#ifndef _DRAWSEQ_ #define _DRAWSEQ_ /*local include files*/ #include #include #include /* #include */ #include #include /************************************************************************** * * DrawSequinMap(slp_list, sep, scale) * return a picture with the interface defined by Jonathan K. * slp_list: a ValNode list of Seq-loc * sep: the Seq-entry pointer * scale: the scale of the picture * **************************************************************************/ SegmenT DrawSequinMap PROTO((ValNodePtr slp_list, SeqEntryPtr sep, Int4 scale, GeneDataPtr gdata, ValNodePtr PNTR ftype_list)); SegmenT DrawSequinMapEx PROTO((ValNodePtr slp_list, SeqEntryPtr sep, Int4 scale, GeneDataPtr gdata, ValNodePtr PNTR ftype_list, Boolean forceSeglevelsTo1, ValNodePtr extraEntityList)); /*###################################################################### # # functions for setting up the color for different object # ######################################################################*/ /************************************************************************ * * get_seg_color(order) * set up the color for a segmented sequence * *************************************************************************/ extern Uint1 MUSK_COLOR[3]; Uint1Ptr get_seg_color PROTO((Int2 order)); /********************************************************************** * * get the color for different enzymes * used in drawing the restriction map * **********************************************************************/ Uint1Ptr get_enz_color PROTO((Int2 enzID)); void add_attribute_pen PROTO((SegmenT seg, Int2 p_class, Int2 sub_class)); /*#################################################################### # # functions related to the drawing of FeatNode and AlignNode # #####################################################################*/ /********************************************************************** * * DrawFlatNode(vnp, seg, label_pos, downward) * Draw a list of FeatNode as a stacked gene view * vnp: a list of FeatNode * seg: the Segment for drawing each item * label_pos: if(TURE), label the position of each cluster * downward: if(TRUE), label the cluster underneath the tickmark * ***********************************************************************/ Boolean DrawFlatNode PROTO((ValNodePtr vnp, SegmenT seg, Uint1 label_type, Int4 scale, GeneDataPtr gdata)); /************************************************************************* * * DrawFeatNode(vnp, type, rec_width, maxScale, seg, label_type, fill) * Draw a list of featnode, return TRUE for success * vnp: a list of featnode * rec_width: width for drawing a rectangle. if <2, draw a line * maxScale: max scale * seg: drawing segment * label_type: Add label on the segment * fill: fill the rectangle? * *************************************************************************/ Boolean DrawFeatNode PROTO((ValNodePtr fnp_node, SegmenT seg, Uint1 label_type, Boolean show_arrow, Int4 scale, GeneDataPtr gdata)); /*********************************************************************** * * DrawFeatures(features, mpp, pic, flat, simple, compact, f_order, * maxScale) * * Draw the features in the a sequence * features: the FeatNdoe contains the features * mpp: the graphic position of the current sequence * pic: the drawing segment * flat: if TRUE, stack features on top * simple: if TRUE, draw the feature intervals as line * compact: if TRUE, does not distinguish subtype of different features * f_order: the order for drawing different features * maxScale: the maximum scale for drawing * image_list: the list of AlignRect to store the image information * *********************************************************************/ Boolean DrawFeatures PROTO((ValNodePtr features, MapPosPtr mpp, SegmenT pic, Boolean flat, Uint1Ptr featureOrder, Uint1Ptr groupOrder, Int4 scale, GeneDataPtr gdata, ValNodePtr PNTR image_list)); /********************************************************************** * * DrawAlignNode(vnp, scale, seg) * Draw a list of AlignNode. * 1) It always labels the sequences * 2) the label is always on top of the sequence * 3) right now, it does NOT show the truncation * **********************************************************************/ Boolean DrawAlignNode PROTO((ValNodePtr vnp, Int4 scale, SegmenT seg)); Boolean DrawFlatAlign PROTO((SegmenT seg, ValNodePtr anp_list)); /*#################################################################### # # functions used in chromoscope to draw the sequences, maps # ####################################################################*/ /************************************************************************* * * DrawGeneticMap(features, mpp, pic, maxScale) * draw the genetic map from featnode * features: the list of FeatNode, will be resorted * mpp: the current map position. The drawing will recalculate * mpp->seq_top and mpp->bottom * pic: the drawing picture * maxScale: the maximum scale in drawing. Will be used in the layout * image_list: the list of AlignRect to store the image information * *************************************************************************/ Boolean DrawGeneticMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, SegmenT pic, Int4 maxScale, GeneDataPtr gdata, ValNodePtr PNTR image_list)); /************************************************************************* * * DrawPhysicalMap(features, mpp, pic, maxScale) * draw the physical map from featnode * features: the list of FeatNode, will be resorted * mpp: the current map position. The drawing will recalculate * mpp->seq_top and mpp->bottom * pic: the drawing picture * maxScale: the maximum scale in drawing. Will be used in the layout * image_list: the list of AlignRect to store the image information * *************************************************************************/ Boolean DrawPhysicalMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, SegmenT pic, Int4 maxScale, ValNodePtr PNTR image_list)); /*********************************************************************** * * DrawRestrictionMap(features, mpp, pic, rsite_flat, strand) * draw the restriction map * features: the FeatNode contains the info for restriction map * mpp: the map position * pic: picture * rsite_flat: if(TRUE), all the enzymes are shown in one line. * strand: the orientation of the map * ***********************************************************************/ Boolean DrawRestrictionMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, SegmenT pic, Boolean rsite_flat, Uint1 strand, Int4 maxScale)); /*********************************************************************** * * DrawCytoMap(features, mpp, maxScale, pic) * draw the cytogenetic map * features: the FeatNode for cytogenetic map * maxScale: maximum scale, used in layout * pic: the drawing segment * ***********************************************************************/ Boolean DrawCytoMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, Int4 maxScale, SegmenT pic)); /********************************************************************* * * DrawSeqMap(features, mpp, pic, flat, maxScale, is_raw_seq) * Draw the real sequence map * features: FeatNode from which the Bioseqs can be extracted * mpp: the MapPos that contains the current map position * pic: the picture * flat: if TRUE, draw the map with features stacked on top * maxScale: maximum scale of the sequence * is_raw_seq: if TRUE, it is a raw DNA sequence. (This is * used to distinguish raw sequence from virtual sequence * *********************************************************************/ Boolean DrawSeqMap PROTO((ValNodePtr PNTR features, MapPosPtr mpp, SegmenT pic, Int4 scale, Boolean is_raw_seq, Boolean show_segment, ValNodePtr PNTR image_list)); /*********************************************************************** * * DrawSeqScale(seg, slp, left, ypos, scaleX) * draw a scale for the Seq-loc. It can be a list of Seq-loc * seg: the drawing segment * slp: the Seq-loc * left: the left offset * ypos: the top position * scaleX: the current scale of the picture * ************************************************************************/ void DrawSeqScale PROTO((SegmenT seg, SeqLocPtr slp, Int4 left, Int4 ypos, Int4 scaleX, Boolean add_x_line)); /************************************************************************* * * DrawVerticalAlign (align, pic, mlp) * draw alignment among the sequences. (connecting aligned seg by line) * align: the Seq-align which contains the alignment among sequence * It is assumed to be a Std-seg * pic: the drawing segment * mlp: the list of the layout of the sequences * *************************************************************************/ Boolean DrawVerticalAlign PROTO((SeqAlignPtr align, SegmenT pic, MapLayoutPtr mlp)); /************************************************************ * * collect_alignnode_from_alp(m_loc) * collect all the alignment stored as the history of the * master sequence * m_loc: the selected location of the master sequence * return a list of AlignNode * ************************************************************/ ValNodePtr collect_alignnode_from_slp PROTO((SeqLocPtr m_loc, Uint2Ptr t_entityID, Boolean flat_insert)); SegmenT DrawSeqHistoryAlignment PROTO((SeqLocPtr m_loc, Int4 scale, ValNodePtr PNTR anp_list, Uint2Ptr entityID, Boolean flat_insert)); Boolean load_align_option_for_graphic PROTO((CollectAlignOptionPtr caop, CollectSeqOptionPtr csop, Int4 style, Boolean flat_insert)); 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)); Boolean DrawHistory PROTO((ValNodePtr aligns, MapPosPtr mpp, Int4 seq_label_len, SegmenT pic, Int4 scale, ValNodePtr PNTR image_list)); /********************************************************************* * * DrawGenomeMap(slp_list, e_align_list, scale, mlp) * * draw all the SeqLocs in the list and show their alignment (if any) * slp_list: the list of Seq-locs * e_align_list: the list of alignment among the Seq-locs * scale: the scale for the picture * mlp: store the layout of the current picture * return the picture of the genome map * ftype_list: return a list of type of features for the current * Seq-loc. This is going to be used for drawing the legend * image_list: the list to store the image mapping information * *********************************************************************/ SegmenT DrawGenomeMap PROTO((ValNodePtr slp_list, ValNodePtr e_align_list, Int4 scale, GeneDataPtr gdata, MapLayoutPtr PNTR mlp, ValNodePtr PNTR ftyle_list, ValNodePtr PNTR image_list)); SegmenT DrawGenomeMapEx PROTO((ValNodePtr slp_list, ValNodePtr e_align_list, Int4 scale, GeneDataPtr gdata, MapLayoutPtr PNTR mlp, ValNodePtr PNTR ftyle_list, ValNodePtr PNTR image_list, Boolean forceSeglevelsTo1, ValNodePtr extraEntityList)); /************************************************************************* * * Label_GData(): Label the gene_data node specified by the user * *************************************************************************/ Boolean Label_GData PROTO((GeneDataPtr gdata, SeqLocPtr slp, Int4 left, Int4 top, SegmenT seg)); #define MAX_SCALE 5000 Int4 FigureMaxScale PROTO((ValNodePtr slp_list, Int2 view_width, Int4 max_width)); Int4 FigureMinScale PROTO((ValNodePtr slp_list, Int4 max_label)); Int4 CountMaxSeqLabel PROTO((ValNodePtr slp_list)); /************************************************************************* * * Find_segment_IDs(): Returns identifier triplet given a mouse point * *************************************************************************/ /* extern Boolean Find_segment_IDs PROTO((VieweR viewer, PoinT pt, Uint2Ptr entityID, Uint2Ptr itemID, Uint2Ptr itemType)); */ void draw_one_align PROTO((AlignPos ap, Int2 num, Int2 order, SegmenT seg)); #define UNKNOWN_DB 0 #define ENTREZ_DB 1 /*entrez is the database*/ #define THC_DB 2 /*db is the THC tigr database*/ #define ENTREZ_KLUDGE_ID 3 /*for kludge id in Entrez */ #define ENTREZ_DB_P 4 /*entrez proteins is the database*/ typedef struct alignlabelrect { Uint1 link_db; /*database for the gi*/ Int4 gi; Int4 left; Int4 top; Int4 right; Int4 bottom; Uint2 itemType; Uint2 itemID; CharPtr label; Int4 from, to; /*the interval on the sequence. For showing partial Seq-loc*/ }AlignLabelRect, PNTR AlignLabelRectPtr; /************************************************************************ * * load the information for image mapping * ************************************************************************/ Boolean load_align_label_rectangle PROTO((ValNodePtr data_list, ValNodePtr PNTR arect_list, Int4 scale, Boolean flat)); /* * for the contig maps, the real contig length may not correspond * with the mapped interval on the graphics. Need a way to find the * store the interval mapped in proportion to what is in the graphic * the intervals are mapped by the function: FindContigList */ void AddIntervalForImage PROTO((ValNodePtr contig_list, ValNodePtr image_list)); SegmenT PicForAlignNode PROTO((ValNodePtr anp_list, SeqLocPtr m_loc, Int4 width, Int4Ptr p_scale, Int4Ptr p_maxwidth, ValNodePtr PNTR arect_list)); /*********************************************************************** * * functions to draw a compressed alignment viewer * ************************************************************************/ SegmenT DrawCompressAlignment PROTO((ValNodePtr anp_list, SeqLocPtr m_loc, Int4 width, Int4Ptr p_scale, Int4Ptr p_maxwidth, Uint2 entityID, ValNodePtr PNTR arect_list)); ValNodePtr MakeCompressAlignList PROTO((BioseqPtr query_bsp, SeqAnnotPtr annot, Uint2Ptr p_entityID)); /*produce a picture which shows the contigs that align to the * cytogenetic band. It will expand left to the half band size and * right to the half band size. pic_width is the width of the picture */ SegmenT DrawCytoContigMap PROTO((ValNodePtr slp_list, BioseqPtr cyto_bsp, Int4 pic_width, Int4Ptr pscale, ValNodePtr PNTR image_list)); #endif