/usr/include/ncbi/glbpic.h is in libvibrant6-dev 6.1.20170106-2.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 | #ifndef _GLBPIC_
#define _GLBPIC_
#include <maputil.h>
#include <gather.h>
#include <jzcoll.h>
#include <picture.h>
#ifdef __cplusplus
extern "C" {
#endif
typedef struct globalbsp{ /*the map drawing unit for global view*/
BioseqPtr bsp;
CharPtr label; /*label for the sequence*/
RecT rec; /*for drawing a linear molecule*/
Int2 radius; /*for drawing a circular molecule*/
Uint1 map_type; /*determine the type of the map*/
Boolean show_map_unit; /*show the map unit??*/
Boolean check_cyto; /*check if it is a cyto-genetic map*/
ValNodePtr l_marks; /*the list of MapMarks, such as landmarks, band in
cytogenetic map*/
ValNodePtr g_marks; /*the list of marks that are picked by the user*/
ValNodePtr cyto_marks; /*marks for the cytogenetic map*/
Boolean hide; /*hide the current Bioseq*/
Uint2 priority; /*priority for search a particular gene*/
ValNodePtr rrp_list; /*list for showing the repeat regions*/
ValNodePtr arp_list; /*list for showing the alignment in the global view*/
Boolean has_fish_align; /*the arp_list is a FISH alignment*/
Boolean is_seqindex_map; /*is it a sequence index map*/
Boolean align_has_status; /*if the alignment arp_list has status*/
Int2 num_lod_score; /*number of the LOD scores for a genethon map*/
}GlobalBsp, PNTR GlobalBspPtr;
typedef struct globaldraw{
Boolean is_circle;
PoinT center;
ValNodePtr gbp_list; /*the list of the globalbsp data*/
GeneDataPtr g_data;
ValNodePtr g_list; /*list of user-selected genes*/
Boolean free_data; /*if TRUE, free msp_list and equiv_align_list*/
ValNodePtr msp_list; /*manually loaded Seq-entry*/
ValNodePtr equiv_align_list; /*manually loaded Seq-annot + alignment parsed out*/
ValNodePtr ext_align; /*alignment taken from the external*/
ValNodePtr slp_list; /*list of selected intervals */
Uint1 release_choice; /* 0 = graphic view, 1=alignment view*/
Boolean draw_align_legend; /*add the legend for the colors used in different score scale*/
}GlobalDraw, PNTR GlobalDrawPtr;
typedef struct mapmark{ /*marks labeled on the global view*/
Char label[20]; /*label the mark*/
Int4 pos; /*position in basepair coordinate*/
Boolean inward; /*the orientation for mark label*/
}MapMark, PNTR MapMarkPtr;
/*************************************************************************
*
* default variables associated with the layout of the global picture
*
**************************************************************************/
#define LINEAR_BSP 1 /*a linear Bioseq*/
#define CIRCLE_BSP 2 /* a circular Bioseq*/
#define PI ((FloatHi)3.14159)
/*options for showing the Equiv-align */
#define EQUIV_ALIGN_DEFAULT 0 /*show the consistent markers and only
some of the inconsistent markers*/
#define EQUIV_ALIGN_ALL 1 /*show all the equiv-aligns*/
/***************************************************************************
*
* CreateGlobalDrawData(msp_list, ext_align, user_list, need_free)
* Create the GlobalDrawPtr structure to draw the global view
* msp_list: externally loaded Seq-entry and its file name (used for saving)
* ext_align: the externally loaded sequence-alignment for equiv maps
* user_list: a list of user-selected gene symbols
* need_free: if TRUE, the free callback will free msp_list, ext_align and
* user_list.
*
****************************************************************************/
GlobalDrawPtr CreateGlobalDrawData PROTO((ValNodePtr msp_list, ValNodePtr ext_align, ValNodePtr user_list, Boolean need_free, Boolean for_picture, Uint1 equiv_align_option));
/**************************************************************************
*
* ree_global_draw(gdraw_p)
* free all the data related to the global draw
*
***************************************************************************/
GlobalDrawPtr free_global_draw PROTO((GlobalDrawPtr gdraw_p));
BioseqPtr has_cyto_map PROTO((GlobalDrawPtr gdraw_p));
/***************************************************************************
*
* functions related to the layout of GlobalDrawPtr
*
* LayoutGlobalDrawData(gdraw_p, pan_width, pan_height)
* gdraw_p: the GlobalDrawPtr
* pan_width: the width of the viewer
* pan_height: the height of the viewer
*
****************************************************************************/
Boolean LayoutGlobalDrawData PROTO((GlobalDrawPtr gdraw_p, Int2 pan_width, Int2 pan_height));
/************************************************************************
*
* Draw_Global(gdraw_p)
* return a picture created from GlobalDrawPtr
*
************************************************************************/
SegmenT Draw_Global PROTO((GlobalDrawPtr gdraw_p));
SegmenT MuskGlobalPicture PROTO((ValNodePtr msp_list, ValNodePtr ext_align, Boolean need_free, Int2 panel_width, Int2 panel_height, ValNodePtr user_list, GlobalDrawPtr PNTR vwr_extra, Uint1 equiv_align_option, Boolean draw_align_legend));
SegmenT SequinGlobalPicture PROTO((SeqEntryPtr sep, Int2 panel_width, Int2 panel_height, ValNodePtr user_list, GlobalDrawPtr PNTR vwr_extra, Boolean draw_align_legend));
SegmenT GlobalPictureUpdate PROTO((GlobalDrawPtr gdraw_p, ValNodePtr new_gene_list, Int2 panel_width, Int2 panel_height));
/*********************************************************************
*
*
* find_map_pos(convert the start_pnt, stop_pnt into a list of
* Seq-locs)
*
*********************************************************************/
ValNodePtr find_map_pos PROTO((GlobalDrawPtr gdraw_p, PntInfo start_pnt, PntInfo stop_pnt));
GeneDataPtr create_gene_data PROTO((ValNodePtr msp_list, ValNodePtr mark_list));
#ifdef __cplusplus
}
#endif
#endif
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