ó Y_Sc@sbdZdefd„ƒYZdefd„ƒYZdefd„ƒYZdefd„ƒYZd S( sàProvides functionality of a linked list. Each node has one (or none) predecessor, and an arbitrary number of successors. Nodes can store arbitrary data in a NodeData class. Subclassed by Trees to store phylogenetic trees. tChainExceptioncBseZRS((t__name__t __module__(((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyRst NodeExceptioncBseZRS((RR(((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_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.iÿÿÿÿN(tchaintid(tself((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyt__init__s cCs|jd7_|jS(s&Gets a new id for a node in the chain.i(R(R((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyt_get_idscCst|jjƒƒS(sReturn a list of all node ids.(tlistRtkeys(R((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pytall_ids$scCsŽ|dk r4||jkr4tdt|ƒƒ‚nV|jƒ}|j|ƒ|j|ƒ|dk r}|j|j|ƒn||j|<|S(sAttaches node to another.sUnknown predecessor: N(tNoneRRtstrR tset_idtset_prevtadd_succ(RtnodetprevR((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pytadd(s     cCs¹||jkr(tdt|ƒƒ‚n|j|jƒ}|j|j|ƒ|j|jƒ}x"|D]}|j|j|ƒqiW|j|j|ƒ|j|}|j|ƒ|S(s>Deletes node from chain and relinks successors to predecessor.s Unknown ID: ( RRRtget_prevt remove_succtget_succRRtkill(RRtprev_idtsucc_idstiR((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pytcollapse5s   cCs6||jkr(tdt|ƒƒ‚n |j|=dS(s?Kills a node from chain without caring to what it is connected.s Unknown ID: N(RRR(RR((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyRCscCs‰||jkr(tdt|ƒƒ‚n]|j|j}|dk rq|j|jj|j|jj|ƒƒnd|j|_|SdS(s&Disconnects node from his predecessor.s Unknown ID: N(RRRRR tsucctpoptindex(RRR((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pytunlinkJs -cCsŒ||jkr(tdt|ƒƒ‚n`||jkrPtdt|ƒƒ‚n8|j|ƒ|j|jj|ƒ|j|j|ƒdS(sConnects son to parent.s Unknown ID: N(RRRR RtappendR(Rtparenttchild((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pytlinkUs cCse||ks%||j|jƒkr)tSx5|j|jƒD]}|j||ƒr=tSq=WtSdS(s+Check if grandchild is a subnode of parent.N(RRtTruet is_parent_oftFalse(RR"t grandchildtsn((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyR&`s %cCs›||jks||jkr-tdƒ‚n|j||ƒ sL||krPgSxD|j|jƒD]/}|j||ƒrd|g|j||ƒSqdWdS(sRReturns a list of all node_ids between two nodes (excluding start, including end).s Unknown node.N(RRR&Rttrace(RtstarttfinishR)((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyR*ksN(RRt__doc__RR R R RRRR R$R&R*(((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_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(s?Represents a node with one predecessor and multiple successors.N(R RtdataRR(RR/((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyRys   cCs+|jdk rtdƒ‚n||_dS(s&Sets the id of a node, if not set yet.sNode id cannot be changed.N(RR R(RR((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyR€scCs|jS(sReturns the node's id.(R(R((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pytget_id†scCs|jS(s(Returns a list of the node's successors.(R(R((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyRŠscCs|jS(s)Returns the id of the node's predecessor.(R(R((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyRŽscCs<t|tgƒƒr(|jj|ƒn|jj|ƒdS(s(Adds a node id to the node's successors.N(t isinstancettypeRtextendR!(RR((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyR’scCs|jj|ƒdS(s-Removes a node id from the node's successors.N(Rtremove(RR((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyR™scCs1t|tgƒƒs$tdƒ‚n||_dS(sSets the node's successors.s$Node successor must be of list type.N(R1R2RR(Rtnew_succ((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pytset_succscCs ||_dS(sSets the node's predecessor.N(R(RR((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyR£scCs|jS(sReturns a node's data.(R/(R((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pytget_data§scCs ||_dS(sSets a node's data.N(R/(RR/((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pytset_data«sN(RRR-R RRR0RRRRR6RR7R8(((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyR.vs          N(R-t ExceptionRRtobjectRR.(((sE/home/psgendb/BIRCHDEV/pkg/weblogo-3.4/corebio/seq_io/_nexus/Nodes.pyt s_