Interface FastaMapper
- All Known Implementing Classes:
FMIndex
public interface FastaMapper
Interface for a class mapping peptides and tags to a protein.
- Author:
- Marc Vaudel, Dominik Kopczynski
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Method Summary
Modifier and Type Method Description ArrayList<PeptideProteinMapping>
getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.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.
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Method Details
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getProteinMapping
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. 0 is the first amino acid.- Parameters:
peptideSequence
- the peptide sequenceproteinInferencePreferences
- the sequence matching preferences- Returns:
- the peptide to protein mapping: peptide sequence > protein accession > index in the protein An empty map if not
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getProteinMapping
ArrayList<PeptideProteinMapping> getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)Returns the protein mappings for the given peptide sequence. Peptide sequence | Protein accession | Index in the protein. An empty map if not found.- Parameters:
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 preferences- Returns:
- the protein mapping for the given peptide sequence
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