Uses of Class
com.compomics.util.experiment.identification.protein_inference.PeptideProteinMapping

Packages that use PeptideProteinMapping

Package	Description
com.compomics.cli.peptide_mapper	Command line for PeptideMapper.
com.compomics.util.experiment.identification.protein_inference	Classes related to protein inference.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.

Uses of PeptideProteinMapping in com.compomics.cli.peptide_mapper

Methods in com.compomics.cli.peptide_mapper with parameters of type PeptideProteinMapping

Modifier and Type	Method	Description
String	MappingWorker.flanking(PeptideProteinMapping peptideProteinMapping, FastaMapper peptideMapper)

Uses of PeptideProteinMapping in com.compomics.util.experiment.identification.protein_inference

Methods in com.compomics.util.experiment.identification.protein_inference that return types with arguments of type PeptideProteinMapping

Modifier and Type	Method	Description
ArrayList<PeptideProteinMapping>	FastaMapper.getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)	Returns the protein mappings for the given peptide sequence.
ArrayList<PeptideProteinMapping>	FastaMapper.getProteinMapping(String peptideSequence, SequenceMatchingParameters proteinInferencePreferences)	Returns the protein mapping in the FASTA file loaded in the sequence factory for the given peptide sequence in a map: peptide sequence found in the FASTA file | protein accession | list of indexes of the peptide sequence on the protein sequence.

Method parameters in com.compomics.util.experiment.identification.protein_inference with type arguments of type PeptideProteinMapping

Modifier and Type	Method	Description
static HashMap<String,HashMap<String,int[]>>	PeptideProteinMapping.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.
static HashMap<String,HashSet<String>>	PeptideProteinMapping.getPeptideProteinMap(ArrayList<PeptideProteinMapping> peptideProteinMappings)	Returns a map made from the given mappings containing protein accessions for every peptide sequence.
static Collection<Peptide>	PeptideProteinMapping.getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings, SequenceMatchingParameters sequenceMatchingPreferences)	Aggregates the given mapping into a list of peptides.
static HashMap<String,HashMap<Integer,PeptideVariantMatches>>	PeptideProteinMapping.getVariantMatches(ArrayList<PeptideProteinMapping> peptideProteinMappings)	Returns the variant matches summarized in a map indexed by protein accession and peptide index on the protein sequence.

Uses of PeptideProteinMapping in com.compomics.util.experiment.identification.protein_inference.fm_index

Methods in com.compomics.util.experiment.identification.protein_inference.fm_index that return types with arguments of type PeptideProteinMapping

Modifier and Type	Method	Description
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMapping(String peptide, SequenceMatchingParameters sequenceMatchingParameters)
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithoutVariants(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences, int indexPart)	Mapping tags against proteome without variants.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithoutVariants(String peptide, SequenceMatchingParameters seqMatchPref, int indexPart)	Exact mapping peptides against the proteome.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithVariants(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences, int indexPart)	Mapping tags against proteome with variants.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithVariantsFixed(String peptide, SequenceMatchingParameters seqMatchPref, int indexPart)	Variant tolerant mapping peptides against the proteome.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithVariantsGeneric(String peptide, SequenceMatchingParameters seqMatchPref, int indexPart)	Variant tolerant mapping peptides against the proteome.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithVariantsSpecific(String peptide, SequenceMatchingParameters seqMatchPref, int indexPart)	Variant tolerant mapping peptides against the proteome

Methods in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type PeptideProteinMapping

Modifier and Type	Method	Description
boolean	FMIndex.checkModificationPattern(PeptideProteinMapping peptideProteinMapping)	Checking if peptide-protein should be discarded due to pattern modification conflict.