Compact descriptor of a peptide instance held by the FragmentIndex. More...

Collaboration diagram for FragmentIndex::Peptide:

Public Member Functions
	Peptide (UInt32 protein_idx, UInt32 modification_idx, std::pair< uint16_t, uint16_t > sequence, float precursor_mz)

Public Attributes
UInt32	protein_idx
	0-based index into FASTA entries provided to build(); identifies the source protein More...

UInt32	modification_idx_
	Index into variant list produced by ModifiedPeptideGenerator for this subsequence (0 = unmodified) More...

std::pair< uint16_t, uint16_t >	sequence_
	{start, length} within the source protein sequence (start is 0-based; length in residues) More...

float	precursor_mz_
	Mono-isotopic m/z at charge 1 (M+H)+ of this peptide; used for sorting/filtering. More...

Detailed Description

Compact descriptor of a peptide instance held by the FragmentIndex.

Field semantics and how they relate to the braced initializer lists used in tests {a, b, {c, d}, e}:

protein_idx .......... 'a' Index into the FASTA entries vector passed to build(); identifies the source protein.
modification_idx_ .... 'b' Index into the list of generated modification variants for the given unmodified subsequence. In tests, this maps to mod_peptides[modification_idx_] created by ModifiedPeptideGenerator.
sequence_ ............ '{c, d}' 0-based start offset and length (in residues) of the peptide subsequence within the protein. Note: length (d) is used like std::string::substr(start, length).
precursor_mz_ ........ 'e' Mono-isotopic m/z at charge 1 (M+H)+; used for ordering/slicing in the index. Many tests use a dummy value here since only ordering invariants are asserted.

Constructor & Destructor Documentation

inline

UInt32 modification_idx_

Index into variant list produced by ModifiedPeptideGenerator for this subsequence (0 = unmodified)

float precursor_mz_

Mono-isotopic m/z at charge 1 (M+H)+ of this peptide; used for sorting/filtering.

UInt32 protein_idx

0-based index into FASTA entries provided to build(); identifies the source protein

std::pair<uint16_t , uint16_t> sequence_

{start, length} within the source protein sequence (start is 0-based; length in residues)