/usr/include/ncbi/needleman.h is in libncbi6-dev 6.1.20120620-7.
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 62 63 64 65 66 67 68 69 70 71 72 73 74 | /*
Compute the a global alignment between two SeqLocs using
the Needleman-Wunsch algorithm.
This algorithms requires temporary storage of order
N*M/4 bytes for the traceback. Do not use it for large
SeqLocs!!
The alignment is assumed to exist between the orientation specified
in the slp.. If one of the sequences need to be reversed, then the
slp should be on the minus strand.
In finding the optimal alignments end-gaps are scored.. but
they are not counted in the returned score.
The alignment returned will start and end at the endpoints of the
SeqLocs, but may include terminal gaps in order to do so.
One way to obtain the correct Karlin Altschul parameters is to
call the function in blastkar.c, given a valid matric name.
Int2 LIBCALL BlastKarlinGetMatrixValues(CharPtr matrix, Int4Ptr open, Int4Ptr extension, FloatHiPtr lambda, FloatHiPtr K, FloatHiPtr H)
if Kappa || Lambda ==0, defaults are provided.. appropriate for nucleotides.
$Revision: 6.7 $
$Log: needleman.h,v $
Revision 6.7 2000/10/31 21:20:05 vakatov
[WIN32] DLL'zation
Revision 6.6 2000/08/28 19:36:52 kans
moved revision log into comment section
Revision 6.5 2000/08/28 17:59:44 sicotte
added revision log
*/
#ifndef _NEEDLEMAN_
#define _NEEDLEMAN_
#include <ncbi.h>
#include <objseq.h>
#include <objsset.h>
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
#ifdef __cplusplus
extern "C" {
#endif
/* BLAST_Score must be a signed datatype
typedef Int4 BLAST_Score, PNTR BLAST_ScorePtr;
*/
NLM_EXTERN SeqAlignPtr LIBCALL NeedlemanWunschQuadraticByLoc(SeqLocPtr slp1,SeqLocPtr slp2, Int4 **matrix, Int4 gapOpen, Int4 gapExtend, Int4 *score, Nlm_FloatHi Kappa, Nlm_FloatHi Lambda);
Uint1Ptr FetchSequenceByLoc(SeqLocPtr slp,Int4* length,Int4* BspLength);
#ifdef __cplusplus
}
#endif
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif
|