/usr/include/ncbi/salsa.h is in libncbi6-dev 6.1.20120620-8.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information (NCBI)
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government do not place any restriction on its use or reproduction.
* We would, however, appreciate having the NCBI and the author cited in
* any work or product based on this material
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* ===========================================================================
*
* File Name: salsa.h
*
* Author: Colombe Chappey
*
* Version Creation Date: 1/27/96
*
* $Revision: 6.6 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
#ifndef _SALSA_
#define _SALSA_
#include <ncbi.h>
#include <objseq.h>
#include <objfdef.h>
#include <objmgr.h>
#include <gather.h>
#define COMPSEG 6
#define TypeEmpty 0
#define TypeSeqInt 1
#define TypeSeqId 2
#define TypeSeqLoc 3
#define TypeSelStruct 4
#define TypeSelEdStruct 5
#define NO_RESIDUE -9
#define GAP_RESIDUE -1
#define SEQ_VIEW 0
#define SEQ_EDIT 1
#define ALIGN_EDIT 2
#define BLOCK_EDIT 3
#define PRETTY_EDIT 4
#define TMP_BUFFERLENGTH 6000
#define TMP_EDITBUFFER 200
#define WINPERBUF 3
#define MAXCharLine 200
#define MAXLineWindow 150
#define LENGTHMAX 10000
#define SALSALENLIMIT 50000
#define HRZ_BORDER_WIDTH 4
#define VER_BORDER_WIDTH 4
#define EDIT_MARGIN_RIGHT 10
#define EDIT_MARGIN_BOT 5
#define SEQ_SHOW1 1
#define SEQ_SHOWALG 2
#define SEQ_FEAT0 0
#define SEQ_FEAT1 1
#define SEQ_FEATALL 2
#define SEQ_NUM0 0
#define SEQ_NUM1 1
#define SEQ_NUM2 2
#define SALSA_ND 0
#define SALSA_FASTA 1
#define SALSA_ASN1 2
#define SALSA_CONTIGUOUS 3
#define SALSA_FASTGAP 4
#define SALSA_PAUP 5
#define SALSA_MACAW 6
#define SALSA_INTERLEAVE 7
#define SALSA_NEXUS 8
#define SALSA_PHYLIP 9
#define SALSA_CLUSTALV 10
#define SALSA_SHWTXT 11
#define SALSAA_FASTA 12
#define SALSAA_CONTIGUOUS 13
#define SALSAA_FASTGAP 14
#define SALSAA_INTERLEAVE 15
#define SALSAA_PHYLIP 16
#define SALSAA_NEXUS 17
#define SALSAA_GCG 18
#define PRG_ANYALIGN 0
#define PRG_FASTA_IMPORT 1
#define PRGALIGNBANDBL 6
#define PRG_BLAST 7
#define PRGALIGNALL 8
#define PRGALIGNDEFAULT 10
#define PROPAG_SETSTOP 1
#define PROPAG_GETSTOP 2
#define LINE0 0
#define COLOR_STAR 0
#define COLOR_SCALE 1
#define COLOR_ID 2
#define COLOR_GAP 3
#define COLOR_ID_MASTER 4
#define COLOR_CDS 5
#define COLOR_SELECT 6
#define ALLPROTAA 1
#define MPROTAA 2
#define PUTPROT 3
#define EDITDEF_SCA 101
#define EDITDEF_SCB 102
#define EDITDEF_CPL 103
#define EDITDEF_RF1 104
#define EDITDEF_RF2 105
#define EDITDEF_RF3 106
#define EDITDEF_RF4 107
#define EDITDEF_RF5 108
#define EDITDEF_RF6 109
#define FEATDEF_TRSL 110
#define LINE_NOGAP 1
#define LINE_WITHGAP 2
#define LINE_ONLYGAP 3
#define PRINTID_GIcc 99
/******************************
** Types define
*******************************/
typedef struct seledstruct
{
Boolean dirty;
Boolean visible;
Uint2 entityID,
itemtype,
itemsubtype;
Uint4 itemID;
Uint4 bsp_itemID;
Pointer region;
Uint1 regiontype; /* 0 = not set
1 = SeqLocPtr of type SEQLOC_INT */
Char label[101];
ValNodePtr data;
Uint1 codonstart;
Int4 offset;
struct seledstruct PNTR prev,
PNTR next;
} SelEdStruct, PNTR SelEdStructPtr;
typedef struct seqparam {
Uint2 entityID;
Uint4 itemID;
Boolean complement;
Boolean rf[10];
Uint2 group;
SeqIdPtr sip_cons;
}
SeqParam, PNTR SeqParamPtr;
typedef struct alignstyle {
Handle font;
Int2 interline; /* space between lines */
Boolean marginwithindex; /* index in left margin */
Boolean marginwithIds; /* Ids in left margin */
Boolean marginwithfeatid;
Boolean marginwithpos; /* position in left margin */
Boolean marginwithgroup;
Int2 marginleft; /* left margin (char) */
Boolean draw_scale;
Boolean draw_bars;
Uint1 rowpcell; /* rows per cell */
Uint1 columnpcell; /* columns per cell */
Uint4 colorRefs[256];
} AlignStyle, PNTR AlignStylePtr;
typedef struct rectc {
Int2 left;
Int2 top;
Int2 right;
Int2 bottom;
} RecTc, PNTR RectcPtr;
typedef struct editaligndata {
Boolean Cn3D_On;
Pointer wdp;
Uint2 input_entityID,
input_itemtype;
Uint4 input_itemID;
Int2 seqnumber; /* number of sequences */
Int4 length; /* alignment length */
Boolean seg_bioseq;
Uint1 mol_type; /* NA, DNA, RNA, AA */
ValNodePtr anp_list; /* list of AlignNode / sequence */
ValNodePtr anp_graph;
SelEdStructPtr seq_info;
ValNodePtr sqloc_list; /* SeqLocPtr list on sequences*/
ValNodePtr bsqloc_list;
Int2 size_labels;
SelStruct master; /* entityID, item, SeqLoc of master seq*/
GatherRange gr;
SeqAnnotPtr sap_align; /* SeqAnnotPtr-SeqAlignPtr-CompSeg */
SeqAnnotPtr sap_original; /* SeqAnnotPtr-SeqAlignPtr-DenSeg */
SeqAnnotPtr sap1_original; /* SeqAnnotPtr-SeqAlignPtr-DenDiag */
SeqAlignPtr blocks; /* list of DenDiag to be aligned */
Boolean dirty;
/* Features */
Uint1 featOrder[FEATDEF_ANY]; /* features displayed */
Uint1 groupOrder[FEATDEF_ANY]; /* ? */
Uint1 gap_choice; /* used only for propagation features */
/* through the Dialog */
/* PaneL */
Int4 x, xoff, y, yoff;
Int4 ybutt;
Boolean vscrollbar_mode;
Int4 hoffset; /* horizontal offset - align coordi. */
Int4 voffset; /* vertical offset - align coordina. */
Int4 pnlLine; /* number of visible lines */
Int4 pnlWidth; /* number of visible characters*/
Int4 vPage; /* lines/page = pnlLine - 1 */
Int4 hPage; /* car/page = pnlWidth- 1 */
Int4 nlines;
Int4 curalignline;
SelStructPtr firstssp;
SelEdStructPtr lastses;
Int4 numberalignline;
Uint4Ptr item_id; /* array of itemID / line */
Uint2Ptr seqEntity_id; /* array of entityID / line */
Uint2Ptr itemtype; /* array of feattype / line */
Uint2Ptr itemsubtype; /* array of feattype / line */
Uint4Ptr alignline; /* array of alignment line index*/
/* text */
Handle font; /* font type */
Int2 ascent;
Int2 leading;
Int2 charw;
Int2 lineheight;
Uint4 colorRefs[256];
Int2 popcolor[10];
Int2 scaleheight; /* scale height= 2 x lineheight */
Int2 interline; /* space between lines */
RecTc margin; /* margin (pix) around sequences*/
Int2 marginleft; /* left margin (char) */
Int2 intersalpwidth;
/* buffer of aligned char - alignment coordinates */
SelStructPtr buffer;
SelStructPtr buffertail;
ValNodePtr linebuff;
Int4 minbufferlength; /* MIN (2 screens or .length) */
Int4 bufferlength; /* varies with edit inser-del */
Int4 bufferstart; /* in alignment coordinates */
Int4 editbuffer; /* length of edit buffer */
Int4Ptr colonne; /* seq position in the buffer */
/* visible part of the buffer - buffer coordinates */
Int4 visibleWidth; /* alignt length per line in Panel*/
Int4 visibleLength;
/* options */
Int2 styleNum;
SelStruct edit_item;
AlignStylePtr newstyle;
Boolean showfeat;
Boolean drawrfp, drawrfm;
Boolean drawcomplt;
Boolean draw_scale;
Boolean draw_bars;
Uint1 nscaleline;
Uint1 rowpcell; /* rows per cell */
Uint1 columnpcell; /* columns per cell */
Boolean displaytype;
Boolean charmode; /* diff y/n >>> SetStatus ItemI */
Boolean marginwithindex; /* index in left margin */
Boolean marginwithIds; /* Ids in left margin */
Boolean marginwithfeatid;
Boolean marginwithpos; /* position in left margin */
Boolean marginwithgroup;
Int4 edit_pos;
Int4 feat_pos;
Int4 start_select;
Uint1 click_feat;
Uint1 clickwhat;
Uint1 mouse_mode;
DenseDiagPtr select_block;
SelStruct caret; /* cursor within alignment */
Uint2 caret_line;
Uint2 feat_line;
Int4 caret_orig;
ValNodePtr feat;
ValNodePtr seqfeat;
ValNodePtr allseqfeat;
Uint4 nfeat;
Uint1 prot_mode;
Uint1 printid;
Int4 stoptransl;
ValNodePtr params;
Boolean spliteditmode;
SelEdStructPtr curfeat;
Uint1 align_format; /* PHYLIP, MACAW, FASTA, ..*/
Uint2 ngroup;
CharPtr current_pattern;
SelStructPtr match_pat;
SelStructPtr cur_pat;
/* dialog */
VoidPtr extra_data;
Int4 int4value2; /* any value from dialog */
Int4 int4value; /* any value from dialog */
Uint1 display_panel;
Boolean all_sequences;
Uint1 edit_mode;
Uint1 input_format;
Boolean draw_emptyline;
Char tmpfile [PATH_MAX]; /* path + filename */
} EditAlignData, PNTR EditAlignDataPtr;
typedef struct compressseg {
Int2 dim,
numseg;
SeqIdPtr ids;
Int4Ptr from;
Int4Ptr lens;
BoolPtr starts;
Uint1Ptr strands;
ScorePtr scores;
} CompSeg, PNTR CompSegPtr;
typedef struct propastruct {
SeqAnnotPtr sap;
Uint2 source_entityID,
source_bspitemID,
target_entityID,
target_bsp_itemID;
SeqEntryPtr target_sep,
source_sep;
ValNodePtr source_seqfeat,
target_seqfeat;
Uint1 gap_choice;
Int4 stoptransl;
Boolean keep_protID;
} PropaStruct, PNTR PropaStructPtr;
#endif
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