o RŀgkH@sdZddlmZddlmZddlmZddlmZddlmZddl m Z ddl m Z d d Z d d Z e jd d fddZde jd fddZe jd d fddZe jd dddd fddZddZddZddZGdd d Zd S)!aHAbstractDrawer module (considered to be a private module, the API may change!). Provides: - AbstractDrawer - Superclass for methods common to the Drawer objects - page_sizes - Method that returns a ReportLab pagesize when passed a valid ISO size - draw_box - Method that returns a closed path object when passed the proper coordinates. For HORIZONTAL boxes only. - angle2trig - Method that returns a tuple of values that are the vector for rotating a point through a passed angle, about an origin - intermediate_points - Method that returns a list of values intermediate between the points in a passed dataset For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com For dealing with biological information, the package expects Biopython objects like SeqFeatures. )islice)cos)pi)sin)Polygon)colors) pagesizescCsidtjdtjdtjdtjdtjdtjdtjdtjd tj d tj d tj d tj d tj dtjdtjdtjdtj}z||WStyZt|ddw)zConvert size string into a Reportlab pagesize. Arguments: - size - A string representing a standard page size, eg 'A4' or 'LETTER' A0A1A2A3A4A5A6B0B1B2B3B4B5B6ELEVENSEVENTEENLEGALLETTERz not in list of page sizesN)rr r r r r rrrrrrrrrrrrKeyError ValueError)sizesizesr^/var/www/html/myenv/lib/python3.10/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py page_sizes2sP       r cCst|tjs td||tjkr|durtj}||fS|dur'|}||fS|r) list_of_pointsr%r&r1r2r'xy_listxyrrr draw_polygons"   rKg?rightcKs|\} } |\} } |dksd|krtd|dkrtd|dur#|}~t||\} }t| | t| | }}t| | t| | }}|dkrO||||f\} } } } n|dkr^||||f\} } } } ntd|d | | }| | }||}tt||t|}|dkr|d 9}d ||}||}||}d |}| | || || || || | | || || | || || | |g}tt|f| dd|d |S) a`Draw an arrow. Returns a closed path object representing an arrow enclosed by the box with corners at {point1=(x1,y1), point2=(x2,y2)}, a shaft height given by shaft_height_ratio (relative to box height), a head length given by head_length_ratio (also relative to box height), and an orientation that may be 'left' or 'right'. rr:z2Arrow shaft height ratio should be in range 0 to 1r9NrLleftzInvalid orientation z, should be 'left' or 'right'r8r;)rr(r-r.absrr>)r/r0r%r&shaft_height_ratiohead_length_ratio orientationr1r2r3r4r5r6r'xminyminxmaxymaxr@rA shaftheight headlengthshafttop shaftbaseheadbase midheightrDrrr draw_arrowsl  r]cCst|ddks Jt|dkr|S|dd}tt|dddt|dddD]\}}||dks7||dkrA||||q'|S)a Remove adjacent duplicate points. This is important for use with the Polygon class since reportlab has a bug with duplicate points. Arguments: - points - list of points [x1, y1, x2, y2,...] Returns a list in the same format with consecutive duplicates removed rNrN)lenziprrF)rD newpointsrIrJrrrr>7s  &  r>cCs.t|td}t|td}||| |fS)a&Convert angle to a reportlab ready tuple. Arguments: - theta - Angle in degrees, counter clockwise from horizontal Returns a representation of the passed angle in a format suitable for ReportLab rotations (i.e. cos(theta), sin(theta), -sin(theta), cos(theta) tuple) )rrr)thetacsrrr angle2trigMs rhc Csg}|||dd|dd|ddd|ddftdt|dD],}||d\}}||\}}||d\} } ||||d|| |d|fq)||| |d||ddf|S)zGenerate intermediate points describing provided graph data.. Returns a list of (start, end, value) tuples describing the passed graph data as 'bins' between position midpoints. rr:@rN)rFrangera) startend graph_datanewdataindexlastxvallastyvalxvalyvalnextxvalnextyvalrrrintermediate_points\s &   $rvc@sbeZdZdZ            dddZd d Zd d Zd dZddZddZ ddZ dS)AbstractDraweraAbstract Drawer. Attributes: - tracklines Boolean for whether to draw lines delineating tracks - pagesize Tuple describing the size of the page in pixels - x0 Float X co-ord for leftmost point of drawable area - xlim Float X co-ord for rightmost point of drawable area - y0 Float Y co-ord for lowest point of drawable area - ylim Float Y co-ord for topmost point of drawable area - pagewidth Float pixel width of drawable area - pageheight Float pixel height of drawable area - xcenter Float X co-ord of center of drawable area - ycenter Float Y co-ord of center of drawable area - start Int, base to start drawing from - end Int, base to stop drawing at - length Size of sequence to be drawn - cross_track_links List of tuples each with four entries (track A, feature A, track B, feature B) to be linked. r landscape皙?NrcCsR||_|||||||||| || | | |_| dur$g} dS| |_dS)aCreate the object. Arguments: - parent Diagram object containing the data that the drawer draws - pagesize String describing the ISO size of the image, or a tuple of pixels - orientation String describing the required orientation of the final drawing ('landscape' or 'portrait') - x Float (0->1) describing the relative size of the X margins to the page - y Float (0->1) describing the relative size of the Y margins to the page - xl Float (0->1) describing the relative size of the left X margin to the page (overrides x) - xr Float (0->1) describing the relative size of the right X margin to the page (overrides x) - yt Float (0->1) describing the relative size of the top Y margin to the page (overrides y) - yb Float (0->1) describing the relative size of the lower Y margin to the page (overrides y) - start Int, the position to begin drawing the diagram at - end Int, the position to stop drawing the diagram at - tracklines Boolean flag to show (or not) lines delineating tracks on the diagram - cross_track_links List of tuples each with four entries (track A, feature A, track B, feature B) to be linked. N)_parent set_page_size set_margins set_bounds tracklinescross_track_links)selfparentpagesizerRrIrJxlxrytybrkrlr~rrrr__init__s,   zAbstractDrawer.__init__cCst|tr t|}nt|trntd|dt|t|}}|}|dvr1td|d|dkr<||f|_dS||f|_dS)aSet page size of the drawing.. Arguments: - pagesize Size of the output image, a tuple of pixels (width, height, or a string in the reportlab.lib.pagesizes set of ISO sizes. - orientation String: 'landscape' or 'portrait' z Page size z not recognised)rxportraitz Orientation rxN) r!strr tuplerr-r.lowerr)rrrR shortsidelongsiderrrr{s  zAbstractDrawer.set_page_sizec Cs|p|}|p|}|p |} |p|} |jd||jd| |_|_|jdd||jdd| |_|_|j|j|_|j|j|_|j|jd|j|jd|_|_dS)atSet page margins. Arguments: - x Float(0->1), Absolute X margin as % of page - y Float(0->1), Absolute Y margin as % of page - xl Float(0->1), Left X margin as % of page - xr Float(0->1), Right X margin as % of page - yt Float(0->1), Top Y margin as % of page - yb Float(0->1), Bottom Y margin as % of page Set the page margins as proportions of the page 0->1, and also set the page limits x0, y0 and xlim, ylim, and page center xorigin, yorigin, as well as overall page width and height rr:riN) rx0y0xlimylim pagewidth pageheightxcenterycenter) rrIrJrrrr xmargin_l xmargin_r ymargin_top ymargin_btmrrrr|s" zAbstractDrawer.set_marginscCs|j\}}|dur|dur||kr||}}|dus |dkr"d}|dus*|dkr.|d}t|t||_|_|j|jd|_dS)zSet start and end points for the drawing as a whole. Arguments: - start - The first base (or feature mark) to draw from - end - The last base (or feature mark) to draw to Nrr:)rzrjintrkrllength)rrkrllowhighrrrr}s zAbstractDrawer.set_boundscCs||jkr ||jkr dSdS)zCheck if given value is within the region selected for drawing. Arguments: - value - A base position r:r)rkrl)rvaluerrr is_in_boundsszAbstractDrawer.is_in_boundscCs|jS)z,Return the length of the region to be drawn.)r)rrrr__len__'szAbstractDrawer.__len__cCsZ|j|j}|jdur|j}nt|j|j}|jdur"|j}||fSt|j|j}||fS)N)rzcurrent_track_levelrkr.rlr-)rtrackrkrlrrr_current_track_start_end+s   z'AbstractDrawer._current_track_start_end) r rxryryNNNNNNrN) __name__ __module__ __qualname____doc__rr{r|r}rrrrrrrrw}s* 8" rw)r itertoolsrmathrrrreportlab.graphics.shapesr reportlab.librrr r( lightgreenr7rErKr]r>rhrvrwrrrrs6         $ 0 % \!