/usr/lib/emboss/include/embword.h is in emboss-lib 6.3.1-6ubuntu3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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extern "C"
{
#endif
#ifndef embWord_h
#define embWord_h
/* @data EmbPWordMatch ********************************************************
**
** NUCLEUS data structure for word matches
**
** @attr seq1start [ajuint] match start point in original sequence
** @attr seq2start [ajuint] match start point in comparison sequence
** @attr sequence [const AjPSeq] need in case we build multiple matches here
** so we know which one the match belongs to
** @attr length [ajint] length of match
** @attr Padding [char[4]] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EmbSWordMatch {
ajuint seq1start;
ajuint seq2start;
const AjPSeq sequence;
ajint length;
char Padding[4];
} EmbOWordMatch;
#define EmbPWordMatch EmbOWordMatch*
/* @data EmbPWord *************************************************************
**
** NUCLEUS data structure for words
**
** @attr fword [const char*] Original word
** @attr seqlocs [AjPTable] Table of word start positions in multiple sequences
** @attr count [ajint] Total number of locations in all sequences
** @attr Padding [char[4]] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct EmbSWord {
const char *fword;
AjPTable seqlocs;
ajint count;
char Padding[4];
} EmbOWord;
#define EmbPWord EmbOWord*
/* @data EmbPWordSeqLocs ******************************************************
**
** NUCLEUS data structure for word locations in a given sequence
**
** @attr seq [const AjPSeq] Sequence for word start positions
** @attr locs [AjPList] List of word start positions in the sequence
** @@
******************************************************************************/
typedef struct EmbSWordSeqLocs {
const AjPSeq seq;
AjPList locs;
} EmbOWordSeqLocs;
#define EmbPWordSeqLocs EmbOWordSeqLocs*
/* @data EmbPWordRK ***********************************************************
**
** Data structure that extends EmbPWord objects for efficient access
** by Rabin-Karp search. It is constructed using embWordInitRabinKarpSearch
** method for a given sequence-set.
**
** Possible improvements could be achieved by scanning all other words
** during preprocessing to find out a minimum length that can be skipped
** safely when a word is matched.
**
** The first 5 fields (seqindxs-nseqs) are set during initialisation,
** and the last 3 fields (nMatches, lenMatches, nSeqMatches) are calculated
** during search.
**
** @attr word [const EmbPWord] Original word object
** @attr seqindxs [ajuint*] Positions in the seqset
** for each sequence the word has been seen
** @attr nnseqlocs [ajuint*] Number of word start positions for each sequence
** @attr locs [ajuint**] List of word start positions for each sequence
** @attr hash [ajulong] Hash value for the word
** @attr nseqs [ajuint] Number of pattern-sequences word has been seen
** @attr nMatches [ajuint] Number of matches in query sequences
** @attr lenMatches [ajulong] Total length of extended matches
** @attr nSeqMatches [ajuint*] Number of matches
** recorded on per pattern-sequence base
** @@
******************************************************************************/
typedef struct EmbSWordRK {
const EmbPWord word;
ajuint* seqindxs;
ajuint* nnseqlocs;
ajuint** locs;
ajulong hash;
ajuint nseqs;
ajuint nMatches;
ajulong lenMatches;
ajuint* nSeqMatches;
} EmbOWordRK;
#define EmbPWordRK EmbOWordRK*
/*
** Prototype definitions
*/
AjPList embWordBuildMatchTable (const AjPTable seq1MatchTable,
const AjPSeq seq2, ajint orderit);
void embWordClear (void);
void embWordExit(void);
void embWordFreeTable(AjPTable *table);
AjBool embWordGetTable (AjPTable *table, const AjPSeq seq);
void embWordLength (ajint wordlen);
AjBool embWordMatchIter (AjIList iter, ajint* start1, ajint* start2,
ajint* len, const AjPSeq* seq);
EmbPWordMatch embWordMatchNew(const AjPSeq seq, ajuint seq1start,
ajuint seq2start, ajint length);
void embWordMatchListDelete (AjPList* plist);
void embWordMatchListPrint (AjPFile file, const AjPList list);
void embWordPrintTable (const AjPTable table);
void embWordPrintTableF (const AjPTable table, AjPFile outf);
void embWordPrintTableFI (const AjPTable table, ajint mincount,
AjPFile outf);
void embWordMatchListConvToFeat(const AjPList list,
AjPFeattable *tab1, AjPFeattable *tab2,
const AjPSeq seq1, const AjPSeq seq2);
void embWordMatchMin(AjPList matchlist);
void embWordUnused(void);
EmbPWordMatch embWordMatchFirstMax(const AjPList matches);
ajuint embWordRabinKarpSearch(const AjPStr sseq,
const AjPSeqset seqset,
const EmbPWordRK* patterns,
ajuint plen, ajuint nwords,
AjPList* l, ajuint* lastlocation,
AjBool checkmode);
ajuint embWordRabinKarpInit(const AjPTable table,
EmbPWordRK**, ajuint wordlen,
const AjPSeqset seqset);
__deprecated EmbPWordMatch embWordMatchListAppend(AjPList hitlist,
const AjPSeq seq,const ajuint seq1start,ajuint seq2start,ajint length);
/*
** End of prototype definitions
*/
#endif
#ifdef __cplusplus
}
#endif
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