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root/gclib/gfview/FXGView.h
Revision: 45
Committed: Tue Sep 6 18:19:20 2011 UTC (8 years, 6 months ago) by gpertea
File size: 13732 byte(s)
Log Message:
added gfview files

Line File contents
1 /********************************************************************************
2 * *
3 * (light) Table W i d g e t *
4 * *
5 *********************************************************************************/
6 #ifndef FXCLVIEW_H
7 #define FXCLVIEW_H
8 #include "GList.hh"
9 #include <ctype.h>
10 #include "LayoutParser.h"
11 #define MISMATCH_CLRIDX 16
12 #define NOCTG_CLRIDX 16
13
14 struct FXTimer;
15
16 struct CScale {
17 double sx;
18 double sy;
19 };
20
21 struct CRect {
22 double x,y;
23 double w,h;
24 CRect() {
25 x=0;y=0;w=0;h=0;
26 }
27 CRect(FXint ax,FXint ay,FXint aw,FXint ah) {
28 x=ax;y=ay;w=aw;h=ah;
29 }
30 CRect(const FXRectangle& r) {
31 x=r.x;y=r.y;w=r.w;h=r.h;
32 }
33 int ix() { return (int)x; };
34 int iy() { return (int)y; };
35 int iw() { return (int)w; };
36 int ih() { return (int)h; };
37 };
38
39 class FXGView;
40 class ClSeq;
41 /*
42 class ClAlign {
43 public:
44 ClSeq* seq1; //pointers to ClSeq objects sharing this overlap
45 ClSeq* seq2;
46 FXint l1,r1; // left/right overlap coordinates on seq1
47 FXint l2,r2; // left/right overlap coordinates on seq2
48 FXdouble pid;
49 FXint score;
50 FXdouble pvalue;
51 ClAlign(ClSeq* nseq1, ClSeq* nseq2,
52 FXint nl1, FXint nr1, FXint nl2, FXint nr2,
53 FXdouble npid,FXint nscore,FXdouble npvalue) {
54 seq1=nseq1;seq2=nseq2; l1=nl1; r1=nr1;
55 l2=nl2; r2=nr2; pid=npid; score=nscore; pvalue=npvalue;
56 }
57 bool operator==(const ClAlign& s) const {
58 return pvalue==s.pvalue;
59 }
60 bool operator<(const ClAlign& s) const {
61 return pvalue<s.pvalue;
62 }
63 bool operator>(const ClAlign& s) const {
64 return pvalue>s.pvalue;
65 }
66 };*/
67
68
69 class ClSeqSegment {
70 public:
71 char splL, splR;
72 FXint xL,xR; // left/right column coordinates in the layout
73 FXint clipL,clipR; // left/right end clipping length
74 FXint len() { return xR-xL+1; }
75 int seqofs; //offset to the first nucleotide of this segment in the sequence string
76 ClSeqSegment(FXint xl, FXint xr, FXint cl=0, FXint cr=0,
77 char sl=0, char sr=0, int segpos=0) {
78 xL=xl;xR=xr;
79 clipL=cl;clipR=cr;
80 splL=sl;splR=sr;
81 seqofs=segpos;
82 }
83 /*
84 bool operator==(const ClSeqSegment& s) const {
85 return xL==s.xL;
86 }
87 bool operator<(const ClSeqSegment& s) const {
88 return xL<s.xL;
89 }
90 bool operator>(const ClSeqSegment& s) const {
91 return xL>s.xL;
92 }*/
93 };
94
95
96
97 class ClSeq {
98 public:
99 FXGView* view;
100 //GList<ClAlign> aligns; //list of pointers to ClAlign objects
101 FXString name;
102 //FXString sequence; //nt sequence itself!
103 char* sequence; //nt sequence could be in fact pulled from the contig sequence
104 // e.g. in the case of GFF files
105 FXString comment; //any annotation given
106 FXint len; //total length of sequence [in chars = column span],
107 //includes clipping
108 //if segmented: total span of all segments+inter-segment gaps
109 FXint slen; //like len, but without intron (sum of segment lengths)
110 int numsegs; //numsegs MUST be at least 1
111 // >1 means segmented!
112 ClSeqSegment* segs; //array of seq segments -- with at least one element!
113 FXint cl_xpos; //left position in cluster [in chars] (to be determined)
114 FXint cl_ypos; //line order number in cluster (to be determined)
115 unsigned int ins, dels; //gaps and deletions for this within the assembly
116 FXint clipL;
117 FXint clipR;
118 short group; //or track_id for GFF files
119 int cdsofs; //offset of cds start, relative to the beginning of this ClSeq
120 unsigned char reversed;
121 unsigned char isET;
122 FXint flag;
123 ClSeq(FXGView* v, const char* vname, FXint vlen, FXint offs=0,
124 bool minus=false, int l_clip=0, int r_clip=0, const char* seq=NULL,
125 unsigned int ains=0, unsigned int adels=0) {
126 name=vname;
127 len=vlen;
128 //sequence=seq;
129 sequence=Gstrdup(seq); //no need to make a copy?
130 view=v;
131 flag=0;
132 group = -1;
133 cdsofs=0;
134 clipL=l_clip;
135 clipR=r_clip;
136 cl_xpos=offs;
137 cl_ypos=-1;
138 ins=ains;
139 numsegs=0;
140 segs=NULL;
141 addSegment(offs,offs+len-1,clipL, clipR);
142 reversed=minus?1:0;
143
144 isET= (name.find("np|")>=0 || name.find("et|")>=0 ||
145 name.find("egad|")>=0)?1:0;
146 dels=adels;
147 }
148 void addSegment(int xl, int xr, int clipl=0, int clipr=0,
149 char lspl=0, char rspl=0, int seqp=0) {
150 GREALLOC(segs,(numsegs+1)*sizeof(ClSeqSegment));
151 segs[numsegs].xL=xl; segs[numsegs].xR=xr;
152 segs[numsegs].clipL=clipl;
153 segs[numsegs].clipR=clipr;
154 segs[numsegs].splL=lspl;
155 segs[numsegs].splR=rspl;
156 segs[numsegs].seqofs=seqp;
157 slen+=xr-xl+1;
158 numsegs++;
159 }
160 ~ClSeq() {
161 GFREE(segs);
162 GFREE(sequence);
163 }
164 ClSeq(FXGView* v, LytSeqInfo* seqinfo, const char* seq=NULL);
165 //FXbool InRect(const CRect& rect, CRect& seqrect);
166 //for testing if repainting is needed for this object
167 //rect is in pixels, but already offset to the whole cluster area
168
169 //sort by y coordinate
170 void calcViewRect(CRect& seqrect); //compute the sequence position
171 //within the view
172 void calcSegView(int segidx, CRect& segrect);//compute a seq segment's position
173 //within the view
174 bool operator==(const ClSeq& s) const {
175 return (name==s.name);
176 }
177 bool operator>(const ClSeq& s) const {
178 return name>s.name;
179 }
180 bool operator<(const ClSeq& s) const {
181 return name<s.name;
182 }
183 };
184
185 // utility class for layout compaction:
186 // a collection of these must always be stored and kept in cl_ypos order
187 class CLayoutRow {
188 public:
189 GList<ClSeq> seqs; //sequences shown on this row
190 int rpos; //coordinate for the righmost end for any of seqs
191 //(where the room starts)
192 CLayoutRow(ClSeq* s, int idx): seqs(false,false,false) {
193 s->cl_ypos=idx;
194 seqs.Add(s);
195 rpos=s->cl_xpos + s->len;
196 }
197
198 void addSeq(ClSeq* s, int idx) {
199 s->cl_ypos=idx;
200 seqs.Add(s);
201 rpos=s->cl_xpos + s->len;
202 }
203
204 char getNuc(int c) {
205 for (int i=0;i<seqs.Count(); i++) {
206 ClSeq* s=seqs[i];
207 if (c<s->cl_xpos) return 0;
208 if (c>=s->cl_xpos+s->clipL && c<s->cl_xpos+s->len-s->clipR)
209 //return s->sequence.empty() ? ' ' :
210 return s->sequence==NULL ? ' ' :
211 toupper(s->sequence[c-s->cl_xpos]);
212 // toupper(s->getNuc(c-s->cl_xpos));
213 }
214 return 0;
215 }
216
217 bool operator==(const CLayoutRow& s) const {
218 return this==&s;
219 }
220 bool operator<(const CLayoutRow& s) const {
221 return this<&s;
222 }
223 bool operator>(const CLayoutRow& s) const {
224 return this>&s;
225 }
226 };
227
228 //layout column info:
229 //this is extended to include SNP candidate detection
230
231 struct NTColumn {
232 char letter;
233 int count;
234 };
235
236 class ColumnData {
237 public:
238 char letter; //the consensus letter
239 int thickness; //how many active layers in this column
240 int mismatches; //how many mismatches among these
241 NTColumn ntdata[5]; //sorted - largest counts first!
242 int nN;
243 int gap;
244 ColumnData() {
245 letter=0;
246 thickness=0;
247 mismatches=0;
248 memset(&ntdata,0,5*sizeof(NTColumn));
249 nN=0;
250 gap=0;
251 }
252 bool operator==(const ColumnData& s) const {
253 return this==&s;
254 }
255 bool operator<(const ColumnData& s) const {
256 return this<&s;
257 }
258 bool operator>(const ColumnData& s) const {
259 return this>&s;
260 }
261 };
262
263 class FXAPI FXGView : public FXScrollArea {
264 FXDECLARE(FXGView)
265 friend class ClSeq;
266 protected:
267 FXFont *font; // Font
268 FXFont *seqfont; // Font
269 FXColor textColor; // Text color
270 FXImage *backbuf;
271 CScale scale;
272 FXColor* grpColors[2];
273 bool hasSeqs;
274 bool canShowSeq;
275 int maxThickness;
276 // non-scrollable grid area at the top
277 FXColor gridColor;
278 FXColor gridColorSh; //shadow
279 FXColor gridColorH; //highlight
280 int content_w;
281 int content_h;
282 int gridStep;
283 int gridH;
284 /* -- this section was moved to mainwin.h :
285 FXColor baseColors[6]; //base colors
286 FXColor seqColors[12];
287 buffer for color array to pass to
288 the Seq Paint method
289 0 = seq color
290 1 = seq highlight
291 2 = seq shadow
292 3 = seqtext color
293 4 = seqtrim color
294 5 = seq range color
295 6 = seq select color
296 7 = alternate seq color (ET)
297 8 = inter-segment connector color
298 9 = internal trim color
299 10 = major consensus splice site
300 11 = minor consensus splice site
301
302
303 FXColor matchColors[MISMATCH_CLRIDX+1]; //luminance ramp
304 FXColor ctgQuals[NOCTG_CLRIDX+1]; //also a ramp, for contig
305 */
306 FXColor* baseColors;
307 FXColor* seqColors;
308 FXColor* matchColors; //luminance ramp for coverage
309 FXColor* ctgQuals; //luminance ramp for contig colors
310 protected:
311 FXGView();
312 void calcLayout();
313 private:
314 FXGView(const FXGView&);
315 FXGView &operator=(const FXGView&);
316 FXPoint lastMousePos;
317 public:
318 enum {
319 ID_TIPTIMER=FXScrollArea::ID_LAST,
320 ID_LOOKUPTIMER,
321 ID_TREELIST,
322 ID_LAST
323 };
324 enum ColorStyle {
325 csDefault,
326 csBaseColor,
327 csDensity,
328 csMismatch //only if contig is available
329 };
330 protected:
331 ColorStyle colorStyle;
332 public:
333 void initColors(FXColor* seqcolors, FXColor* basecolors,
334 FXColor* matchcolors, FXColor* ctgquals, FXColor* grpcolors, FXColor* grpgapcolors);
335 void scrollBy(int x,int y);
336 //void initGrpColors(int num);
337 bool setSeqGrp(FXString& seq, int grp);
338 void paintGrid(FXDCWindow* dc, FXRectangle& gridR);
339 void paintGap(FXDCWindow* dc, FXColor gapcolor, FXRectangle& ClpRct, int y, int x1, int x2,
340 int gapl, int gapr, char splL, char splR);
341 void paintSeq(FXDCWindow* dc, FXRectangle& clipR, ClSeq* seq,
342 ColorStyle colorstyle);
343 void paintSeqBorder(FXDCWindow* dc, FXRectangle& clipR, ClSeq* seq,
344 ColorStyle colorstyle);
345 long onPaint(FXObject*,FXSelector,void*);
346 long onLeftBtnPress(FXObject*,FXSelector,void*);
347 long onLeftBtnRelease(FXObject*,FXSelector,void*);
348 long onClicked(FXObject*,FXSelector,void*);
349 long onCommand(FXObject*,FXSelector,void*);
350 long onMotion(FXObject*,FXSelector,void*);
351 long onEnter(FXObject*,FXSelector,void*);
352 long onLeave(FXObject*,FXSelector,void*);
353 long onQueryTip(FXObject*,FXSelector,void*);
354 long onQueryHelp(FXObject*,FXSelector,void*);
355 long onTipTimer(FXObject*,FXSelector,void*);
356 virtual bool canFocus() const {return true;}
357
358 ClSeq* getSeqAt(int x, int y, int& colno);
359 void drawColumn(int colno);
360 void drawSeq(ClSeq* seq);
361 void makeVisible(ClSeq* seq);
362 void selectSeq(ClSeq* seq, bool showIt=false);
363 void drawTriangle(FXDCWindow& dc, FXColor color, FXint l,FXint t,FXint r,FXint b);
364 public:
365 /// Constructor
366 GList<ClSeq>* seqlist;
367 GList<CLayoutRow> rows;
368 GList<ColumnData> columns;
369 char filetype; //type of the file loaded in the view ('L'=*.lyt, 'A'=*.ace)
370 bool showContig; //if true, only shown within the grid, if canShowSeq
371 ClSeq* contig; // this will point to the sequence which is actually
372 // the contig (if loaded)
373 ClSeq* selSeq; //selected sequence
374 ClSeq* btnSeq; //seq which was pressed left btn on
375 int selCol;
376 int btnCol;
377 //default values
378 int seqfntW; //seqfont char width
379 int seqfntH; //seqfont char height
380
381 int seqH; //sequence bar height (pixels)
382 double seqW; //sequence char width (pixels)
383 int vSpace;
384 FXint XRight; //maximum right margin (in chars)
385 //given by max(cl_xpos+len)
386 FXint XLeft; //maximum left column (in chars)
387 //minimum offset
388 ClSeq* addSeq(const char* name, FXint len, FXint offs, bool reversed=false,
389 int trim_l=0, int trim_r=0, const char* sequence=NULL,
390 unsigned int ains=0, unsigned int adels=0);
391 //supporting segmented sequence addition:
392 ClSeq* addSeq(LytSeqInfo* seqinfo, const char* sequence=NULL);
393 void addContig(const char* name, FXint len, const char* sequence=NULL, FXint offs=0);
394 void buildLayout();
395 FXGView(FXComposite *p,FXObject* tgt=NULL,FXSelector sel=0,FXuint opts=0,FXint x=0,FXint y=0,FXint w=0,FXint h=0);
396 /// Destructor
397 virtual ~FXGView();
398 /// Save list to a stream
399 virtual void save(FXStream& store) const;
400 /// Load list from a stream
401 virtual void load(FXStream& store);
402 virtual void create();
403 virtual void detach();
404 virtual void resize(FXint w,FXint h);
405 virtual void position(FXint x, FXint y, FXint w,FXint h);
406 virtual void moveContents(FXint x,FXint y);
407 //---------------
408 /// Change text font
409 void setFont(FXFont* fnt);
410 /// Return text font
411 FXFont* getFont() const { return font; }
412 /// Return normal text color
413 FXColor getTextColor() const { return textColor; }
414 /// Change normal text color
415 void setTextColor(FXColor clr);
416 //determine when to show scroll bars
417
418 virtual FXint getContentWidth();
419 virtual FXint getContentHeight();
420
421 void RecalcContent(bool repaint=true);
422 FXdouble getZoomX() { return scale.sx; }
423 FXdouble getZoomY() { return scale.sy; }
424 void ZoomX(FXdouble zx, int fromX=-1);
425 void ZoomY(FXdouble zy, int fromY=-1);
426 void Zoom(FXdouble zx, FXdouble zy, int fromX=-1, int fromY=-1);
427 void setColorStyle(ColorStyle cs) { colorStyle=cs; update(); }
428 void Clear() {
429 rows.Clear();
430 seqlist->Clear();
431 //seqaligns->Clear();
432 XRight=XLeft=0;
433 columns.Clear();
434 hasSeqs=false;
435 selSeq=NULL;
436 selCol=-1;
437 RecalcContent();
438 }
439 int getXLeft() { return XLeft; }
440 bool HasSeqs() { return hasSeqs; }
441 int getSelCol() { return selCol; }
442 void set1pxZoom(int fromX=-1, int fromY=-1) {
443 if (rows.Count()==0 || XRight-XLeft==0) return;
444 Zoom(1.00/(double)seqfntW, 1.00/(double)seqfntH,
445 fromX, fromY);
446 }
447 ColumnData* getColumnData(int cidx) { return columns[cidx]; }
448 };
449
450 #endif