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#include "../inst/include/Biostrings_defines.h"
#include <string.h>
#define INIT_STATIC_SYMBOL(NAME) \
{ \
if (NAME ## _symbol == NULL) \
NAME ## _symbol = install(# NAME); \
}
/* utils.c */
void _init_ByteTrTable_with_lkup(
ByteTrTable *byte_tr_table,
SEXP lkup
);
SEXP _new_lkup_from_ByteTrTable(const ByteTrTable *byte_tr_table);
void _init_byte2offset_with_INTEGER(
ByteTrTable *byte2offset,
SEXP bytes,
int error_on_dup
);
void _init_byte2offset_with_Chars_holder(
ByteTrTable *byte2offset,
const Chars_holder *seq,
const BytewiseOpTable *bytewise_match_table
);
TwobitEncodingBuffer _new_TwobitEncodingBuffer(
SEXP base_codes,
int buflength,
int endianness
);
void _reset_twobit_signature(TwobitEncodingBuffer *teb);
int _shift_twobit_signature(
TwobitEncodingBuffer *teb,
char c
);
int _get_twobit_signature(
TwobitEncodingBuffer *teb,
const Chars_holder *seq
);
int _get_twobit_signature_at(
TwobitEncodingBuffer *teb,
const Chars_holder *seq,
const int *at,
int at_length
);
/* RoSeqs_utils.c */
RoSeqs _alloc_RoSeqs(int nelt);
/* XString_class.c */
const ByteTrTable *get_enc_byte2code(const char *classname);
const ByteTrTable *get_dec_byte2code(const char *classname);
SEXP init_DNAlkups(SEXP enc_lkup, SEXP dec_lkup);
char _DNAencode(char c);
char _DNAdecode(char code);
SEXP init_RNAlkups(SEXP enc_lkup, SEXP dec_lkup);
char _RNAencode(char c);
char _RNAdecode(char code);
void _copy_CHARSXP_to_Chars_holder(
Chars_holder *dest,
SEXP src,
int start_in_src,
const int *lkup,
int lkup_length
);
SEXP _new_CHARSXP_from_Chars_holder(
const Chars_holder *x,
SEXP lkup
);
SEXP new_XString_from_CHARACTER(
SEXP classname,
SEXP x,
SEXP start,
SEXP width,
SEXP lkup
);
SEXP new_CHARACTER_from_XString(
SEXP x,
SEXP lkup
);
/* XStringSet_class.c */
int _get_XStringSet_length(SEXP x);
SEXP _get_XStringSet_width(SEXP x);
const char *_get_XStringSet_xsbaseclassname(SEXP x);
XStringSet_holder _hold_XStringSet(SEXP x);
int _get_length_from_XStringSet_holder(const XStringSet_holder *x_holder);
Chars_holder _get_elt_from_XStringSet_holder(
const XStringSet_holder *x_holder,
int i
);
XStringSet_holder _get_linear_subset_from_XStringSet_holder(
const XStringSet_holder *x_holder,
int offset,
int length
);
void _set_XStringSet_names(
SEXP x,
SEXP names
);
SEXP new_XStringSet_from_CHARACTER(
SEXP classname,
SEXP element_type,
SEXP x,
SEXP start,
SEXP width,
SEXP lkup
);
SEXP new_CHARACTER_from_XStringSet(
SEXP x,
SEXP lkup
);
RoSeqs _new_RoSeqs_from_XStringSet(
int nelt,
SEXP x
);
SEXP XStringSet_unlist(SEXP x);
/* XStringSetList_class.c */
XStringSetList_holder _hold_XStringSetList(SEXP x);
int _get_length_from_XStringSetList_holder(
const XStringSetList_holder *x_holder
);
XStringSet_holder _get_elt_from_XStringSetList_holder(
const XStringSetList_holder *x_holder,
int i
);
/* xscat.c */
SEXP XString_xscat(SEXP args);
SEXP XStringSet_xscat(SEXP args);
/* XStringSet_io.c */
SEXP fasta_index(
SEXP filexp_list,
SEXP nrec,
SEXP skip,
SEXP seek_first_rec,
SEXP lkup
);
SEXP read_XStringSet_from_fasta_blocks(
SEXP seqlength,
SEXP filexp_list,
SEXP nrec_list,
SEXP offset_list,
SEXP elementType,
SEXP lkup
);
SEXP write_XStringSet_to_fasta(
SEXP x,
SEXP filexp_list,
SEXP width,
SEXP lkup
);
SEXP fastq_geometry(
SEXP filexp_list,
SEXP nrec,
SEXP skip,
SEXP seek_first_rec
);
SEXP read_XStringSet_from_fastq(
SEXP filexp_list,
SEXP nrec,
SEXP skip,
SEXP seek_first_rec,
SEXP use_names,
SEXP elementType,
SEXP lkup
);
SEXP write_XStringSet_to_fastq(
SEXP x,
SEXP filexp_list,
SEXP qualities,
SEXP lkup
);
/* letter_frequency.c */
SEXP XString_letter_frequency(
SEXP x,
SEXP codes,
SEXP with_other
);
SEXP XStringSet_letter_frequency(
SEXP x,
SEXP collapse,
SEXP codes,
SEXP with_other
);
SEXP XString_letterFrequencyInSlidingView(
SEXP x,
SEXP view_width,
SEXP single_codes,
SEXP colmap,
SEXP colnames
);
SEXP XStringSet_letterFrequency(
SEXP x,
SEXP single_codes,
SEXP colmap,
SEXP colnames,
SEXP collapse
);
SEXP XString_oligo_frequency(
SEXP x,
SEXP width,
SEXP step,
SEXP as_prob,
SEXP as_array,
SEXP fast_moving_side,
SEXP with_labels,
SEXP base_codes
);
SEXP XStringSet_oligo_frequency(
SEXP x,
SEXP width,
SEXP step,
SEXP as_prob,
SEXP as_array,
SEXP fast_moving_side,
SEXP with_labels,
SEXP simplify_as,
SEXP base_codes
);
SEXP XStringSet_nucleotide_frequency_at(
SEXP x,
SEXP at,
SEXP as_prob,
SEXP as_array,
SEXP fast_moving_side,
SEXP with_labels,
SEXP base_codes
);
SEXP XStringSet_consensus_matrix(
SEXP x,
SEXP shift,
SEXP width,
SEXP with_other,
SEXP codes
);
SEXP XString_two_way_letter_frequency(
SEXP x,
SEXP y,
SEXP x_codes,
SEXP y_codes,
SEXP with_other
);
SEXP XStringSet_two_way_letter_frequency(
SEXP x,
SEXP y,
SEXP collapse,
SEXP x_codes,
SEXP y_codes,
SEXP with_other
);
SEXP XStringSet_two_way_letter_frequency_by_quality(
SEXP x,
SEXP y,
SEXP x_quality,
SEXP y_quality,
SEXP codes,
SEXP quality_codes,
SEXP with_other
);
/* gtestsim.c */
void gtestsim(
int *nrow,
int *ncol,
int *nrowt,
int *ncolt,
int *n,
int *b,
double *expected,
int *observed,
double *fact,
int *jwork,
double *results
);
/* translate.c */
SEXP DNAStringSet_translate(
SEXP x,
SEXP skip_code,
SEXP dna_codes,
SEXP lkup,
SEXP if_non_ambig,
SEXP if_ambig
);
/* replaceAt.c */
SEXP XString_replaceAt(
SEXP x,
SEXP at,
SEXP value
);
SEXP XStringSet_replaceAt(
SEXP x,
SEXP at,
SEXP value
);
/* replace_letter_at.c */
SEXP XString_replace_letter_at(
SEXP x,
SEXP at,
SEXP letter,
SEXP lkup,
SEXP if_not_extending,
SEXP verbose
);
SEXP XString_inplace_replace_letter_at(
SEXP x,
SEXP at,
SEXP letter,
SEXP lkup
);
/* inject_code.c */
SEXP XString_inject_code(
SEXP x,
SEXP start,
SEXP width,
SEXP code
);
/* unstrsplit_methods.c */
SEXP XStringSetList_unstrsplit(
SEXP x,
SEXP sep,
SEXP seqtype
);
/* SparseList_utils.c */
SEXP _SparseList_int2symb(int symb_as_int);
int _SparseList_symb2int(SEXP symbol);
SEXP _get_val_from_env(
SEXP symbol,
SEXP env,
int error_on_unbound_value
);
SEXP _get_val_from_SparseList(
int symb_as_int,
SEXP env,
int error_on_unbound_value
);
int _get_int_from_SparseList(
int symb_as_int,
SEXP env
);
void _set_env_from_IntAE(
SEXP env,
const IntAE *int_ae
);
void _set_env_from_IntAEAE(
SEXP env,
const IntAEAE *int_aeae
);
/* match_reporting.c */
int _get_match_storing_code(const char *ms_mode);
MatchBuf _new_MatchBuf(
int ms_code,
int nPSpair
);
void _MatchBuf_report_match(
MatchBuf *match_buf,
int PSpair_id,
int start,
int width
);
void _MatchBuf_flush(MatchBuf *match_buf);
void _MatchBuf_append_and_flush(
MatchBuf *match_buf1,
MatchBuf *match_buf2,
int view_offset
);
SEXP _MatchBuf_which_asINTEGER(const MatchBuf *match_buf);
SEXP _MatchBuf_counts_asINTEGER(const MatchBuf *match_buf);
SEXP _MatchBuf_starts_asLIST(const MatchBuf *match_buf);
SEXP _MatchBuf_ends_asLIST(const MatchBuf *match_buf);
SEXP _MatchBuf_as_Ranges(const MatchBuf *match_buf);
SEXP _MatchBuf_as_SEXP(
const MatchBuf *match_buf,
SEXP env
);
void _init_match_reporting(const char *ms_mode, int nPSpair);
void _set_active_PSpair(int PSpair_id);
void _set_match_shift(int shift);
void _report_match(int start, int width);
void _drop_reported_matches();
int _get_match_count();
SEXP _reported_matches_asSEXP();
MatchBuf *_get_internal_match_buf();
/* MIndex_class.c */
MIndex_holder _hold_MIndex(SEXP x);
int _get_length_from_MIndex_holder(const MIndex_holder *x_holder);
int _get_width0_elt_from_MIndex_holder(
const MIndex_holder *x_holder,
int i
);
IRanges_holder _get_elt_from_MIndex_holder(
const MIndex_holder *x_holder,
int i
);
SEXP ByPos_MIndex_endIndex(
SEXP x_high2low,
SEXP x_ends,
SEXP x_width0
);
SEXP SparseMIndex_endIndex(
SEXP x_ends_envir,
SEXP x_width0,
SEXP x_names,
SEXP all_names
);
SEXP ByPos_MIndex_combine(SEXP ends_listlist);
/* lowlevel_matching.c */
void _init_bytewise_match_tables();
const BytewiseOpTable *_select_bytewise_match_table(int fixedP, int fixedS);
int _nmismatch_at_Pshift(
const Chars_holder *P,
const Chars_holder *S,
int Pshift,
int max_nmis,
const BytewiseOpTable *bytewise_match_table
);
int _nedit_for_Ploffset(
const Chars_holder *P,
const Chars_holder *S,
int Ploffset,
int max_nedit,
int loose_Ploffset,
int *min_width,
const BytewiseOpTable *bytewise_match_table
);
int _nedit_for_Proffset(
const Chars_holder *P,
const Chars_holder *S,
int Proffset,
int max_nedit,
int loose_Proffset,
int *min_width,
const BytewiseOpTable *bytewise_match_table
);
SEXP XString_match_pattern_at(
SEXP pattern,
SEXP subject,
SEXP at,
SEXP at_type,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
SEXP ans_type,
SEXP auto_reduce_pattern
);
SEXP XStringSet_vmatch_pattern_at(
SEXP pattern,
SEXP subject,
SEXP at,
SEXP at_type,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
SEXP ans_type,
SEXP auto_reduce_pattern
);
SEXP XStringSet_dist_hamming(SEXP x);
/* match_pattern_boyermoore.c */
int _match_pattern_boyermoore(
const Chars_holder *P,
const Chars_holder *S,
int nfirstmatches,
int walk_backward
);
/* match_pattern_shiftor.c */
SEXP bits_per_long();
void _match_pattern_shiftor(
const Chars_holder *P,
const Chars_holder *S,
int max_nmis,
int fixedP,
int fixedS
);
/* match_pattern_indels.c */
void _match_pattern_indels(
const Chars_holder *P,
const Chars_holder *S,
int max_nmis,
int fixedP,
int fixedS
);
/* match_pattern.c */
void _match_pattern_XString(
const Chars_holder *P,
const Chars_holder *S,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
const char *algo
);
void _match_pattern_XStringViews(
const Chars_holder *P,
const Chars_holder *S,
SEXP views_start,
SEXP views_width,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
const char *algo
);
SEXP XString_match_pattern(
SEXP pattern,
SEXP subject,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
SEXP algorithm,
SEXP count_only
);
SEXP XStringViews_match_pattern(
SEXP pattern,
SEXP subject,
SEXP views_start,
SEXP views_width,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
SEXP algorithm,
SEXP count_only
);
SEXP XStringSet_vmatch_pattern(
SEXP pattern,
SEXP subject,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
SEXP algorithm,
SEXP ms_mode
);
/* match_PWM.c */
SEXP PWM_score_starting_at(
SEXP pwm,
SEXP subject,
SEXP starting_at,
SEXP base_codes
);
SEXP XString_match_PWM(
SEXP pwm,
SEXP subject,
SEXP min_score,
SEXP count_only,
SEXP base_codes
);
SEXP XStringViews_match_PWM(
SEXP pwm,
SEXP subject,
SEXP views_start,
SEXP views_width,
SEXP min_score,
SEXP count_only,
SEXP base_codes
);
/* find_palindromes.c */
SEXP find_palindromes(
SEXP x,
SEXP min_armlength,
SEXP max_looplength,
SEXP max_mismatch,
SEXP L2R_lkup
);
SEXP palindrome_arm_length(
SEXP x,
SEXP max_mismatch,
SEXP L2R_lkup
);
/* BitMatrix.c */
void _BitCol_set_val(
BitCol *bitcol,
BitWord val
);
BitCol _new_BitCol(
int nbit,
BitWord val
);
int _BitCol_get_bit(
const BitCol *bitcol,
int i
);
void _BitCol_set_bit(
BitCol *bitcol,
int i,
int bit
);
void _BitCol_A_gets_BimpliesA(
BitCol *A,
const BitCol *B
);
BitCol _BitMatrix_get_col(
const BitMatrix *bitmat,
int j
);
void _BitMatrix_set_col(
BitMatrix *bitmat,
int j,
const BitCol *bitcol
);
void _BitMatrix_set_val(
BitMatrix *bitmat,
BitWord val
);
BitMatrix _new_BitMatrix(
int nrow,
int ncol,
BitWord val
);
int _BitMatrix_get_bit(
const BitMatrix *bitmat,
int i,
int j
);
void _BitMatrix_set_bit(
BitMatrix *bitmat,
int i,
int j,
int bit
);
void _BitMatrix_Rrot1(BitMatrix *bitmat);
void _BitMatrix_grow1rows(
BitMatrix *bitmat,
const BitCol *bitcol
);
/* PreprocessedTB_class.c */
SEXP _get_PreprocessedTB_tb(SEXP x);
SEXP _get_PreprocessedTB_dups(SEXP x);
SEXP _get_PreprocessedTB_base_codes(SEXP x);
int _get_PreprocessedTB_length(SEXP x);
int _get_PreprocessedTB_width(SEXP x);
SEXP _get_PreprocessedTB_low2high(SEXP x);
SEXP _get_Twobit_sign2pos_tag(SEXP x);
SEXP _get_ACtree2_nodebuf_ptr(SEXP x);
SEXP _get_ACtree2_nodeextbuf_ptr(SEXP x);
void _init_ppdups_buf(int length);
void _report_ppdup(
int poffset,
int P_id
);
SEXP _get_ppdups_buf_asINTEGER();
/* match_pdict_utils.c */
TBMatchBuf _new_TBMatchBuf(
int tb_length,
int tb_width,
const int *head_widths,
const int *tail_widths
);
void _TBMatchBuf_report_match(
TBMatchBuf *buf,
int PSpair_id,
int end
);
void _TBMatchBuf_flush(TBMatchBuf *buf);
MatchPDictBuf _new_MatchPDictBuf(
SEXP matches_as,
int tb_length,
int tb_width,
const int *head_widths,
const int *tail_widths
);
void _MatchPDictBuf_report_match(
MatchPDictBuf *buf,
int PSpair_id,
int tb_end
);
void _MatchPDictBuf_flush(MatchPDictBuf *buf);
void _MatchPDictBuf_append_and_flush(
MatchBuf *buf1,
MatchPDictBuf *buf2,
int view_offset
);
HeadTail _new_HeadTail(
SEXP pdict_head,
SEXP pdict_tail,
SEXP pptb,
SEXP max_mismatch,
SEXP fixed,
int with_ppheadtail
);
void _match_pdict_flanks_at(
int key0,
SEXP low2high,
HeadTail *headtail,
const Chars_holder *S,
int tb_end,
int max_nmis,
int min_nmis,
int fixedP,
int fixedS,
MatchPDictBuf *matchpdict_buf
);
void _match_pdict_all_flanks(
SEXP low2high,
HeadTail *headtail,
const Chars_holder *S,
int max_nmis,
int min_nmis,
int fixedP,
int fixedS,
MatchPDictBuf *matchpdict_buf
);
/* match_pdict_Twobit.c */
SEXP build_Twobit(
SEXP tb,
SEXP pp_exclude,
SEXP base_codes
);
void _match_Twobit(
SEXP pptb,
const Chars_holder *S,
int fixedS,
TBMatchBuf *tb_matches
);
/* BAB_class.c */
SEXP IntegerBAB_new(SEXP max_nblock);
int *_get_BAB_nblock_ptr(SEXP x);
int *_get_BAB_lastblock_nelt_ptr(SEXP x);
SEXP _get_BAB_blocks(SEXP x);
SEXP _IntegerBAB_addblock(
SEXP x,
int block_length
);
/* match_pdict_ACtree2.c */
SEXP ACtree2_nodebuf_max_nblock();
SEXP ACtree2_nodeextbuf_max_nblock();
SEXP ACtree2_nnodes(SEXP pptb);
SEXP ACtree2_print_nodes(SEXP pptb);
SEXP ACtree2_summary(SEXP pptb);
SEXP ACtree2_build(
SEXP tb,
SEXP pp_exclude,
SEXP base_codes,
SEXP nodebuf_ptr,
SEXP nodeextbuf_ptr
);
SEXP ACtree2_has_all_flinks(SEXP pptb);
SEXP ACtree2_compute_all_flinks(SEXP pptb);
void _match_tbACtree2(
SEXP pptb,
const Chars_holder *S,
int fixedS,
TBMatchBuf *tb_matches
);
void _match_pdictACtree2(
SEXP pptb,
HeadTail *headtail,
const Chars_holder *S,
int max_nmis,
int min_nmis,
int fixedP,
int fixedS,
MatchPDictBuf *matchpdict_buf
);
/* match_pdict.c */
SEXP match_PDict3Parts_XString(
SEXP pptb,
SEXP pdict_head,
SEXP pdict_tail,
SEXP subject,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP fixed,
SEXP matches_as,
SEXP envir
);
SEXP match_XStringSet_XString(
SEXP pattern,
SEXP subject,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
SEXP algorithm,
SEXP matches_as,
SEXP envir
);
SEXP match_PDict3Parts_XStringViews(
SEXP pptb,
SEXP pdict_head,
SEXP pdict_tail,
SEXP subject,
SEXP views_start,
SEXP views_width,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP fixed,
SEXP matches_as,
SEXP envir
);
SEXP match_XStringSet_XStringViews(
SEXP pattern,
SEXP subject,
SEXP views_start,
SEXP views_width,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
SEXP algorithm,
SEXP matches_as,
SEXP envir
);
SEXP vmatch_PDict3Parts_XStringSet(
SEXP pptb,
SEXP pdict_head,
SEXP pdict_tail,
SEXP subject,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP fixed,
SEXP collapse,
SEXP weight,
SEXP matches_as,
SEXP envir
);
SEXP vmatch_XStringSet_XStringSet(
SEXP pattern,
SEXP subject,
SEXP max_mismatch,
SEXP min_mismatch,
SEXP with_indels,
SEXP fixed,
SEXP algorithm,
SEXP collapse,
SEXP weight,
SEXP matches_as,
SEXP envir
);
/* align_utils.c */
SEXP PairwiseAlignments_nmatch(
SEXP nchar,
SEXP nmismatch,
SEXP ninsertion,
SEXP ndeletion
);
SEXP AlignedXStringSet_nchar(SEXP alignedXStringSet);
SEXP AlignedXStringSet_align_aligned(
SEXP alignedXStringSet,
SEXP gapCode
);
SEXP PairwiseAlignmentsSingleSubject_align_aligned(
SEXP alignment,
SEXP gapCode,
SEXP endgapCode
);
SEXP align_compareStrings(
SEXP patternStrings,
SEXP subjectStrings,
SEXP maxNChar,
SEXP insertionCode,
SEXP deletionCode,
SEXP mismatchCode
);
/* pmatchPattern.c */
SEXP lcprefix(
SEXP s1_xp,
SEXP s1_offset,
SEXP s1_length,
SEXP s2_xp,
SEXP s2_offset,
SEXP s2_length
);
SEXP lcsuffix(
SEXP s1_xp,
SEXP s1_offset,
SEXP s1_length,
SEXP s2_xp,
SEXP s2_offset,
SEXP s2_length
);
/* align_pairwiseAlignment.c */
SEXP XStringSet_align_pairwiseAlignment(
SEXP pattern,
SEXP subject,
SEXP type,
SEXP typeCode,
SEXP scoreOnly,
SEXP gapOpening,
SEXP gapExtension,
SEXP useQuality,
SEXP substitutionArray,
SEXP substitutionArrayDim,
SEXP substitutionLookupTable,
SEXP fuzzyMatrix,
SEXP fuzzyMatrixDim,
SEXP fuzzyLookupTable
);
SEXP XStringSet_align_distance(
SEXP string,
SEXP type,
SEXP typeCode,
SEXP gapOpening,
SEXP gapExtension,
SEXP useQuality,
SEXP substitutionArray,
SEXP substitutionArrayDim,
SEXP substitutionLookupTable,
SEXP fuzzyMatrix,
SEXP fuzzyMatrixDim,
SEXP fuzzyLookupTable
);
/* align_needwunsQS.c */
SEXP align_needwunsQS(
SEXP s1,
SEXP s2,
SEXP mat,
SEXP mat_nrow,
SEXP lkup,
SEXP gap_cost,
SEXP gap_code
);
/* strutils.c (belonged originally to old matchprobes package) */
char compbase(char c);
SEXP MP_longestConsecutive(SEXP x, SEXP letter);
/* matchprobes.c (belonged originally to old matchprobes package) */
SEXP MP_matchprobes(SEXP query, SEXP records, SEXP probepos);
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