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/* ingengraph.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: ingengraph.h
*
* Author: Fasika Aklilu
*
* Version Creation Date: 4/26/01
*
* $Revision: 6.6 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
#ifndef _INGENGRAPH_
#define _INGENGRAPH_
#ifdef __cplusplus
extern "C" {
#endif
#include <seqmgr.h>
#include <ncbi.h>
#include <vibrant.h>
#include <picture.h>
#include <viewer.h>
#include <objmgr.h>
#include <sequtil.h>
#include <explore.h>
#include <gather.h>
#include <seqport.h>
#include <sqnutils.h>
#include <alignmgr2.h>
#include <jsavlt.h>
/******************************************************
*
* defines for the Genome Viewer of UDV
*
******************************************************/
#define FEATURE_SEGMENT_MAXSIZE 500 /*a segment contains a max of 500 features*/
#define Ing_FEAT_LINEDECAL 20/* was 8 */ /*on the Feature Viewer, the line height is 8 pixels*/
#define Ing_FEAT_HEIGHT 2 /*on the Feature Viewer the height of a Feature is 3 pixels*/
#define LEVEL1_MAXNUM 20 /* top level segment contains max of 20 level 2 segments */
#define LEVEL2_MAXNUM 20 /* second level segment contains max of 20 level 3 segments */
#define COMPRESS_SCALE 500
#define Ing_black 121
#define Ing_red 122
#define Ing_blue 123
#define Ing_green 124
#define Ing_cyan 125
#define Ing_magenta 126
#define Ing_purple 127
#define Ing_yellow 128
#define Ing_grey 129
#define Ing_MAX 130
#define Ing_GENSCAN 110
#define ALIGN_ANNOT 111 /* alignment from running blast vs. db */
#define Ing_SPIDEY 112
#define ALIGN_FILE 113/* alignment from asn file */
#define ALIGN_BLAST 114/* alignment annotated on sequence */
#define ALIGN_BLAST2SEQ 115 /* alignment from running blast2seq */
#define Ing_ORF 116
#define Ing_SUMMARY 117
#define Ing_FEAT_TABLE 118
#define Ing_TBDL 119
#define Ing_SEQIDLISTFORSPIDEY 120
#define Ing_SEQIDLISTFORBLAST 121
#define Ing_DOTMATRIX 122
/******************************************************
*
* data structures for the Genome Viewer
*
******************************************************/
typedef struct gvpopfeat{/*data structure used to populate features viewer*/
SegmenT pictRuler;
SegmenT pictMain;
SegmenT CurrentSeg;
SegmenT seg1;
SegmenT seg2;
Uint1Ptr PNTR pClr;
Boolean showLabels;
Boolean bSaved;
Boolean bTrim;
Uint4 nSegs; /* number of subsegments below Current segment */
Uint4 nPrims; /* prim counter */
Uint4 nLevel3; /* level 3 segments counter */
Uint4 nLevel2; /* level 2 segments counter */
Uint4 nLevel1; /* level 1 segments counter */
ValNodePtr PopRowsList;
ValNodePtr vnp_top10; /* used to trim linked list */
ValNodePtr vnp_last;
ValNodePtr group1;
ValNodePtr group1_last;
ValNodePtr group2;
ValNodePtr group2_last;
ValNodePtr group3;
ValNodePtr group3_last;
Int4 nPopRows; /* feature row counter */
Int4 yBase;
Int4 scaleX;
Int4 max_label; /* width of largest label */
SeqLocPtr slp;
Int4 left;
Int4 right;
} IngPopFeat, PNTR IngPopFeatPtr;
typedef struct gvgraphdata{
/*font size*/
Int2 cxChar;
Int2 cyChar;
FonT hFnt;
/*values used to draw the rulers*/
Int2 SegBoxHeight;
Int2 SegRulerTick;
Int2 SegRulerIn;
Int4 DecalSegRuler;
Int4 DecalZoomRuler;
Uint1Ptr PNTR pClr;
} IngGraphData, PNTR IngGraphDataPtr;
typedef struct gvpopnames{/*used to populate the Segments in Viewer*/
VieweR viewer;
SegmenT seg;
Uint1Ptr seqbuf;
Int4 scaleX;
Uint1 comp;
Boolean bRegister;
Uint2 procID;
Uint2 userKey;
OMMessageFunc messagefunc;
Pointer data;
SeqLocPtr slp;
BioseqPtr bsp;
ValNodePtr slp_list;
Boolean bPopSlp;
Boolean bShowGC;
Boolean bLabels;
Boolean bTop;
Int4 idx;
Int4 left, right;
IngGraphDataPtr GrData;
} IngExploreSegs, PNTR IngExploreSegsPtr;
typedef struct ing_trackaligns{
ValNodePtr hidelist;
ValNodePtr showlist;
CharPtr PNTR namelist;
CharPtr PNTR hnamelist;
Boolean update;
Int4 showindex;
Int4 hideindex;
} IngTrackAligns, PNTR IngTrackAlignsPtr;
typedef struct ingseqannotdata{
Int4 sindex;
Int4 hindex;
ValNodePtr aln_hidelist;
ValNodePtr aln_showlist;
CharPtr PNTR aln_namelist;
CharPtr PNTR aln_hnamelist;
IngTrackAlignsPtr tap;
}IngSeqAnnotData;
typedef struct ing_entitylist{
ValNode *Sips; /* list of sips in SeqEntry */
Uint2 entityID;
Uint4 itemID;
Int4 bspcount;
struct ing_entitylist PNTR next;
} IngEntity, PNTR IngEntityPtr;
typedef struct win_data{
MenU Edit;
MenU Run;
MenU Options;
MenU Analysis;
MenU Annotate;
MenU Feat;
GrouP Goto;
IteM labels;
IteM mrnaorexons;
IteM GC;
} IngWinData, PNTR IngWinDataPtr;
typedef struct ing_genomeviewer{
WindoW hMain;
WindoW hReport;
GrouP gMain;
/*graphic elements*/
VieweR vRuler1;
VieweR vTop;
VieweR vRuler2;
VieweR vBottom;
SegmenT pictRuler1;
SegmenT pictTop;
SegmenT pictRuler2;
SegmenT pictBottom;
VieweR vZoom;
SegmenT pictZoom;
PrompT featInfo[4];
CharPtr defline;
CharPtr defline2;
GrouP deflineg;
PopuP pageControl;
Uint2 sel_entityID;
Uint4 sel_itemID;
GrouP Buttons;
IteM item_usenetwork;
Boolean update;
Boolean bOverviewSelected;
/*data to display*/
Uint2 procID;
Uint2 userKey;
Uint2 entityID;
Uint4 itemID;
Uint2 itemType;
BioseqPtr bsp;
Boolean bspIsLocked;
Int4 from;
Int4 to;
Int4 SeqLength;/* length of user specified region*/
Int4 bspLength; /* total sequence length */
Int4 scale_index;
Int4Ptr scale_array;
Int4 scaleX;
Int4 maxScaleX;
Boolean bMaxScale;
IngEntityPtr entity_list;
Int4 numseqs;
Int4 ZoomedVal;
Int4 last_feat_position_top;
Int4 last_feat_position_bottom;
Int2 TopHeight;
Int4 xposition;
Char title[50];
Boolean bLabels;
Boolean isExons;
Boolean user_defined;
SeqLocPtr slp;
IngGraphData GrData;
IngTrackAligns talign;
IngWinDataPtr d_Win;
/* variables for imported features -- from sequence analysis */
Boolean bDustExists;
Boolean bOrfExists;
Boolean bShowGC;
Pointer data;
Uint1Ptr seqbuf;
Uint1 comp;
LisT bsp_list; /* listbox of bsps */
SeqIdPtr cur_sip;
Int2 cur_target;
IteM imemory;
/* data info */
Int4 filetype; /* reading in output files */
Int2 nAnnotFeats;
/* zoom */
PrimitivE zoomFbar;
/*internal use only*/
Int4 idx;
Boolean bSegmented;
/* progress notice vars */
CharPtr progress_string;
Boolean progress_running;
Int4 progress_timer;
PrompT progress_prompt;
Char progress_counter[20];
} IngGenomeViewer , * IngGenomeViewerPtr;
extern Boolean IngfeatDefFilter[FEATDEF_MAX];/* filter parameter for SeqMgrExploreFeatures() */
extern Boolean IngfeatDefTrack2[FEATDEF_MAX];/* used by Ing_AddToOverviewPage() when scale is greater than COMPRESS_SCALE */
extern Uint1 IngfeatDefTrack[FEATDEF_MAX];/* track features 1=exists 2=exists and is visible */
/*******************************************************************************
Static Function Declarations
*******************************************************************************/
extern void Ing_AddGCRect(SegmenT seg, SeqIdPtr sip, Uint2 entityID, Uint4 itemID, Uint2 itemtype, Uint1Ptr seq, Int4 left, Int4 top, Int4 right, Int4 bottom, Int4 scaleX, Uint1 strand, Boolean needs_label, Boolean clickable, Int4 idx, Boolean bShowGC);
extern SegmenT Ing_PopulateSequinGraphic(SegmenT seg, BioseqPtr bsp, Uint2 entityID, Uint4 itemID, Int4 scaleX);
extern void Ing_AddRuler(SegmenT seg, Int4 height, Int4 xstart,Int4 xstop, Int4 scaleX, Int4 scaleY, Boolean add_whitespace);
extern void Ing_InitGrData(IngGraphDataPtr gdp);
extern Uint4 Ing_PopDetailedPage(BioseqPtr bsp, SegmenT pictBottom, Int4 left, Int4 right, Uint1Ptr PNTR pClr, Int4 scaleX, Int4 start_row, Boolean Labels, Boolean isExons, IngTrackAlignsPtr tap);
extern Uint4 Ing_PopOverviewPage(BioseqPtr bsp, SegmenT pictTop, Int4 left, Int4 right, Uint1Ptr PNTR pClr, Int4 maxScaleX, IngTrackAlignsPtr tap);
extern Uint1Ptr PNTR Ing_BuildColorTable(void);
extern Uint1Ptr PNTR Ing_FreeColorTable(Uint1Ptr PNTR pClr);
extern Uint1Ptr Ing_PutColor(Uint1 r, Uint1 g, Uint1 b);
extern Boolean LIBCALLBACK Ing_ExploreSegments(SeqLocPtr slp, SeqMgrSegmentContextPtr context);
extern void Ing_InitfeatDefFilter(void);
extern void Ing_SearchAli(SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent);
extern Uint8 Ing_BigEncodeIdxFeat (Uint4 val1,Uint4 val2);
extern void Ing_BigDecodeIdxFeat (Uint8 index_g, Uint4Ptr val1, Uint4Ptr val2);
extern Boolean Ing_PopOverviewRuler(VieweR vRuler1, SegmenT pictRuler1, BioseqPtr bsp, IngGraphData GrData, Int4 from, Int4 to, Uint1Ptr seqbuf, Int4 scaleX);
extern Int4 Ing_GetValue (TexT t);
#ifdef __cplusplus
}
#endif
#endif /* ndef _INGENGRAPH_ */
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