o RŀgD@sdZddlZddlZddlmZzddlmZddlmZWne y0ddl m Z e ddwzddl m Z Wne yKddl m Z e d dwdd lmZdd lmZdd dZddZddZGdddZdS)zClasses and functions to visualise a KGML Pathway Map. The KGML definition is as of release KGML v0.7.1 (http://www.kegg.jp/kegg/xml/docs/) Classes: N)BytesIO)colors)canvas)MissingPythonDependencyErrorz.Install reportlab if you want to use KGML_vis.)Imagez+Install pillow if you want to use KGML_vis.)urlopen)Pathwayffffff?cCs,t|}dD] }t|||t||q|S)zReturn darkened color as a ReportLab RGB color. Take a passed color and returns a Reportlab color that is darker by the factor indicated in the parameter. )redgreenblue)color_to_reportlabsetattrgetattr)colorfactornewcolarI/var/www/html/myenv/lib/python3.10/site-packages/Bio/Graphics/KGML_vis.pydarken+srcCst|tjr|St|tr8|dr|ddt|dkr#t|Sztj|ddWSty7t ddwt|t rBtj|S|S)anReturn the passed color in Reportlab Color format. We allow colors to be specified as hex values, tuples, or Reportlab Color objects, and with or without an alpha channel. This function acts as a Rosetta stone for conversion of those formats to a Reportlab Color object, with alpha value. Any other color specification is returned directly 0x#T)hasAlphaz3Your reportlab seems to be too old, try 2.7 onwardsN) isinstancerColorstr startswithreplacelenHexColor TypeError RuntimeErrortuple)rrrrr 7s&         r cCsFt|}tt|}tjddd}|j}|| |d|S)zReturn filename of temporary file containing downloaded image. Create a new temporary file to hold the image file at the passed URL and return the filename. Fz.png)deletesuffixPNG) rreadropenrtempfileNamedTemporaryFilenameclosesave)urlimgimffnamerrrget_temp_imagefilenameUs  r4c@seZdZdZ              dddZd d Zd d Zd dZddZddZ ddZ ddZ ddZ ddZ ddZdS) KGMLCanvaszr?r@rJrrr__init__hs  zKGMLCanvas.__init__c Cs|jr!tj|jjr|jj}nt|jj}t|}|j \}}n|jj dd|jj dd}}t j |d|dd|j d|dd|j dfd|_|j|j|j|j|j d|jj dd|j d|jj dd|jr|j|jdd|jd| |j|dd|j|jr||jr||jr||jr||jr| |j!dS)z$Add the map elements to the drawing.r)bottomuppagesizeN)"rIospathisfiler;imager4rr)sizeboundsrCanvasrJdrawingsetFontrErF translate saveStatescale drawImage restoreStater<_KGMLCanvas__add_mapsr@!_KGMLCanvas__add_reaction_entriesr=_KGMLCanvas__add_orthologsr>_KGMLCanvas__add_compoundsr?_KGMLCanvas__add_genesr.)rKfilename imfilenamer1cwidthcheightrrrdrawsH    "  zKGMLCanvas.drawcCs\|jjD]'}|jD]!}|jd|jd|||jr*|jd||q qdS)a+Add maps to the drawing of the map (PRIVATE). We do this first, as they're regional labels to be overlaid by information. Also, we want to set the color to something subtle. We're using Hex colors because that's what KGML uses, and Reportlab doesn't mind. z#888888z#DDDDDDN) r;mapsgraphicsrYsetStrokeColor setFillColor_KGMLCanvas__add_graphicsrD_KGMLCanvas__add_labels)rKmgrrr __add_mapss      zKGMLCanvas.__add_mapsc CsN|jdkrD|j}|jd\}}|jdur|j|jn|jd||||jD] \}}|||q-|j||jd|jdkr[|jj |j |j |jdddddS|jdkr|jj |j |jd|j |j d|j|j t|j|j d ddddS|jd kr|jj|j |jd|j |j d|j|j ddddSdS) zAdd the passed graphics object to the map (PRIVATE). Add text, add after the graphics object, for sane Z-ordering. linerNrMcircle?)strokefillroundrectangleg? rectangle)typerY beginPathcoordswidth setLineWidthmoveTolineTodrawPathrtxy roundRectheightminrect)rKrkprrrrr__add_graphicssF           zKGMLCanvas.__add_graphicsc Cs8|jdkrGt|jd}t||kr t|dt|d}}n t|dt|}}|j|\}}|j|\}}d||d||} } n|jdkrT|j|j} } n |jdvr`|j|j} } |jjdkru|j} |j |j |j dnt|jdkr|j} n |jd d d } |j | | | |j |j |j d S) zAdd labels for the passed graphics objects to the map (PRIVATE). We don't check that the labels fit inside objects such as circles/ rectangles/roundrectangles. rsrurMrt)ryrxmaprNN z...) rzr r|intrr_parentr,rYrZrErFdrawCentredString) rKrkmid_idxidx1idx2x1y1x2y2rrtextrrr __add_labelss(     zKGMLCanvas.__add_labelscCn|jjD]0}|jD]*}|jt|j|jt|j| ||j r3|jt |j| |q qdS)zAdd 'ortholog' Entry elements to the drawing of the map (PRIVATE). In KGML, these are typically line objects, so we render them before the compound circles to cover the unsightly ends/junctions. N) r; orthologsrkrYrlr fgcolorrmbgcolorrnrBrro)rKorthologrqrrr__add_orthologs+    zKGMLCanvas.__add_orthologscCr)zAdd Entry elements for Reactions to the map drawing (PRIVATE). In KGML, these are typically line objects, so we render them before the compound circles to cover the unsightly ends/junctions N) r;reaction_entriesrkrYrlr rrmrrnrCrro)rKreactionrqrrr__add_reaction_entries<rz!KGMLCanvas.__add_reaction_entriesc Cs|jjD]H}|jD]B}t|j}|js|j|j9_|j t|j |j || ||j rK|js8d}nd}|j tddd|||q qdS)z:Add compound elements to the drawing of the map (PRIVATE).r:rMg?N)r; compoundsrkr r is_reactantalpharHrYrlrrmrnrArrro)rKcompoundrq fillcolortrrr__add_compoundsMs"      zKGMLCanvas.__add_compoundscCr)z6Add gene elements to the drawing of the map (PRIVATE).N) r;genesrkrYrlr rrmrrnrArro)rKgenerqrrr __add_genesas    zKGMLCanvas.__add_genescCsrt|jjD]0}|jdkr|jddn|j|jD]}|jj|d}||j ||||j qqdS)aAdd relations to the map (PRIVATE). This is tricky. There is no defined graphic in KGML for a relation, and the corresponding entries are typically defined as objects 'to be connected somehow'. KEGG uses KegSketch, which is not public, and most third-party software draws straight line arrows, with heads to indicate the appropriate direction (at both ends for reversible reactions), using solid lines for ECrel relation types, and dashed lines for maplink relation types. The relation has: - entry1: 'from' node - entry2: 'to' node - subtype: what the relation refers to Typically we have entry1 = map/ortholog; entry2 = map/ortholog, subtype = compound. maplinkr7rMN) listr; relationsrzrYsetDashsubtypesentries_KGMLCanvas__draw_arrowentry1entry2)rKrelationssubtyperrr__add_relationsls   zKGMLCanvas.__add_relationscCs|j|j}}d|dd|ddd|dd|ddf}d|dd|ddd|dd|ddf}|j}|dd|dkrX|ddkrnn:|d|dkr{||d|dd||d|ddnh||d|dd||d|ddnO|dd|dkr|ddkrnn9|d|dkr||d|dd||d|ddn||d|dd||d|dd|j|dS)zDraw an arrow between given Entry objects (PRIVATE). Draws an arrow from the g_from Entry object to the g_to Entry object; both must have Graphics objects. rurrMN)rWrYr{rrr)rKg_fromg_to bounds_from bounds_to centre_from centre_torrrr __draw_arrows* ,,zKGMLCanvas.__draw_arrowN)FTTTTFr6r7TTTTTr8)__name__ __module__ __qualname____doc__rLrir`rnrorbrarcrd_KGMLCanvas__add_relationsrrrrrr5es6 &:.# "r5)r )rrRr*ior reportlab.librreportlab.pdfgenr ImportErrorBiorPILrurllib.requestrBio.KEGG.KGML.KGML_pathwayrrr r4r5rrrrs>