o Rŀg-@sHdZddlmZddlmZddlmZedddZGdddZ d S) zTrack module. Provides: - Track - Container for a single track on the diagram, containing FeatureSet and GraphSet objects For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com )colors) FeatureSet)GraphSetg333333?c@seZdZdZddddddddeddejddd d dd d d dddddddfddZddZd#ddZ ddZ ddZ ddZ ddZ d$ddZdd Zd!d"ZdS)%Tracka Track. Attributes: - height Int describing the relative height to other trackscale_fontsizes in the diagram - name String describing the track - hide Boolean, 0 if the track is not to be drawn - start, end Integers (or None) specifying start/end to draw just a partial track. - greytrack Boolean, 1 if a grey background to the track is to be drawn - greytrack_labels Int describing how many track-identifying labels should be placed on the track at regular intervals - greytrack_font String describing the font to use for the greytrack labels - greytrack_fontsize Int describing the font size to display the labels on the grey track - greytrack_font_rotation Int describing the angle through which to rotate the grey track labels (Linear only) - greytrack_font_color colors.Color describing the color to draw the grey track labels - scale Boolean, 1 if a scale is to be drawn on the track - scale_format String, defaults to None, when scale values are written as numerals. Setting this to 'SInt' invokes SI unit-like multiples, such as Mbp, Kbp and so on. - scale_color colors.Color to draw the elements of the scale - scale_font String describing the font to use for the scale labels - scale_fontsize Int describing the size of the scale label font - scale_fontangle Int describing the angle at which to draw the scale labels (linear only) - scale_ticks Boolean, 1 if ticks should be drawn at all on the scale - scale_largeticks Float (0->1) describing the height of large scale ticks relative to the track height. - scale_smallticks Float (0->1) describing the height of large scale ticks relative to the track height. - scale_largetick_interval Int, describing the number of bases that should separate large ticks - scale_smalltick_interval Int, describing the number of bases that should separate small ticks - scale_largetick_labels Boolean describing whether position labels should be written over large ticks - scale_smalltick_labels Boolean describing whether position labels should be written over small ticks - axis_labels Boolean describing whether the value labels should be placed on the Y axes Nrr Helvetica-g?g333333?g.Ag@cCs|dur|} |dur |} d|_i|_||_|durt||_nd|_||_||_||_||_||_ ||_ ||_ ||_ | |_ | |_| |_| |_| |_||_||_||_||_||_||_||_||_||_||_dS)a( Initialize. Arguments: - height Int describing the relative height to other tracks in the diagram - name String describing the track - hide Boolean, 0 if the track is not to be drawn - greytrack Boolean, 1 if a grey background to the track is to be drawn - greytrack_labels Int describing how many track-identifying labels should be placed on the track at regular intervals - greytrack_font String describing the font to use for the greytrack labels - greytrack_fontsize Int describing the font size to display the labels on the grey track - greytrack_font_rotation Int describing the angle through which to rotate the grey track labels (Linear only) - greytrack_font_color colors.Color describing the color to draw the grey track labels (overridden by backwards compatible argument with UK spelling, colour). - scale Boolean, 1 if a scale is to be drawn on the track - scale_color colors.Color to draw the elements of the scale (overridden by backwards compatible argument with UK spelling, colour). - scale_font String describing the font to use for the scale labels - scale_fontsize Int describing the size of the scale label font - scale_fontangle Int describing the angle at which to draw the scale labels (linear only) - scale_ticks Boolean, 1 if ticks should be drawn at all on the scale - scale_largeticks Float (0->1) describing the height of large scale ticks relative to the track height. - scale_smallticks Float (0->1) describing the height of large scale ticks relative to the track height. - scale_largetick_interval Int, describing the number of bases that should separate large ticks - scale_smalltick_interval Int, describing the number of bases that should separate small ticks - scale_largetick_labels Boolean describing whether position labels should be written over large ticks - scale_smalltick_labels Boolean describing whether position labels should be written over small ticks - name String to help identify the track - height Relative height to draw the track - axis_labels Boolean describing whether the value labels should be placed on the Y axes Nrr)_next_id_setsheightstrnamehidestartend greytrackgreytrack_labelsgreytrack_fontsizegreytrack_fontgreytrack_font_rotationgreytrack_fontcolorscale scale_format scale_color scale_fontscale_fontsizescale_fontangle scale_ticksscale_largeticksscale_smallticksscale_largetick_intervalscale_smalltick_intervalscale_largetick_labelsscale_smalltick_labels axis_labels)selfrrrrrrrrgreytrack_font_colorrrrrrrr!r r"r#r$r%r&r'rrgreytrack_font_colour scale_colourr,U/var/www/html/myenv/lib/python3.10/site-packages/Bio/Graphics/GenomeDiagram/_Track.py__init__RsBO  zTrack.__init__cCs,|j|_||_||j|j<|jd7_dS)z=Add a preexisting FeatureSet or GraphSet object to the track.rN)r idparentr )r(setr,r,r-add_sets z Track.add_setfeaturecKsZttd}||}|D] }t||||q |j|_||_||j|j<|jd7_|S)zCreate a new FeatureSet or GraphSet object. Create a new FeatureSet or GraphSet object, add it to the track, and return for user manipulation )r3graphr)rrsetattrr r/r0r )r(typeargs type_dictr1keyr,r,r-new_sets   z Track.new_setcCs |j|=dS)z1Remove the set with the passed id from the track.Nr )r(set_idr,r,r-del_sets z Track.del_setcCt|jS)z(Return the sets contained in this track.)listr valuesr(r,r,r-get_setszTrack.get_setscCr>)z3Return the ids of all sets contained in this track.)r?r keysrAr,r,r-get_idsrCz Track.get_idscCsgg}}|jdur||j|jdur||j|jD]}|\}}||||q |r:t|}nd}|rFt|}||fSd}||fS)z@Return the lowest and highest base (or mark) numbers as a tuple.N)rappendrr r@rangeminmax)r(lowshighsr1lowhighr,r,r-rGs"         z Track.rangecCsb|s|Sd|jd|jdg}|dt|j|jD] }|d|j|qd|S)zReturn a formatted string with information about the track. Arguments: - verbose - Boolean indicating whether a short or complete account of the track is required  <: >%d setszset:   __class__rrFlenr join)r(verboseoutstrr9r,r,r- to_strings  zTrack.to_stringcCs |j|S)z"Return the set with the passed id.r;)r(r9r,r,r- __getitem__s zTrack.__getitem__cCs6d|jd|jdg}|dt|jd|S)z;Return a formatted string with information about the Track.rNrOrPrQrRrS)r(rXr,r,r-__str__s z Track.__str__)r3)r)__name__ __module__ __qualname____doc___greyrblackr.r2r:r=rBrErGrYrZr[r,r,r,r-r sN3 y   rN) r_ reportlab.libr _FeatureSetr _GraphSetrColorr`rr,r,r,r-s