/usr/include/ncbi/salign.h is in libncbi6-dev 6.1.20110713-3ubuntu2.
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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 | /** salign.h
***
*** Header file containing external functions of salign.c
***
************/
#ifndef _SALIGN_
#define _SALIGN_
#include <ncbi.h>
#include <objseq.h>
#include <objsset.h>
#include <objalign.h>
/********************************************************
*** BandAlign Data Structure
*********************************************************/
typedef struct mash {
Uint1 band_method;
Int2 reward;
Int2 penalty;
Int4 gap_open;
Int4 gap_extend;
Int4 wordsize;
Int4 filter;
Int4 gap_x_dropoff;
Int4 gap_x_dropoff_final;
Boolean is_prot;
Boolean translate_prot;
SeqAlignPtr transalp;
Boolean use_gapped_blast;
CharPtr matrixname;
Int4 lg1_ext;
Int4 rg1_ext;
Int4 lg2_ext;
Int4 rg2_ext;
Int4 lg1_open;
Int4 lg2_open;
Int4 rg1_open;
Int4 rg2_open;
Int4 blast_threshold;
Uint1 choice_blastfilter;
Boolean splicing;
Boolean multidim;
Boolean map_align;
Boolean align_ends;
} Mash, PNTR MashPtr;
NLM_EXTERN MashPtr MashNew (Boolean is_prot);
NLM_EXTERN SeqAlignPtr SeqLocListToSeqAlign (ValNodePtr sqloc_list, Int2 choice, Pointer param);
NLM_EXTERN SeqLocPtr AlignmRNA2genomic (BioseqPtr bsp1, BioseqPtr bsp2);
NLM_EXTERN SeqAnnotPtr BlastBandAlignFromBlastSeqAlign (SeqAlignPtr salpblast, Boolean align_ends);
#endif
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