public interface FastaMapper
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
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> |
getProteinMapping(Tag tag,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
ArrayList<PeptideProteinMapping> getProteinMapping(String peptideSequence, SequenceMatchingParameters proteinInferencePreferences)
peptideSequence
- the peptide sequenceproteinInferencePreferences
- the sequence matching preferencesArrayList<PeptideProteinMapping> getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)
tag
- the tag to look for in the tree. Must contain a consecutive
amino acid sequence of longer or equal size than the initialTagSize of
the treesequenceMatchingPreferences
- the sequence matching preferencesCopyright © 2021. All rights reserved.