o Rŀg=@svdZzddlmZWn eydZYnwddlmZddlmZddlm Z ddl m Z d d Z Gd d d Z dS) aProvides a container for information concerning the tracks to be drawn in a diagram. It also provides the interface for defining the diagram (possibly split these functions in later version?). 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 - namely SeqRecord objects containing SeqFeature objects. )renderPMN)_write)CircularDrawer) LinearDrawer)TrackcGs|D] }|dur |SqdS)z-Return the first non-null argument (PRIVATE).N)argsargrrW/var/www/html/myenv/lib/python3.10/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py_first_defined&s r c@seZdZdZ                d0d d ZddZ                  d1ddZd2ddZd3ddZddZ ddZ ddZ dd Z d!d"Z d4d$d%Zd&d'Zd(d)Zd*d+Zd,d-Zd.d/ZdS)5DiagramaDiagram container. Arguments: - name - a string, identifier for the diagram. - tracks - a list of Track objects comprising the diagram. - format - a string, format of the diagram 'circular' or 'linear', depending on the sort of diagram required. - pagesize - a string, the pagesize of output describing the ISO size of the image, or a tuple of pixels. - orientation - a string describing the required orientation of the final drawing ('landscape' or 'portrait'). - x - a float (0->1), the proportion of the page to take up with even X margins t the page. - y - a float (0->1), the proportion of the page to take up with even Y margins to the page. - xl - a float (0->1), the proportion of the page to take up with the left X margin to the page (overrides x). - xr - a float (0->1), the proportion of the page to take up with the right X margin to the page (overrides x). - yt - a float (0->1), the proportion of the page to take up with the top Y margin to the page (overrides y). - yb - a float (0->1), the proportion of the page to take up with the bottom Y margin to the page (overrides y). - circle_core - a float, the proportion of the available radius to leave empty at the center of a circular diagram (0 to 1). - start - an integer, the base/aa position to start the diagram at. - end - an integer, the base/aa position to end the diagram at. - tracklines - a boolean, True if track guidelines are to be drawn. - fragments - and integer, for a linear diagram, the number of equal divisions into which the sequence is divided. - fragment_size - a float (0->1), the proportion of the space available to each fragment that should be used in drawing. - track_size - a float (0->1), the proportion of the space available to each track that should be used in drawing with sigils. - circular - a boolean, True if the genome/sequence to be drawn is, in reality, circular. NcircularA3 landscape皙?F ?TcCsi|_||_||_||_||_||_||_||_||_| |_ | |_ | |_ | |_ | |_ ||_|dur5||_n |jdkr>d|_nd|_||_||_||_g|_d|_dS)z6Initialize. gdd = Diagram(name=None) Nrg?)tracksnameformatpagesize orientationxyxlxrytybstartend tracklines fragments fragment_size track_sizer circle_corecross_track_linksdrawing)selfrrrrrrrrrrr r!r"r#r$r%rr&rrr __init__Vs2  zDiagram.__init__cCs*|jD] }t||rt|||qdS)zSet the passed attribute of all tracks in the set to the passed value. Arguments: - attr - An attribute of the Track class. - value - The value to set that attribute. set_all_tracks(self, attr, value) N)rvalueshasattrsetattr)r)attrvaluetrackrrr set_all_trackss   zDiagram.set_all_trackscCsZ|dkrTt|t||jt||jt||jt||jt||jt||jt||jt| |j t| |j t| |j t| |j t| |j t||jt||jt||j}nOt|t||jt||jt||jt||jt||jt||jt||jt| |j t| |j t| |j t| |j t||jt||jt||jt||j}||j|_dS)zvDraw the diagram, with passed parameters overriding existing attributes. gdd.draw(format='circular') linearN)rr rrrrrrrrr r!r"r#r$r%r'rrr&drawr()r)rrrrrrrrrr r!r"r#r$r%rr&r'drawerrrr r3sN                               z Diagram.drawtest1.psPSHcCst|j|||dS)aWrite the drawn diagram to a specified file, in a specified format. Arguments: - filename - a string indicating the name of the output file, or a handle to write to. - output - a string indicating output format, one of PS, PDF, SVG, or provided the ReportLab renderPM module is installed, one of the bitmap formats JPG, BMP, GIF, PNG, TIFF or TIFF. The format can be given in upper or lower case. - dpi - an integer. Resolution (dots per inch) for bitmap formats. Returns: No return value. write(self, filename='test1.ps', output='PS', dpi=72) )dpi)rr()r)filenameoutputr8rrr writesz Diagram.writecCs(ddlm}|}|||||S)aReturn a byte string containing the diagram in the requested format. Arguments: - output - a string indicating output format, one of PS, PDF, SVG, JPG, BMP, GIF, PNG, TIFF or TIFF (as specified for the write method). - dpi - Resolution (dots per inch) for bitmap formats. Returns: Return the completed drawing as a bytes string in a prescribed format. r)BytesIO)ior<r;getvalue)r)r:r8r<handlerrr write_to_strings zDiagram.write_to_stringcCs||durtd||jvr||j|<n#t|}||D]}||jkr0|j||j|d<q||j|<||j|_dS)aAdd a Track object to the diagram. It also accepts instructions to place it at a particular level on the diagram. Arguments: - track - Track object to draw. - track_level - an integer. The level at which the track will be drawn (above an arbitrary baseline). add_track(self, track, track_level) NzMust specify trackr) ValueErrorrsorted get_levelsreverse track_level)r)r0rEoccupied_levelsvalrrr add_tracks     zDiagram.add_trackcKst}|D] }t||||q||jvr||j|<n"t|}||D]}||kr7|j||j|d<q'||j|<||j|_|S)a3Add a new Track to the diagram at a given level. The track is returned for further user manipulation. Arguments: - track_level - an integer. The level at which the track will be drawn (above an arbitrary baseline). new_track(self, track_level) r)rr-rrBrCrDrE)r)rEr newtrackkeyrFrGrrr new_track+s      zDiagram.new_trackcCs |j|=dS)zRemove the track to be drawn at a particular level on the diagram. Arguments: - track_level - an integer. The level of the track on the diagram to delete. del_track(self, track_level) Nr)r)rErrr del_trackHs zDiagram.del_trackcCst|jS)z5Return a list of the tracks contained in the diagram.)listrr+r)rrr get_tracksSszDiagram.get_trackscCs"|j|}|j|=|||dS)zMove a track from one level on the diagram to another. Arguments: - from_level - an integer. The level at which the track to be moved is found. - to_level - an integer. The level to move the track to. N)rrH)r) from_levelto_levelauxrrr move_trackWs zDiagram.move_trackrcCsD|}|}i}|D]}|j|||<|||_||7}q ||_dS)a Renumber all tracks consecutively. Optionally from a passed lowest number. Arguments: - low - an integer. The track number to start from. - step - an integer. The track interval for separation of tracks. N)rCrrE)r)lowstepr0levels conversionlevelrrr renumber_tracksds    zDiagram.renumber_trackscCs t|jS)zAReturn a sorted list of levels occupied by tracks in the diagram.rBrrOrrr rCy zDiagram.get_levelscstfddjDS)zlReturn a sorted list of levels occupied by tracks. These tracks are not explicitly hidden. c3s |] }j|js|VqdS)N)rhide).0rJrOrr sz+Diagram.get_drawn_levels..r[rOrrOr get_drawn_levels}szDiagram.get_drawn_levelscCsJgg}}|jD]}|\}}||||q t|t|fS)zgReturn lowest and highest base numbers from track features. Returned type is a tuple. )rr+rangeappendminmax)r)lowshighsr0rUhighrrr ras    z Diagram.rangecCs |j|S)z:Return the track contained at the level of the passed key.rL)r)rJrrr __getitem__r\zDiagram.__getitem__cCs`d|jd|jdg}|dt|j|D]}|d||j|fqd|}|S)z1Return a formatted string describing the diagram.z z %d tracksz Track %d: %s  ) __class__rrblenrrCjoin)r)outstrrYrrr __str__s   zDiagram.__str__)NrrrrrNNNNNNFrNrTr)NNNNNNNNNNNNNNNNNN)r5r6r7)r6r7)rr)__name__ __module__ __qualname____doc__r*r1r3r;r@rHrKrMrPrTrZrCr`rarhrorrrr r .sl) 8 F    r )rsreportlab.graphicsr ImportError Bio.Graphicsr_CircularDrawerr _LinearDrawerr_Trackrr r rrrr s