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.
|
Modifier and Type | Method and Description |
---|---|
String |
MappingWorker.flanking(PeptideProteinMapping peptideProteinMapping,
FastaMapper peptideMapper) |
Modifier and Type | Method and Description |
---|---|
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.
|
ArrayList<PeptideProteinMapping> |
FastaMapper.getProteinMapping(Tag tag,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(String peptide,
SequenceMatchingParameters sequenceMatchingParameters) |
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(Tag tag,
SequenceMatchingParameters sequenceMatchingPreferences) |
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithoutVariants(String peptide,
SequenceMatchingParameters seqMatchPref,
int indexPart)
Exact mapping peptides against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithoutVariants(Tag tag,
SequenceMatchingParameters sequenceMatchingPreferences,
int indexPart)
Mapping tags against proteome without variants.
|
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
|
Modifier and Type | Method and Description |
---|---|
boolean |
FMIndex.checkModificationPattern(PeptideProteinMapping peptideProteinMapping)
Checking if peptide-protein should be discarded due to pattern
modification conflict.
|
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