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C/desktop/drawseq.h

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  1 
  2 #ifndef _DRAWSEQ_
  3 #define _DRAWSEQ_
  4 
  5 /*local include files*/
  6 #include <jzcoll.h>
  7 #include <fstyle.h>
  8 #include <layout.h>
  9 
 10 /* #include <viewer.h> */
 11 #include <picture.h>
 12 #include <objmgr.h>
 13 
 14 
 15 /**************************************************************************
 16 *
 17 *       DrawSequinMap(slp_list, sep, scale)
 18 *       return a picture with the interface defined by Jonathan K. 
 19 *       slp_list: a ValNode list of Seq-loc
 20 *       sep: the Seq-entry pointer
 21 *       scale: the scale of the picture
 22 *
 23 **************************************************************************/
 24 SegmenT DrawSequinMap PROTO((ValNodePtr slp_list, SeqEntryPtr sep, Int4 scale, GeneDataPtr gdata, ValNodePtr PNTR ftype_list));
 25 
 26 SegmenT DrawSequinMapEx PROTO((ValNodePtr slp_list, SeqEntryPtr sep, Int4 scale, GeneDataPtr gdata, ValNodePtr PNTR ftype_list,
 27 Boolean forceSeglevelsTo1, ValNodePtr extraEntityList));
 28 
 29 
 30 /*######################################################################
 31 #
 32 #       functions for setting up the color for different object
 33 #
 34 ######################################################################*/
 35 
 36 /************************************************************************
 37 *
 38 *       get_seg_color(order)
 39 *       set up the color for a segmented sequence
 40 *
 41 *************************************************************************/
 42 extern Uint1 MUSK_COLOR[3];
 43 Uint1Ptr get_seg_color PROTO((Int2 order));
 44 
 45 
 46 
 47 /**********************************************************************
 48 *
 49 *       get the color for different enzymes
 50 *       used in drawing the restriction map
 51 *
 52 **********************************************************************/
 53 Uint1Ptr get_enz_color PROTO((Int2 enzID));
 54 
 55 
 56 void add_attribute_pen PROTO((SegmenT seg, Int2 p_class, Int2 sub_class));
 57 
 58 
 59 /*####################################################################
 60 #
 61 #       functions related to the drawing of FeatNode and AlignNode
 62 #
 63 #####################################################################*/
 64 
 65 /**********************************************************************
 66 *
 67 *       DrawFlatNode(vnp, seg, label_pos, downward)
 68 *       Draw a list of FeatNode as a stacked gene view
 69 *       vnp: a list of FeatNode
 70 *       seg: the Segment for drawing each item
 71 *       label_pos: if(TURE), label the position of each cluster
 72 *       downward: if(TRUE), label the cluster underneath the tickmark
 73 *
 74 ***********************************************************************/
 75 Boolean DrawFlatNode PROTO((ValNodePtr vnp, SegmenT seg, Uint1 label_type, Int4 scale, GeneDataPtr gdata));
 76 
 77 /*************************************************************************
 78 *
 79 *       DrawFeatNode(vnp, type, rec_width, maxScale, seg, label_type, fill)
 80 *       Draw a list of featnode, return TRUE for success
 81 *       vnp: a list of featnode
 82 *       rec_width: width for drawing a rectangle. if <2, draw a line
 83 *       maxScale: max scale
 84 *       seg: drawing segment
 85 *       label_type: Add label on the segment
 86 *       fill: fill the rectangle?
 87 *
 88 *************************************************************************/
 89 Boolean DrawFeatNode PROTO((ValNodePtr fnp_node, SegmenT seg, Uint1 label_type, Boolean show_arrow, Int4 scale, GeneDataPtr gdata));
 90 /***********************************************************************
 91 *
 92 *       DrawFeatures(features, mpp, pic, flat, simple, compact, f_order,
 93 *       maxScale)
 94 *
 95 *       Draw the features in the a sequence
 96 *       features: the FeatNdoe contains the features
 97 *       mpp: the graphic position of the current sequence
 98 *       pic: the drawing segment
 99 *       flat: if TRUE, stack features on top
100 *       simple: if TRUE, draw the feature intervals as line
101 *       compact: if TRUE, does not distinguish subtype of different features
102 *       f_order: the order for drawing different features
103 *       maxScale: the maximum scale for drawing
104 *       image_list: the list of AlignRect to store the image information
105 *
106 *********************************************************************/
107 Boolean DrawFeatures PROTO((ValNodePtr features, MapPosPtr mpp, SegmenT pic, Boolean flat, Uint1Ptr featureOrder, Uint1Ptr groupOrder, Int4 scale, GeneDataPtr gdata, ValNodePtr PNTR image_list));
108 
109 
110 /**********************************************************************
111 *
112 *       DrawAlignNode(vnp, scale, seg)
113 *       Draw a list of AlignNode. 
114 *       1) It always labels the sequences
115 *       2) the label is always on top of the sequence
116 *       3) right now, it does NOT show the truncation
117 *
118 **********************************************************************/
119 Boolean DrawAlignNode PROTO((ValNodePtr vnp, Int4 scale, SegmenT seg));
120 Boolean DrawFlatAlign PROTO((SegmenT seg, ValNodePtr anp_list));
121 
122 
123 
124 /*####################################################################
125 #
126 #       functions used in chromoscope to draw the sequences, maps
127 #
128 ####################################################################*/
129 /************************************************************************* 
130 * 
131 *       DrawGeneticMap(features, mpp, pic, maxScale) 
132 *       draw the genetic map from featnode 
133 *       features: the list of FeatNode, will be resorted 
134 *       mpp: the current map position. The drawing will recalculate
135 *       mpp->seq_top and mpp->bottom 
136 *       pic: the drawing picture 
137 *       maxScale: the maximum scale in drawing. Will be used in the layout 
138 *       image_list: the list of AlignRect to store the image information
139 * 
140 *************************************************************************/ 
141 Boolean DrawGeneticMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, SegmenT pic, Int4 maxScale, GeneDataPtr gdata, ValNodePtr PNTR image_list));
142 
143 
144 /*************************************************************************
145 *
146 *       DrawPhysicalMap(features, mpp, pic, maxScale)
147 *       draw the physical map from featnode
148 *       features: the list of FeatNode, will be resorted
149 *       mpp: the current map position. The drawing will recalculate
150 *       mpp->seq_top and mpp->bottom
151 *       pic: the drawing picture
152 *       maxScale: the maximum scale in drawing. Will be used in the layout
153 *       image_list: the list of AlignRect to store the image information
154 *
155 *************************************************************************/
156 Boolean DrawPhysicalMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, SegmenT pic, Int4 maxScale, ValNodePtr PNTR image_list));
157 
158 
159 /*********************************************************************** 
160 * 
161 *       DrawRestrictionMap(features, mpp, pic, rsite_flat, strand) 
162 *       draw the restriction map 
163 *       features: the FeatNode contains the info for restriction map 
164 *       mpp: the map position 
165 *       pic: picture
166 *       rsite_flat: if(TRUE), all the enzymes are shown in one line. 
167 *       strand: the orientation of the map
168 * 
169 ***********************************************************************/ 
170 Boolean DrawRestrictionMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, SegmenT pic, Boolean rsite_flat, Uint1 strand, Int4 maxScale));
171 
172 
173 
174 /*********************************************************************** 
175 * 
176 *       DrawCytoMap(features, mpp, maxScale, pic) 
177 *       draw the cytogenetic map
178 *       features: the FeatNode for cytogenetic map 
179 *       maxScale: maximum scale, used in layout 
180 *       pic: the drawing segment
181 * 
182 ***********************************************************************/
183 Boolean DrawCytoMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, Int4 maxScale, SegmenT pic));
184 
185 
186 /*********************************************************************
187 *
188 *       DrawSeqMap(features, mpp, pic, flat, maxScale, is_raw_seq)
189 *       Draw the real sequence map
190 *       features: FeatNode from which the Bioseqs can be extracted
191 *       mpp: the MapPos that contains the current map position 
192 *       pic: the picture 
193 *       flat: if TRUE, draw the map with features stacked on top
194 *       maxScale: maximum scale of the sequence
195 *       is_raw_seq: if TRUE, it is a raw DNA sequence. (This is  
196 *       used to distinguish raw sequence from virtual sequence 
197 * 
198 *********************************************************************/ 
199 Boolean DrawSeqMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, SegmenT pic, Int4 scale, Boolean is_raw_seq, Boolean show_segment, ValNodePtr PNTR image_list));
200 
201 
202 /***********************************************************************
203 *
204 *       DrawSeqScale(seg, slp, left, ypos, scaleX) 
205 *       draw a scale for the Seq-loc. It can be a list of Seq-loc 
206 *       seg: the drawing segment
207 *       slp: the Seq-loc
208 *       left: the left offset 
209 *       ypos: the top position 
210 *       scaleX: the current scale of the picture 
211 * 
212 ************************************************************************/
213 void DrawSeqScale PROTO((SegmenT seg, SeqLocPtr slp, Int4 left, Int4 ypos, Int4 scaleX, Boolean add_x_line));
214 
215 
216 
217 /*************************************************************************
218 *
219 *       DrawVerticalAlign (align, pic, mlp)
220 *       draw alignment among the sequences. (connecting aligned seg by line)
221 *       align: the Seq-align which contains the alignment among sequence 
222 *       It is assumed to be a Std-seg 
223 *       pic: the drawing segment 
224 *       mlp: the list of the layout of the sequences
225 *
226 *************************************************************************/
227 Boolean DrawVerticalAlign PROTO((SeqAlignPtr align, SegmenT pic, MapLayoutPtr mlp));
228 
229 /************************************************************
230 *
231 * collect_alignnode_from_alp(m_loc)
232 * collect all the alignment stored as the history of the
233 * master sequence
234 * m_loc: the selected location of the master sequence
235 * return a list of AlignNode
236 *
237 ************************************************************/
238 ValNodePtr collect_alignnode_from_slp PROTO((SeqLocPtr m_loc, Uint2Ptr t_entityID, Boolean flat_insert));
239 
240 SegmenT DrawSeqHistoryAlignment PROTO((SeqLocPtr m_loc, Int4 scale, ValNodePtr PNTR anp_list, Uint2Ptr entityID, Boolean flat_insert));
241 
242 Boolean load_align_option_for_graphic PROTO((CollectAlignOptionPtr caop, CollectSeqOptionPtr csop, Int4 style, Boolean flat_insert));
243 
244 Boolean DrawMPAlignment PROTO((ValNodePtr anp_node, Int4 left, Int4 right, SeqLocPtr m_loc, Uint2 entityID, Int4 scale, Int4Ptr cur_pos, Uint1 style, Boolean compress, SegmenT pic));
245 
246 Boolean DrawHistory PROTO((ValNodePtr aligns, MapPosPtr mpp, Int4 seq_label_len, SegmenT pic, Int4 scale, ValNodePtr PNTR image_list));
247 
248 
249 
250 /*********************************************************************
251 *
252 *       DrawGenomeMap(slp_list, e_align_list, scale, mlp)
253 *
254 *       draw all the SeqLocs in the list and show their alignment (if any)
255 *       slp_list: the list of Seq-locs
256 *       e_align_list: the list of alignment among the Seq-locs
257 *       scale: the scale for the picture
258 *       mlp: store the layout of the current picture
259 *       return the picture of the genome map
260 *       ftype_list: return a list of type of features for the current
261 *       Seq-loc. This is going to be used for drawing the legend
262 *       image_list: the list to store the image mapping information
263 
264 *
265 *********************************************************************/
266 SegmenT DrawGenomeMap PROTO((ValNodePtr slp_list, ValNodePtr e_align_list, Int4
267 scale, GeneDataPtr gdata, MapLayoutPtr PNTR mlp, ValNodePtr PNTR ftyle_list, ValNodePtr PNTR image_list));
268 
269 SegmenT DrawGenomeMapEx PROTO((ValNodePtr slp_list, ValNodePtr e_align_list, Int4
270 scale, GeneDataPtr gdata, MapLayoutPtr PNTR mlp, ValNodePtr PNTR ftyle_list, ValNodePtr PNTR image_list,
271 Boolean forceSeglevelsTo1, ValNodePtr extraEntityList));
272 
273 /*************************************************************************
274 *
275 *       Label_GData(): Label the gene_data node specified by the user
276 *
277 *************************************************************************/
278 Boolean Label_GData PROTO((GeneDataPtr gdata, SeqLocPtr slp, Int4 left, Int4 top, SegmenT seg));
279 
280 #define MAX_SCALE       5000
281 Int4 FigureMaxScale PROTO((ValNodePtr slp_list, Int2 view_width, Int4 max_width));
282 Int4 FigureMinScale PROTO((ValNodePtr slp_list, Int4 max_label));
283 
284 Int4 CountMaxSeqLabel PROTO((ValNodePtr slp_list));
285  
286 /*************************************************************************
287 *
288 *       Find_segment_IDs(): Returns identifier triplet given a mouse point
289 *
290 *************************************************************************/
291 /* extern Boolean Find_segment_IDs PROTO((VieweR viewer, PoinT pt, Uint2Ptr entityID, Uint2Ptr itemID, Uint2Ptr itemType)); */
292 
293 void draw_one_align PROTO((AlignPos ap, Int2 num, Int2 order, SegmenT seg));
294 
295 
296 #define UNKNOWN_DB      0
297 #define ENTREZ_DB       1       /*entrez is the database*/
298 #define THC_DB          2       /*db is the THC tigr database*/
299 #define ENTREZ_KLUDGE_ID        3       /*for kludge id in Entrez */
300 #define ENTREZ_DB_P     4       /*entrez proteins is the database*/
301 typedef struct alignlabelrect {
302         Uint1 link_db;  /*database for the gi*/
303         Int4 gi;
304         Int4 left;
305         Int4 top;
306         Int4 right;
307         Int4 bottom;
308         Uint2 itemType;
309         Uint4 itemID;
310         CharPtr label;
311         Int4 from, to;  /*the interval on the sequence. For showing partial Seq-loc*/
312 }AlignLabelRect, PNTR AlignLabelRectPtr;
313 
314 /************************************************************************
315 *
316 *       load the information for image mapping
317 *
318 ************************************************************************/
319 Boolean load_align_label_rectangle PROTO((ValNodePtr data_list, ValNodePtr PNTR arect_list, Int4 scale, Boolean flat));
320 /*
321 *       for the contig maps, the real contig length may not correspond
322 *       with the mapped interval on the graphics. Need a way to find the 
323 *       store the interval mapped in proportion to what is in the graphic
324 *       the intervals are mapped by the function: FindContigList
325 */
326 void AddIntervalForImage PROTO((ValNodePtr contig_list, ValNodePtr image_list));
327 
328 
329 SegmenT PicForAlignNode PROTO((ValNodePtr anp_list, SeqLocPtr m_loc, Int4 width, Int4Ptr p_scale, Int4Ptr p_maxwidth, ValNodePtr PNTR arect_list));
330 
331 
332 /***********************************************************************
333 *
334 *       functions to draw a compressed alignment viewer
335 *
336 ************************************************************************/
337 SegmenT DrawCompressAlignment PROTO((ValNodePtr anp_list, SeqLocPtr m_loc, Int4 width, 
338                                                                         Int4Ptr p_scale, Int4Ptr p_maxwidth, Uint2 entityID, ValNodePtr PNTR arect_list));
339 
340 ValNodePtr MakeCompressAlignList PROTO((BioseqPtr query_bsp, SeqAnnotPtr annot, Uint2Ptr p_entityID));
341 
342 /*produce a picture which shows the contigs that align to the 
343 * cytogenetic band. It will expand left to the half band size and 
344 * right to the half band size. pic_width is the width of the picture
345 */
346 SegmenT DrawCytoContigMap PROTO((ValNodePtr slp_list, BioseqPtr cyto_bsp, 
347                         Int4 pic_width, Int4Ptr pscale, ValNodePtr PNTR image_list));
348 #endif
349
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