/* 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: 6.5 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #ifndef _INGENGRAPH_ #define _INGENGRAPH_ #ifdef __cplusplus extern "C" { #endif #include #include #include #include #include #include #include #include #include #include #include #include #include /****************************************************** * * 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; Uint2 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; Uint2 sel_itemID; GrouP Buttons; IteM item_usenetwork; Boolean update; Boolean bOverviewSelected; /*data to display*/ Uint2 procID; Uint2 userKey; Uint2 entityID; Uint2 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, Uint2 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, Uint2 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_ */