/usr/lib/emboss/include/embnmer.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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 | #ifdef __cplusplus
extern "C"
{
#endif
/*
* This set of routines was written primarily for the compseq program.
* Feel free to use it for anything you want.
*
* compseq counts the frequency of n-mers (or words) in a sequence.
*
* The easiest way to do this was to make a big ajulong array
* to hold the counts of each type of word.
*
* I needed a way of converting a sequence word into an integer so that I
* could increment the appropriate element of the array.
* (embNmerNuc2int and embNmerProt2int)
*
* I also needed a way of converting an integer back to a short sequence
* so that I could display the word.
* (embNmerInt2nuc and embNmerInt2prot)
*
* embNmerGetNoElements returns the number of elements required to store the
* results.
* In other words it is the number of possible words of size n.
*
* Gary Williams
*
*/
#ifndef embnmer_h
#define embnmer_h
/*
** Prototype definitions
*/
ajulong embNmerNuc2int (const char *seq, ajint wordsize, ajint offset,
AjBool *otherflag);
ajint embNmerInt2nuc (AjPStr *seq, ajint wordsize,
ajulong value);
ajulong embNmerProt2int (const char *seq, ajint wordsize, ajint offset,
AjBool *otherflag, AjBool ignorebz);
ajint embNmerInt2prot (AjPStr *seq, ajint wordsize,
ajulong value, AjBool ignorebz);
AjBool embNmerGetNoElements (ajulong *no_elements,
ajint word, AjBool seqisnuc,
AjBool ignorebz);
/*
** End of prototype definitions
*/
#endif
#ifdef __cplusplus
}
#endif
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