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1 /* ingengraph.h
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information (NCBI)
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
12 * Government do not place any restriction on its use or reproduction.
13 * We would, however, appreciate having the NCBI and the author cited in
14 * any work or product based on this material
15 *
16 * Although all reasonable efforts have been taken to ensure the accuracy
17 * and reliability of the software and data, the NLM and the U.S.
18 * Government do not and cannot warrant the performance or results that
19 * may be obtained by using this software or data. The NLM and the U.S.
20 * Government disclaim all warranties, express or implied, including
21 * warranties of performance, merchantability or fitness for any particular
22 * purpose.
23 *
24 * ===========================================================================
25 *
26 * File Name: ingengraph.h
27 *
28 * Author: Fasika Aklilu
29 *
30 * Version Creation Date: 4/26/01
31 *
32 * $Revision: 6.6 $
33 *
34 * File Description:
35 *
36 * Modifications:
37 * --------------------------------------------------------------------------
38 * Date Name Description of modification
39 * ------- ---------- -----------------------------------------------------
40 *
41 *
42 * ==========================================================================
43 */
44
45 #ifndef _INGENGRAPH_
46 #define _INGENGRAPH_
47
48 #ifdef __cplusplus
49 extern "C" {
50 #endif
51
52 #include <seqmgr.h>
53 #include <ncbi.h>
54 #include <vibrant.h>
55 #include <picture.h>
56 #include <viewer.h>
57 #include <objmgr.h>
58 #include <sequtil.h>
59 #include <explore.h>
60 #include <gather.h>
61 #include <seqport.h>
62 #include <sqnutils.h>
63 #include <alignmgr2.h>
64 #include <jsavlt.h>
65
66 /******************************************************
67 *
68 * defines for the Genome Viewer of UDV
69 *
70 ******************************************************/
71 #define FEATURE_SEGMENT_MAXSIZE 500 /*a segment contains a max of 500 features*/
72 #define Ing_FEAT_LINEDECAL 20/* was 8 */ /*on the Feature Viewer, the line height is 8 pixels*/
73 #define Ing_FEAT_HEIGHT 2 /*on the Feature Viewer the height of a Feature is 3 pixels*/
74 #define LEVEL1_MAXNUM 20 /* top level segment contains max of 20 level 2 segments */
75 #define LEVEL2_MAXNUM 20 /* second level segment contains max of 20 level 3 segments */
76 #define COMPRESS_SCALE 500
77
78 #define Ing_black 121
79 #define Ing_red 122
80 #define Ing_blue 123
81 #define Ing_green 124
82 #define Ing_cyan 125
83 #define Ing_magenta 126
84 #define Ing_purple 127
85 #define Ing_yellow 128
86 #define Ing_grey 129
87 #define Ing_MAX 130
88
89 #define Ing_GENSCAN 110
90 #define ALIGN_ANNOT 111 /* alignment from running blast vs. db */
91 #define Ing_SPIDEY 112
92 #define ALIGN_FILE 113/* alignment from asn file */
93 #define ALIGN_BLAST 114/* alignment annotated on sequence */
94 #define ALIGN_BLAST2SEQ 115 /* alignment from running blast2seq */
95 #define Ing_ORF 116
96 #define Ing_SUMMARY 117
97 #define Ing_FEAT_TABLE 118
98 #define Ing_TBDL 119
99 #define Ing_SEQIDLISTFORSPIDEY 120
100 #define Ing_SEQIDLISTFORBLAST 121
101 #define Ing_DOTMATRIX 122
102
103 /******************************************************
104 *
105 * data structures for the Genome Viewer
106 *
107 ******************************************************/
108
109
110 typedef struct gvpopfeat{/*data structure used to populate features viewer*/
111 SegmenT pictRuler;
112 SegmenT pictMain;
113 SegmenT CurrentSeg;
114 SegmenT seg1;
115 SegmenT seg2;
116 Uint1Ptr PNTR pClr;
117 Boolean showLabels;
118 Boolean bSaved;
119 Boolean bTrim;
120 Uint4 nSegs; /* number of subsegments below Current segment */
121 Uint4 nPrims; /* prim counter */
122 Uint4 nLevel3; /* level 3 segments counter */
123 Uint4 nLevel2; /* level 2 segments counter */
124 Uint4 nLevel1; /* level 1 segments counter */
125 ValNodePtr PopRowsList;
126 ValNodePtr vnp_top10; /* used to trim linked list */
127 ValNodePtr vnp_last;
128 ValNodePtr group1;
129 ValNodePtr group1_last;
130 ValNodePtr group2;
131 ValNodePtr group2_last;
132 ValNodePtr group3;
133 ValNodePtr group3_last;
134 Int4 nPopRows; /* feature row counter */
135 Int4 yBase;
136 Int4 scaleX;
137 Int4 max_label; /* width of largest label */
138 SeqLocPtr slp;
139 Int4 left;
140 Int4 right;
141 } IngPopFeat, PNTR IngPopFeatPtr;
142
143
144 typedef struct gvgraphdata{
145 /*font size*/
146 Int2 cxChar;
147 Int2 cyChar;
148 FonT hFnt;
149 /*values used to draw the rulers*/
150 Int2 SegBoxHeight;
151 Int2 SegRulerTick;
152 Int2 SegRulerIn;
153 Int4 DecalSegRuler;
154 Int4 DecalZoomRuler;
155 Uint1Ptr PNTR pClr;
156 } IngGraphData, PNTR IngGraphDataPtr;
157
158
159 typedef struct gvpopnames{/*used to populate the Segments in Viewer*/
160 VieweR viewer;
161 SegmenT seg;
162 Uint1Ptr seqbuf;
163 Int4 scaleX;
164 Uint1 comp;
165 Boolean bRegister;
166 Uint2 procID;
167 Uint2 userKey;
168 OMMessageFunc messagefunc;
169 Pointer data;
170 SeqLocPtr slp;
171 BioseqPtr bsp;
172 ValNodePtr slp_list;
173 Boolean bPopSlp;
174 Boolean bShowGC;
175 Boolean bLabels;
176 Boolean bTop;
177 Int4 idx;
178 Int4 left, right;
179 IngGraphDataPtr GrData;
180 } IngExploreSegs, PNTR IngExploreSegsPtr;
181
182
183 typedef struct ing_trackaligns{
184 ValNodePtr hidelist;
185 ValNodePtr showlist;
186 CharPtr PNTR namelist;
187 CharPtr PNTR hnamelist;
188 Boolean update;
189 Int4 showindex;
190 Int4 hideindex;
191 } IngTrackAligns, PNTR IngTrackAlignsPtr;
192
193
194 typedef struct ingseqannotdata{
195 Int4 sindex;
196 Int4 hindex;
197 ValNodePtr aln_hidelist;
198 ValNodePtr aln_showlist;
199 CharPtr PNTR aln_namelist;
200 CharPtr PNTR aln_hnamelist;
201 IngTrackAlignsPtr tap;
202 }IngSeqAnnotData;
203
204
205
206
207 typedef struct ing_entitylist{
208 ValNode *Sips; /* list of sips in SeqEntry */
209 Uint2 entityID;
210 Uint4 itemID;
211 Int4 bspcount;
212 struct ing_entitylist PNTR next;
213 } IngEntity, PNTR IngEntityPtr;
214
215
216 typedef struct win_data{
217 MenU Edit;
218 MenU Run;
219 MenU Options;
220 MenU Analysis;
221 MenU Annotate;
222 MenU Feat;
223 GrouP Goto;
224 IteM labels;
225 IteM mrnaorexons;
226 IteM GC;
227 } IngWinData, PNTR IngWinDataPtr;
228
229 typedef struct ing_genomeviewer{
230 WindoW hMain;
231 WindoW hReport;
232 GrouP gMain;
233 /*graphic elements*/
234 VieweR vRuler1;
235 VieweR vTop;
236 VieweR vRuler2;
237 VieweR vBottom;
238 SegmenT pictRuler1;
239 SegmenT pictTop;
240 SegmenT pictRuler2;
241 SegmenT pictBottom;
242 VieweR vZoom;
243 SegmenT pictZoom;
244 PrompT featInfo[4];
245 CharPtr defline;
246 CharPtr defline2;
247 GrouP deflineg;
248 PopuP pageControl;
249 Uint2 sel_entityID;
250 Uint4 sel_itemID;
251 GrouP Buttons;
252 IteM item_usenetwork;
253 Boolean update;
254 Boolean bOverviewSelected;
255 /*data to display*/
256 Uint2 procID;
257 Uint2 userKey;
258 Uint2 entityID;
259 Uint4 itemID;
260 Uint2 itemType;
261 BioseqPtr bsp;
262 Boolean bspIsLocked;
263 Int4 from;
264 Int4 to;
265 Int4 SeqLength;/* length of user specified region*/
266 Int4 bspLength; /* total sequence length */
267 Int4 scale_index;
268 Int4Ptr scale_array;
269 Int4 scaleX;
270 Int4 maxScaleX;
271 Boolean bMaxScale;
272 IngEntityPtr entity_list;
273 Int4 numseqs;
274 Int4 ZoomedVal;
275 Int4 last_feat_position_top;
276 Int4 last_feat_position_bottom;
277 Int2 TopHeight;
278 Int4 xposition;
279 Char title[50];
280 Boolean bLabels;
281 Boolean isExons;
282 Boolean user_defined;
283 SeqLocPtr slp;
284 IngGraphData GrData;
285 IngTrackAligns talign;
286 IngWinDataPtr d_Win;
287 /* variables for imported features -- from sequence analysis */
288 Boolean bDustExists;
289 Boolean bOrfExists;
290 Boolean bShowGC;
291 Pointer data;
292 Uint1Ptr seqbuf;
293 Uint1 comp;
294 LisT bsp_list; /* listbox of bsps */
295 SeqIdPtr cur_sip;
296 Int2 cur_target;
297 IteM imemory;
298 /* data info */
299 Int4 filetype; /* reading in output files */
300 Int2 nAnnotFeats;
301 /* zoom */
302 PrimitivE zoomFbar;
303 /*internal use only*/
304 Int4 idx;
305 Boolean bSegmented;
306 /* progress notice vars */
307 CharPtr progress_string;
308 Boolean progress_running;
309 Int4 progress_timer;
310 PrompT progress_prompt;
311 Char progress_counter[20];
312 } IngGenomeViewer , * IngGenomeViewerPtr;
313
314
315
316 extern Boolean IngfeatDefFilter[FEATDEF_MAX];/* filter parameter for SeqMgrExploreFeatures() */
317
318 extern Boolean IngfeatDefTrack2[FEATDEF_MAX];/* used by Ing_AddToOverviewPage() when scale is greater than COMPRESS_SCALE */
319
320 extern Uint1 IngfeatDefTrack[FEATDEF_MAX];/* track features 1=exists 2=exists and is visible */
321
322 /*******************************************************************************
323
324 Static Function Declarations
325
326 *******************************************************************************/
327 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);
328
329 extern SegmenT Ing_PopulateSequinGraphic(SegmenT seg, BioseqPtr bsp, Uint2 entityID, Uint4 itemID, Int4 scaleX);
330
331 extern void Ing_AddRuler(SegmenT seg, Int4 height, Int4 xstart,Int4 xstop, Int4 scaleX, Int4 scaleY, Boolean add_whitespace);
332
333 extern void Ing_InitGrData(IngGraphDataPtr gdp);
334
335 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);
336 extern Uint4 Ing_PopOverviewPage(BioseqPtr bsp, SegmenT pictTop, Int4 left, Int4 right, Uint1Ptr PNTR pClr, Int4 maxScaleX, IngTrackAlignsPtr tap);
337
338 extern Uint1Ptr PNTR Ing_BuildColorTable(void);
339 extern Uint1Ptr PNTR Ing_FreeColorTable(Uint1Ptr PNTR pClr);
340
341 extern Uint1Ptr Ing_PutColor(Uint1 r, Uint1 g, Uint1 b);
342
343 extern Boolean LIBCALLBACK Ing_ExploreSegments(SeqLocPtr slp, SeqMgrSegmentContextPtr context);
344
345 extern void Ing_InitfeatDefFilter(void);
346 extern void Ing_SearchAli(SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent);
347 extern Uint8 Ing_BigEncodeIdxFeat (Uint4 val1,Uint4 val2);
348 extern void Ing_BigDecodeIdxFeat (Uint8 index_g, Uint4Ptr val1, Uint4Ptr val2);
349 extern Boolean Ing_PopOverviewRuler(VieweR vRuler1, SegmenT pictRuler1, BioseqPtr bsp, IngGraphData GrData, Int4 from, Int4 to, Uint1Ptr seqbuf, Int4 scaleX);
350 extern Int4 Ing_GetValue (TexT t);
351
352
353
354 #ifdef __cplusplus
355 }
356 #endif
357
358 #endif /* ndef _INGENGRAPH_ */
359 |
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