Ñò Rá¬Pc@s@dZddkZddkTddklZddkZeidƒZdefd„ƒYZ defd „ƒYZ d efd „ƒYZ d efd „ƒYZ dfd„ƒYZ defd„ƒYZdefd„ƒYZde fd„ƒYZedjo;ddkiiZe ƒZeidƒeeƒGHeiddddddddd d!g ƒeiddfd"d#ƒeiddfd"d$ƒeiddfd"d%ƒeiddfd"d&ƒeiddfd"d'd(d)ƒeidd d!dddfƒeieƒGHHd*d+GHd,eiƒGHd-eiƒGHd.eidƒGHd/ei dƒGHd0gZ!ei"dƒD]Z#e!e#d1qr[!GHd2ei$ƒGHd3ei%ƒGHd4eeƒGHei&d5ƒHd6GHd,eiƒGHd-eiƒGHd2ei$ƒGHd4eeƒGHei'ddfƒHd7GHd,eiƒGHd-eiƒGHd2ei$ƒGHd4eeƒGHei'ddfƒHd8GHd,eiƒGHd-eiƒGHd2ei$ƒGHd4eeƒGHHd9GHei(dƒZ)ee)ƒGHd:e)i*dd fƒGHd;e)i+dd dfƒGHd<e)i+e)i,dgƒGHd=e)i-d!dgƒGHndS(>sá BASIC GRAPH CLASS *********************************** *** *** BASIC GRAPH CLASS *** *** written by Markus Doering *** BGBM, Berlin, 2003 *** *********************************** $RCSfile: graph.py,v $ $Revision: 1231 $ $Author: j.holetschek $ $Date: 2012-11-21 15:12:34 +0100 (Mi, 21. Nov 2012) $ Some classes used for the graph class, a basic class for undirected graphs. It stores the graph as a matrix with the matrix values being a dictionary if filled and None if not. iÿÿÿÿN(t*(tuniquespywrapper.graphtNodeNotExistingErrorcBseZdZd„ZRS(sIException raised when trying to reference a non existing node of a graph.cCsti|ƒdS(N(t Exceptiont__init__(tself((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR"s(t__name__t __module__t__doc__R(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR stNodeAlreadyExistingErrorcBseZdZd„ZRS(sHException raised when trying to add an already existing node of a graph.cCsti|ƒdS(N(RR(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR&s(RRRR(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR $stEdgeNotExistingErrorcBseZdZd„ZRS(sIException raised when trying to reference a non existing edge of a graph.cCsti|ƒdS(N(RR(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR*s(RRRR(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR (stEdgeAlreadyExistingErrorcBseZdZd„ZRS(sHException raised when trying to add an already existing edge of a graph.cCsti|ƒdS(N(RR(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR.s(RRRR(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR ,stgraphcBs7eZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z d „Z d „Z hd!d „Zd „Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zhd„Zd„Zd„Zd„Zd„Z d„Z!d„Z"d „Z#RS("s‰A basic class for undirected graphs. It stores the graph as a matrix with the matrix values being a dictionary if filled and None if not.cCstgƒ|_h|_dS(N(tsymmetricMatrixtmatrixtedges(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR7scCs+y|ii|ƒWntƒ‚nXdS(s(add one node to the graph without edges.N(RtaddRowR (Rtnode((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytaddNode=scCs"x|D]}|i|ƒqWdS(s!add a list of nodes to the graph.N(R(RtnodesR((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytaddNodesDsc Csty]g}|i|ƒD]}||dq~}x|D]}|i|=q8W|ii|ƒWntƒ‚nXdS(s8remove node from graph. also remove all connected edges.iN(tlistAdjacentEdgesRRtdelRowR(RRt_[1]tetadjEdgestedgename((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytdelNodeIs.cCs|iii|ƒpdSdS(Nii(Rt_colsthas_key(RR((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyt nodeExistsSscCs |iiƒS(s3return a list of all nodes (vertices) of the graph.(RtlistRows(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyt listNodesXscCsvg}|ii|ƒ}xW|iƒD]I\}}t|ƒthƒjo$t|ƒdjo|i|ƒq%q%W|S(sList all adjacent nodes.i(RtgetRowtitemsttypetlentappend(RRtadjNodestrowDicttcolR((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytlistAdjacentNodes\s ,cCs&g|_|i||ihƒ|iS(s,List all nodes that are connected to "node".(t_tmptDepthFirstSearcht _listNodes(RR((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytlistConnectedNodeses cCsRh}x|iƒD]}d||y|i|}Wntƒ‚nX|ii|ƒ||fS(sFreturn tuple of 1.value of edge "name" and 2.tuple of connected nodes.(RR RR=(RR?t nodeTuple((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytgetEdge·s  cCsg|ii|ƒp tƒ‚nD|i|}|i|=|ii|ƒ}||=|ii||ƒdS(sdelete edge "name".N(RRR RR=R>(RR?RRB((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytdelEdge¿s   cCscg}|ii|ƒ}t|ƒthƒjo|iƒ}nx|D]}|i|ƒqHWdS(s,delete all edges between two adjacent nodes.N(RR=R#R.RJ(RRt edgesToDelRRA((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyt cut2NodesÊscCs‘|iƒo tƒ‚nttƒ}ti|iƒ}||_ti|iƒ}||_||_x$|i|ƒD]}|i |ƒqrW|SdS(N( t hasClosedWalktCircleExistingErrorttreetcopytdeepcopyRRtrootR1R(RRRttreeObjt newMatrixRR((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytmakeTreeÔs      cCs`|ii|ƒ}d}xA|iƒD]3}t|ƒthƒjo|t|ƒ7}q%q%W|S(s8return the degree (number of edges connected) of a node.i(RR!R2R#R$(RRtrowtdegreeR(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRWãs cCsVxO|iƒD]A}|i|ƒdjo%|i||hƒdjodSq q WdS(sdreturns 1 if the graph allows circular walks - that is its number of possible spanning trees is > 1.ii(R RWt _testClosed(RR((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRMís   cCsdS(sHreturns 1 if the graph is connected, that is if all nodes are connected.N((R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyt isConnected÷scCsŒ|g}h}xvt|ƒdjob|idƒ}d||<||ƒx8|i|ƒD]'}|i|ƒp|i|ƒqXqXWqWdS(s\Traverse the graph in breadth-first search order and apply the function func to every node..iiN(R$tpopR)RR%(RtstarttfunctqueuetseenRtneighbor((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytBreadthFirstSearchýs   cCs|ii|ƒdS(N(R*R%(RR((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR, scCsYd||<||ƒx>|i|ƒD]-}|i|ƒp|i|||ƒq$q$WdS(sZTraverse the graph in depth-first search order and apply the function func to every node..iN(R)RR+(RR[R\t_visitedR((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR+ s   cCsdS(sufind the shortest possible path of two nodes using the single-source or all-pair shortest path (SSSP/APSP) algorithm.N((RRERF((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyt shortestPathscCsdS(sCfind the minimum spanning tree using Kruskal's or Prim's algorithm.N((RRERF((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytminimumSpanningTreescCsdS(sfind the Euler path.N((R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyt EulerPathscCsdS(sfind the Euler path.N((R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytHamiltonianPath scCs|iid|iƒS(s)return simple string output of the graph.s: (t __class__Rt __reprGraph__(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyt__repr__&scCsmd}x"|iƒD]}||d7}qWx;|iiƒD]*\}}||dd|dd7}q;W|S(s)return simple string output of the graph.ts, it-i(R7RR"(RtresultRRAR((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRg*s  "cCs‘|i|ƒ}x{|D]s}|i|dƒpY|d|jodS|iƒ}d||d<|i||d|ƒdjodSqqWdS(s(recursive testing function for each nodeii(RRRPRX(Rt startNodetcurrNodetdictOfUsedEdgesRRAtnewDict((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRX4s   N($RRRRRRRRR R)R-R1R7R;R3R8RCRGRRIRJRLRURWRMRYR`R,R+RbRcRdReRhRgRX(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR 5sB                     RNcBseZdZd„ZRS(sPException raised when trying to change the tree into a graph containing circles.cCsti|ƒdS(N(RR(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRMs(RRRR(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRNKstRootMissingErrorcBseZdZd„ZRS(sPException raised when trying to change the tree into a graph containing circles.cCsti|ƒdS(N(RR(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRQs(RRRR(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRpOsROcBsVeZdZd„Zhdd„Zd„Zd„Zgd„Zd„Z d„Z RS( t.cCsti|ƒd|_dS(N(R RR3RR(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRWs cCsP|}ti||||ƒ|iƒo tƒ‚nti||||ƒdS(s>add edge, but check first if graph is still a tree afterwards.N(R R8RMRN(RRR6R?t testGraph((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyR8[s   cCsŸ|\}}|i|ƒdjo tƒ‚n|i|ƒdjo tƒ‚n|g}||jo|gS|i|||ƒ}|djo|SgSdS(s?return a path (list of nodes) with all nodes between two given.iN(RRt_DFSSearchNodeR3(RRDR[tendt nodesVisitedRk((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytpathBetween2Nodesds      cCsH|d}g}x+|dD]}||i||fƒ7}qWt|ƒS(s9return a path (list of nodes) connecting all nodes given.ii(RvR(RRR[Rktnext((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pytpathConnectingNodesss   c Csæ|idjo tƒ‚ng}|igg}t|ƒ}x-|D]%}|i|i|i|fƒƒqEWxkttg}|D]}|t|ƒq‚~ƒƒD]6}x-|D]%}y|i||ƒWq¯q¯Xq¯Wq¢Wt|ƒS(sŸreturn a list of tuples (node/edge-value) connecting all nodes given to the root node. Order them from root downwards according to distance from root.N( RRR3RpRR%RvtrangeR<R$( RRRktpathsRRtxtdepthtpath((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyt listOrderedNodesConnectedViaRoot{s"  #4 cCsd|id|iƒS(Ns Rooted Tree (s): (RRRg(R((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRhscCs‰x‚|i|ƒD]q}||jo|i|ƒ|S||jo?|}|i|ƒ|i|||ƒ}|djo|SqqWdS(N(R)R%RsR3(RRmtendNodet visitedNodesRtNewVisitedNodestdeeper((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyRs”s      N( RRRRR3R8RvRxR~RhRs(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyROUs     t__main__theiotmarkustpiatbriantsilketpetertstefantewaldtmelittatirenetpaulR6tverliebttext geschwistersschlimm verliebts bald verliebtR?tSilBriRjiPs All Nodes %ss All Edges %ssDegree(markus): %isadjacentNodes(markus): %ssadjacentEdges(pia): %sisgraph has a closed walk ? %isisolated nodes: %ssprint graph: %sisdeleted edge 1scut off nodes silke & brianscut off nodes silke & silkes##### TREE NOW !!! #####smarkus-irene: %ssmarkus-irene-silke: %ssroot brian: %ssroot-ordered paul,brian: %s(.RRPtbiocase.wrapper.graph.matrixtbiocase.tools.various_functionsRtloggingt getLoggertlogRRR R R R RNRpRORtbiocase.tools.showobjectttoolst showobjecttobjtgRtstrRR8R;tviewR RCRWR)RRRRMR7RJRLRUttRvRxRRR~(((sC/srv/www/vhosts/sammlung/BioCase/lib/biocase/wrapper/graph/graph.pyts„    ÿP    + 1