Ri-hdZddlmZddlmZddlmZejdddZGddZ y ) 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?ceZdZdZddddddddeddej ddd d dd d d dddddddfdZdZddZ dZ dZ dZ dZ ddZdZdZy)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@c||} ||} d|_i|_||_|t||_nd|_||_||_||_||_||_ ||_ ||_ ||_ | |_ | |_| |_| |_| |_||_||_||_||_||_||_||_||_||_||_y)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_colorrrrr r!r"r$r#r%r&r'r(r)r*rrgreytrack_font_colour scale_colours Y/home/agent/.friday_env/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Track.py__init__zTrack.__init__Rs^ ! ,#8  #&K    D DIDI  # 0"4,'>$#7  (&$,.& 0 0(@%(@%&<#&<#&c|j|_||_||j|j<|xjdz c_y)z=Add a preexisting FeatureSet or GraphSet object to the track.rN)ridparentr)r+sets r/add_setz Track.add_sets4 $' 4==!  r1c ttd}||}|D]}t|||||j|_||_||j |j<|xjdz c_|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 )featuregraphr)rrsetattrrr3r4r)r+typeargs type_dictr5keys r/new_setz Track.new_setsr !+X> io )C Cd3i ( ) $' 4==!   r1c|j|=y)z1Remove the set with the passed id from the track.Nr)r+set_ids r/del_setz Track.del_sets JJv r1cHt|jjS)z(Return the sets contained in this track.)listrvaluesr+s r/get_setszTrack.get_setssDJJ%%'((r1cHt|jjS)z3Return the ids of all sets contained in this track.)rErkeysrGs r/get_idsz Track.get_idssDJJOO%&&r1cgg}}|j|j|j|j|j|j|jj D]7}|j \}}|j||j|9|r t |}nd}|rt|}||fSd}||fS)z@Return the lowest and highest base (or mark) numbers as a tuple.N)rappendrrrFrangeminmax)r+lowshighsr5lowhighs r/rNz Track.ranges"e :: ! KK # 88  LL "::$$& C IC KK  LL   d)CC u:DDyDDyr1c|s|Sd|jd|jdg}|jdt|jz|jD]#}|jd|j|%dj |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__rrMlenrjoin)r+verboseoutstrr>s r/ to_stringzTrack.to_stringsV DNN+2dii[:;F MM)c$**o5 6zz 9 djjo%678 999V$ $r1c |j|S)z"Return the set with the passed id.rA)r+r>s r/ __getitem__zTrack.__getitem__szz#r1cd|jd|jdg}|jdt|jzdj |S)z;Return a formatted string with information about the Track.rVrWrXrYrZr[)r+r`s r/__str__z Track.__str__sJ'r$))A67 i#djj/12yy  r1)r8)r)__name__ __module__ __qualname____doc___greyrblackr0r6r?rCrHrKrNrarcrer1r/rr s/f " !"LL!$!$   "9w'r )'*%"!r1rN) ri reportlab.libr _FeatureSetr _GraphSetrColorrjrrlr1r/rqs7!$ S#s#|!|!r1