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