ó ž{Ic@sVdefd„ƒYZdefd„ƒYZdd d„ƒYZdd d„ƒYZdS( tChainExceptioncBseZRS((t__name__t __module__(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyRst NodeExceptioncBseZRS((RR(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyRstChaincBskeZdZd„Zd„Zd„Zd d„Zd„Zd„Z d„Z d„Z d „Z d „Z RS( s0Stores a list of nodes that are linked together.cCsi|_d|_dS(sInitiates a node chain: (self).iÿÿÿÿN(tchaintid(tself((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyt__init__s cCs|jd7_|jS(s&Gets a new id for a node in the chain.i(R(R((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyt_get_idscCs |jjƒS(sReturn a list of all node ids.(Rtkeys(R((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pytall_ids$scCsŽ|dk r4||jkr4tdt|ƒƒ‚nV|jƒ}|j|ƒ|j|ƒ|dk r}|j|j|ƒn||j|<|S(s-Attaches node to another: (self, node, prev).sUnknown predecessor: N(tNoneRRtstrR tset_idtset_prevtadd_succ(RtnodetprevR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pytadd(s     cCs¹||jkr(tdt|ƒƒ‚n|j|jƒ}|j|j|ƒ|j|jƒ}x"|D]}|j|j|ƒqiW|j|j|ƒ|j|}|j|ƒ|S(sRDeletes node from chain and relinks successors to predecessor: collapse(self, id).s Unknown ID: ( RRR tget_prevt remove_succtget_succRRtkill(RRtprev_idtsucc_idstiR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pytcollapse5s   cCs6||jkr(tdt|ƒƒ‚n |j|=dS(sNKills a node from chain without caring to what it is connected: kill(self,id).s Unknown ID: N(RRR (RR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyRCscCs‰||jkr(tdt|ƒƒ‚n]|j|j}|dk rq|j|jj|j|jj|ƒƒnd|j|_|SdS(s7Disconnects node from his predecessor: unlink(self,id).s Unknown ID: N(RRR RR tsucctpoptindex(RRR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pytunlinkJs -cCsŒ||jkr(tdt|ƒƒ‚n`||jkrPtdt|ƒƒ‚n8|j|ƒ|j|jj|ƒ|j|j|ƒdS(s.Connects son to parent: link(self,son,parent).s Unknown ID: N(RRR RRtappendR(Rtparenttchild((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pytlinkUs cCse||ks%||j|jƒkr)tSx5|j|jƒD]}|j||ƒr=tSq=WtSdS(sQCheck if grandchild is a subnode of parent: is_parent_of(self,parent,grandchild).N(RRtTruet is_parent_oftFalse(RR!t grandchildtsn((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyR%`s %cCs›||jks||jkr-tdƒ‚n|j||ƒ sL||krPgSxD|j|jƒD]/}|j||ƒrd|g|j||ƒSqdWdS(sdReturns a list of all node_ids between two nodes (excluding start, including end): trace(start,end).s Unknown node.N(RRR%Rttrace(RtstarttfinishR(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyR)ksN(RRt__doc__RR R R RRRRR#R%R)(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyRs      tNodecBsteZdZd d„Zd„Zd„Zd„Zd„Zd„Z d„Z d„Z d „Z d „Z d „ZRS( sA single node.cCs(d|_||_d|_g|_dS(sRRepresents a node with one predecessor and multiple successors: (self, data=None).N(R RtdataRR(RR.((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyRxs   cCs+|jdk rtdƒ‚n||_dS(s1Sets the id of a node, if not set yet: (self,id).sNode id cannot be changed.N(RR R(RR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyRscCs|jS(sReturns the node's id: (self).(R(R((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pytget_id…scCs|jS(s0Returns a list of the node's successors: (self).(R(R((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyR‰scCs|jS(s1Returns the id of the node's predecessor: (self).(R(R((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyRscCs<t|tgƒƒr(|jj|ƒn|jj|ƒdS(s3Adds a node id to the node's successors: (self,id).N(t isinstancettypeRtextendR (RR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyR‘scCs|jj|ƒdS(s8Removes a node id from the node's successors: (self,id).N(Rtremove(RR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyR˜scCs1t|tgƒƒs$tdƒ‚n||_dS(s,Sets the node's successors: (self,new_succ).s$Node successor must be of list type.N(R0R1RR(Rtnew_succ((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pytset_succœscCs ||_dS(s'Sets the node's predecessor: (self,id).N(R(RR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyR¢scCs|jS(sReturns a node's data: (self).(R.(R((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pytget_data¦scCs ||_dS(s Sets a node's data: (self,data).N(R.(RR.((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pytset_dataªsN(RRR,R RRR/RRRRR5RR6R7(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyR-us          N(((t ExceptionRRRR-(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Nexus/Nodes.pyts^