/* udvseq.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: udvseq.h * * Author: Patrick Durand * * Version Creation Date: 5/3/99 * * $Revision: 6.20 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * $Log: udvseq.h,v $ * Revision 6.20 2000/07/08 20:43:55 vakatov * Get all "#include" out of the 'extern "C" { }' scope; other cleanup... * * Revision 6.19 2000/04/13 13:57:33 durand * allowed udv to display reverse complement sequence * * Revision 6.18 2000/02/17 15:54:36 durand * use ~ for an unaligned gap and - for an aligned gap * * Revision 6.17 2000/02/03 15:55:14 hurwitz * added constructor and destructor for MsaTxtDisp * * Revision 6.16 2000/01/24 19:37:18 durand * add field szEditSeq in ParaG * * Revision 6.15 1999/12/02 13:47:32 durand * add new function for Entrez sequence viewer * * Revision 6.14 1999/11/03 13:46:15 durand * add UDV_GetStrandinPGP, UDV_GetStrandinPGPList and UDV_GetBspRangeinPGPList for DDV * * Revision 6.13 1999/10/29 14:14:53 durand * add text styles for DDV * * Revision 6.12 1999/10/20 13:13:54 durand * add new fields in data structure for DDV * * Revision 6.11 1999/10/04 19:52:56 durand * add new text MSA_TXT_STYLE_2 * * Revision 6.9 1999/09/16 18:51:53 durand * move MsaTxtDisp struct from pgppop.h to udvseq.h * * Revision 6.8 1999/09/07 19:39:18 durand * don't display special features * * Revision 6.7 1999/07/30 20:08:28 durand * updates for the new Entrez graphical viewer * * Revision 6.6 1999/06/08 21:21:16 durand * update ParaG structure * * Revision 6.5 1999/06/08 17:02:54 durand * add bspGeneticCode to bspinfo data structure * * Revision 6.4 1999/06/07 15:10:18 durand * add LOG line to keep track of the history * * * * ========================================================================== */ #ifndef _UDVSEQ_ #define _UDVSEQ_ #include #include #include #include #include #include #include #ifdef __cplusplus extern "C" { #endif /******************************************************************************* The major element of this module is: paragraph (or ParaG) This module is Vibrant free and can be used by non-vibrant software. *******************************************************************************/ /***************************************************************************** Structure of a ParaG 10 20 30 Line 0 . | . | . | Line 1 1 GFDEDJSHHF DHGCJFDHCGNJFGJDHFGJ Line 3 |===>......===>.....===>| Line 4 /\/\/\/\ >------< ^ Line n Line 0: numerical scale Line 1: ticks (minor: . ; major: |) Line 3: left scale (if needed) + the sequence Line 4: features Line n: features *****************************************************************************/ /******************************************************************************* DEFINES *******************************************************************************/ /*Error value; if Feature Index failed*/ #define INDEX_CREATION_ERROR FALSE /***************************************************************************** text styles *****************************************************************************/ #define MSA_TXT_STYLE_SEQ 1 /*sequence type */ #define MSA_TXT_STYLE_GAP 2 /*gap type */ #define MSA_TXT_STYLE_NONE 3 /*nothing */ #define MSA_TXT_STYLE_1 4 /*style 1 = 5 "space" char. */ #define MSA_TXT_STYLE_REG_ALIGN 5 /*aligned region */ #define MSA_TXT_STYLE_REG_UNALIGN 6 /*unaligned region */ #define MSA_TXT_STYLE_2 7 /*for a disc. ali, display unaligned seq.*/ #define MSA_TXT_STYLE_UAGAP 8 /*gap type, unaligned regions */ #define SPACER_TXT_BLANK 5 /*use with MSA_TXT_STYLE_1*/ /*text justification for UnAligned region; used only by DDV */ #define DISP_JUST_LEFT ((Uint1)1) #define DISP_JUST_RIGHT ((Uint1)2) #define DISP_JUST_CENTER ((Uint1)3) #define DISP_JUST_SPLIT ((Uint1)4) /******************************************************************************* STRUCTURES *******************************************************************************/ /***************************************************************************** text to display in a MSA_ParaG; line descriptor *****************************************************************************/ typedef struct msatxtdisp { Int4 from; /*bioseq coord - zero-based */ Int4 to; /*or used to compute if gap size */ Int4 SegID; /*identifiers of the Indexed SeqAlign*/ Int4 BspID; Boolean IsGap; /*display a gap */ Boolean IsUnAligned;/*unaligned region */ Uint1 TextStyle; /*seqence/gap_text/gap/... */ Uint1 strand; /*plus, minus, etc.*/ } MsaTxtDisp, PNTR MsaTxtDispPtr; typedef struct parag {/*Paragraph information*/ Int4 NumOrder; /*ParaG graphical values*/ Int4 StartLine; /*this ParaG starts at this line*/ Int4 nLines; /*and contains nLines (scale+seq+feat)*/ Int4 StartLetter; /*first letter of the bioseq to show*/ Int4 StopLetter; /*last letter of the bioseq to show*/ ValNodePtr pFeatList; /*list of itemID,index (Feature Index values)*/ ValNodePtr ptxtList;/*text to draw - MSA*/ SeqIdPtr sip;/*identification of the bioseq - MSA*/ Char *szEditSeq; /*used by DDV only for editi*/ Int4 OccupyTo; /*used to populate features; vertical disp*/ Int2 MinLine; /*used to populate features;horz display*/ Int2 nFeatLines; /*number of lines with features*/ Int2 nFeat; /*number of features*/ Int2 nTrans; /*number of translation*/ Uint1 ScaleStyle;/*scale type (top/left/...)-MSA*/ } ParaG, PNTR ParaGPtr; /*structure used to initialize ParaG with features*/ typedef struct paragfeaturesinloc{ ValNodePtr ParaG_head; ValNodePtr ParaG_next_head; ValNodePtr ParaG_last_head; Int4 OccupyTo[500]; Int4 nTotLines_new; /*Int2 rcP_top;*/ Int4 nFeat; Int2 LineH; Boolean ShowFeatures; Uint1 DispType; Int4 cumOffset; Int4 bsp_part_length; } ParaGFeaturesInLoc,PNTR ParaGFeaturesInLocPtr; typedef struct bspinfo { /*general data*/ Uint2 bsp_entityID; Uint2 bsp_itemID; Uint2 bsp_itemType; BioseqPtr bsp; /* set to NULL if uninitialized */ Char bspName[41]; Char bspAccNum[21]; Char bspRepr[21]; Char bspMol[21]; Boolean bspMolNuc; Char bspTopo[21]; Char bspStrand[21]; Char bspDataType[21]; CharPtr bspGeneticCode;/* set to NULL if uninitialized */ Int4 bspLength; SeqPortPtr spp; /* set to NULL if uninitialized */ SeqIdPtr sip; /* set to NULL if uninitialized */ /*SAM specific data*/ Int4 BspID; /*Sequence Buffer*/ Int4 StartBuf; /*buffer start here in the sequence*/ Int4 StopBuf; /*buffer stop here... (0 based values)*/ Int2 LengthBuf; /*buffer size*/ CharPtr SeqBuf; /*buffer sequence*/ ValNodePtr PgpStartBuf;/*Pgp where start buffer is located*/ struct bspinfo *next; }BspInfo, PNTR BspInfoPtr; /******************************************************************************* FUNCTIONS DECLARATION (see .c module for a complete description) *******************************************************************************/ NLM_EXTERN MsaTxtDispPtr UDV_MsaTxtDispNew(MsaTxtDispPtr pTxtDisp); NLM_EXTERN MsaTxtDispPtr UDV_MsaTxtDispFree(MsaTxtDispPtr pTxtDisp); /*BSP information*/ NLM_EXTERN void UDV_ReadBspDataForViewer(BspInfoPtr bsp_i); /*Feature management*/ NLM_EXTERN void UDV_DecodeIdxFeat (Uint4 index_g, Uint2Ptr val1, Uint2Ptr val2); NLM_EXTERN void UDV_BigDecodeIdxFeat (Uint8 index_g, Uint2Ptr val1, Uint2Ptr val2, Uint2Ptr val3, Uint2Ptr val4); NLM_EXTERN Uint4 UDV_EncodeIdxFeat (Uint2 val1,Uint2 val2); NLM_EXTERN Uint8 UDV_BigEncodeIdxFeat (Uint2 val1,Uint2 val2,Uint2 val3,Uint2 val4); NLM_EXTERN SeqMgrFeatContextPtr UDV_ConvertFeatContext( SeqMgrFeatContextPtr context,Int4 cumOffset,Int4 bsp_part_length); NLM_EXTERN Boolean UDV_IsTranslationNeeded(SeqMgrFeatContextPtr context, ParaGPtr pgp); NLM_EXTERN Boolean LIBCALLBACK UDV_ParaGFTableFeatures (SeqFeatPtr sfp, SeqMgrFeatContextPtr context); NLM_EXTERN Uint2 UDV_CreateOneFeatureIndex(Uint2 entityID_seq, BioseqPtr bsp,Boolean bReverse); NLM_EXTERN void UDV_FreeListParaG(ValNodePtr PNTR vnp_head); NLM_EXTERN ValNodePtr UDV_CreateParaGList(Int2 nCharByLine, Int4 bsp_length,Int4 from,Int4 to, Boolean ShowTop,Boolean ShowTick,Boolean ShowSequence, Boolean ShowBlank,Int4Ptr nTotL,ValNodePtr ParaG_head); NLM_EXTERN Boolean UDV_PopulateParaGFeatures(BioseqPtr bsp, ValNodePtr ParaG_vnp,Boolean ShowFeatures,Int4Ptr nTotL, Uint4 DispType,Int2Ptr nFeatFound); NLM_EXTERN Boolean UDV_PopParaGFeaturesEx(BioseqPtr bsp,ValNodePtr ParaG_vnp, Boolean ShowFeatures,Int4Ptr nTotL,Uint4 DispType,Int2Ptr nFeatFound, BoolPtr FeatDefTable,Int4 from_bsp,Int4 to_bsp); /*Sequence reader*/ NLM_EXTERN CharPtr UDV_Read_SequenceEx (SeqIdPtr sip, Int4 from, Int4 to, Boolean IsProt,Int2 len,Uint1 strand); NLM_EXTERN CharPtr UDV_Read_Sequence (SeqIdPtr sip, Int4 from, Int4 to, Boolean IsProt,Int2 len); NLM_EXTERN void UDV_ComputeBspCoordRangeinPGP(ParaGPtr pgp,Int4Ptr from, Int4Ptr to); NLM_EXTERN void UDV_GetStrandinPGP(ParaGPtr pgp,Uint1Ptr strand); NLM_EXTERN void UDV_GetStrandinPGPList(ValNodePtr pgp_list,Uint1Ptr strand); NLM_EXTERN void UDV_GetBspRangeinPGPList(ValNodePtr pgp_list, Int4Ptr bsp_start,Int4Ptr bsp_stop); NLM_EXTERN Int4 UDV_RevertBioSeqCoord(Int4 bsp_coord,Int4 bsp_length); #ifdef __cplusplus } #endif #endif /* ndef _UDVSEQ_ */