/* salsa.h * =========================================================================== * * 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: 6.5 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #ifndef _SALSA_ #define _SALSA_ #include #include #include #include #include #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, itemID, itemtype, itemsubtype; Uint2 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; Uint2 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_itemID, input_itemtype; 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; Uint2Ptr 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; Uint2 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