideSequence()
Returns the peptide sequence.
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PeptideVariantMatches |
getPeptideVariantMatches()
Returns eventual variants found.
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String |
getProteinAccession()
Returns the accession of the protein.
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ModificationMatch[] |
getVariableModifications()
Returns eventual modifications found.
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static HashMap<String,HashMap<Integer,PeptideVariantMatches>> |
getVariantMatches(ArrayList<PeptideProteinMapping> peptideProteinMappings)
Returns the variant matches summarized in a map indexed by protein
accession and peptide index on the protein sequence.
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public PeptideProteinMapping()
public PeptideProteinMapping(String proteinAccession, String peptideSequence, int index, ModificationMatch[] modificationMatches, PeptideVariantMatches peptideVariantMatches)
proteinAccession
- the accession of the proteinpeptideSequence
- the peptide sequenceindex
- the index on the proteinmodificationMatches
- eventual modification matchespeptideVariantMatches
- eventual sequence variantspublic PeptideProteinMapping(String proteinAccession, String peptideSequence, int index)
proteinAccession
- the accession of the proteinpeptideSequence
- the peptide sequenceindex
- the index on the proteinpublic PeptideProteinMapping(String proteinAccession, String peptideSequence, int index, ModificationMatch[] modificationMatches)
proteinAccession
- the accession of the proteinpeptideSequence
- the peptide sequenceindex
- the index on the proteinmodificationMatches
- modification matchespublic String getProteinAccession()
public String getPeptideSequence()
public int getIndex()
public ModificationMatch[] getVariableModifications()
public PeptideVariantMatches getPeptideVariantMatches()
public static HashMap<String,HashMap<String,int[]>> getPeptideProteinIndexesMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
peptideProteinMappings
- a list of peptide to protein mappingspublic static HashMap<String,HashSet<String>> getPeptideProteinMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)
peptideProteinMappings
- a list of peptide to protein mappingspublic static HashMap<String,HashMap<Integer,PeptideVariantMatches>> getVariantMatches(ArrayList<PeptideProteinMapping> peptideProteinMappings)
peptideProteinMappings
- the protein mappings to grouppublic static Collection<Peptide> getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings, SequenceMatchingParameters sequenceMatchingPreferences)
peptideProteinMappings
- a list of peptides to protein mappingssequenceMatchingPreferences
- the sequence matching preferencesCopyright © 2021. All rights reserved.