/usr/include/ncbi/udvseq.h is in libvibrant6-dev 6.1.20170106-2.
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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: udvseq.h
*
* Author: Patrick Durand
*
* Version Creation Date: 5/3/99
*
* $Revision: 6.21 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* $Log: udvseq.h,v $
* Revision 6.21 2006/07/13 17:06:39 bollin
* use Uint4 instead of Uint2 for itemID values
* removed unused variables
* resolved compiler warnings
*
* 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 <explore.h>
#include <ncbi.h>
#include <objfdef.h>
#include <objloc.h>
#include <objseq.h>
#include <seqport.h>
#include <sequtil.h>
#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;
Uint4 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,
Uint4Ptr val2);
NLM_EXTERN void UDV_BigDecodeIdxFeat (Uint8 index_g, Uint4Ptr 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_ */
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