Index

_

__add_amino_acids() (in module src.alignment.alignment_utils) __get_surrounding_amino_acids() (in module src.alignment.alignment_utils)

__remove_amino_acids() (in module src.alignment.alignment_utils) __replace_ambiguous_hybrid() (in module src.alignment.hybrid_alignment) __split_hybrid() (in module src.utils)

A

align_b_y() (in module src.alignment.alignment) align_overlaps() (in module src.alignment.alignment_utils)

Alignments() (in module src.objects) all_perms_of_s() (in module src.utils) attempt_alignment() (in module src.alignment.alignment)

B

b_ions() (in module src.gen_spectra)

build() (in module src.database)

C

calc_masses() (in module src.gen_spectra)

cosine_similarity() (in module src.utils)

D

Database() (in module src.objects) DatabaseEntry() (in module src.objects) DEV_contains_truth_exact() (in module src.utils)

DEV_contains_truth_parts() (in module src.utils) DEVFallOffEntry() (in module src.objects) digest_score() (in module src.scoring.scoring)

E

extend_base_kmers() (in module src.alignment.alignment)

extend_non_hybrid() (in module src.alignment.alignment_utils) extract_protein_name() (in module src.database)

F

file_exists() (in module src.utils)

G

gen_min_ordering() (in module src.gen_spectra) gen_spectra() (in module src.gen_spectra) gen_spectrum() (in module src.gen_spectra) get_entry_by_name() (in module src.database)

get_parents() (in module src.alignment.alignment_utils) get_precursor() (in module src.gen_spectra) get_proteins_with_subsequence() (in module src.database) get_proteins_with_subsequence_ion() (in module src.database)

H

hashable_boundaries() (in module src.utils) hybrid_alignment() (in module src.alignment.hybrid_alignment)

hybrid_score() (in module src.scoring.scoring) HybridSequenceAlignment() (in module src.objects)

I

id_spectra() (in module src.identification) id_spectrum() (in module src.identification) is_dir() (in module src.utils)

is_fasta() (in module src.utils) is_file() (in module src.utils) is_json() (in module src.utils)

L

load_spectra() (in module src.preprocessing.preprocessing_utils)

M

make_database_set() (in module src.preprocessing.merge_search) make_dir() (in module src.utils) make_sparse_array() (in module src.utils) make_valid_csv_file() (in module src.utils) make_valid_dir_string() (in module src.utils) make_valid_fasta_file() (in module src.utils) make_valid_json_file() (in module src.utils)

make_valid_text_file() (in module src.utils) match_masses() (in module src.preprocessing.merge_search) match_precursor() (in module src.alignment.alignment_utils) max_mass() (in module src.gen_spectra) merge() (in module src.preprocessing.merge_search) mp_id_spectrum() (in module src.identification) MPSpectrumID() (in module src.objects)

O

optimized_compare_masses() (in module src.scoring.mass_comparisons)

overlap_intervals() (in module src.utils)

P

peak_filtering() (in module src.preprocessing.spectra_filtering) ppm_to_da() (in module src.utils)

precursor_distance() (in module src.scoring.scoring) predicted_len() (in module src.utils) predicted_len_precursor() (in module src.utils)

R

refine_alignments() (in module src.alignment.alignment)

relative_abundance_filtering() (in module src.preprocessing.spectra_filtering) replace_ambiguous_hybrids() (in module src.alignment.hybrid_alignment)

S

same_protein_alignment() (in module src.alignment.alignment) score_sequence() (in module src.scoring.scoring)

SequenceAlignment() (in module src.objects) Spectrum() (in module src.objects)

T

total_mass_error() (in module src.scoring.scoring)

Y

y_ions() (in module src.gen_spectra)