RihdZddlmZGddeZGddeZGddZGd d Zy ) aNLinked list functionality for use in Bio.Nexus. Provides 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 Nexus.Trees to store phylogenetic trees. Bug reports to Frank Kauff (fkauff@biologie.uni-kl.de) )OptionalceZdZdZy)ChainExceptionz1Provision for the management of Chain exceptions.N__name__ __module__ __qualname____doc__G/home/agent/.friday_env/lib/python3.12/site-packages/Bio/Nexus/Nodes.pyrrs;r rceZdZdZy) NodeExceptionz0Provision for the management of Node exceptions.Nrr r r rrs:r rcveZdZdZddZdefdZdeefdZdddd edzdefd Z d Z d Z d Z dZ dZdZy)Chainz0Stores a list of nodes that are linked together.returnNc i|_d|_y)zInitialize a node chain.N)chainidselfs r __init__zChain.__init__!s&( r cD|xjdz c_|jS)z/Get a new id for a node in the chain (PRIVATE).rrs r _get_idz Chain._get_id&s 1 wwr cHt|jjS)zReturn a list of all node ids.)listrkeysrs r all_idsz Chain.all_ids+sDJJOO%&&r nodeNodeprevc|%||jvrtdt|z|j}|j ||j |||j|j |||j|<|S)zAttach node to another.zUnknown predecessor: )rrstrrset_idset_prevadd_succ)rr"r$rs r addz Chain.add/sy  DJJ 6 !83t9!DE EB KKO MM$  4 ))"-!DJJrN r c||jvrtdt|z|j|j}|j|j ||j|j }|D] }|j|j |"|j|j||j|}|j||S)z=Delete node from chain and relinks successors to predecessor. Unknown ID: ) rrr&get_prev remove_succget_succr(r)kill)rrprev_idsucc_idsir"s r collapsezChain.collapse<s TZZ  #b'!9: :**R.))+ 7''+::b>**, ,A JJqM " "7 + , 7$$X.zz"~ "  r ch||jvrtdt|z|j|=y)z>Kill a node from chain without caring to what it is connected.r,N)rrr&rrs r r0z Chain.killJs- TZZ  #b'!9: : 2r cJ||jvrtdt|z|j|j}|N|j|jj |j|jj |d|j|_|S)z%Disconnect node from his predecessor.r,N)rrr&r$succpopindex)rrr1s r unlinkz Chain.unlinkQs TZZ  #b'!9: :jjn))G" 7#((,,TZZ-@-E-E-K-KB-OP"&DJJrN Nr cF||jvrtdt|z||jvrtdt|z|j||j|jj ||j|j |y)zConnect son to parent.r,N)rrr&r;r8appendr()rparentchilds r linkz Chain.link\s  " #e*!<= = 4:: % #f+!=> > KK  JJv  # # * *5 1 JJu  & &v .r c||k(s||j|jvry|j|jD]}|j||syy)z+Check if grandchild is a subnode of parent.TF)rr/ is_parent_of)rr> grandchildsns r rBzChain.is_parent_ofgs_  :F1C1L1L1N#Njj(113 $$R4 r c||jvs||jvr td|j||r||k(rgS|j|jD],}|j||s|g|j ||zcSy)zQReturn a list of all node_ids between two nodes (excluding start, including end).z Unknown node.N)rrrBr/trace)rstartfinishrDs r rFz Chain.tracers  "fDJJ&>0 0  /5F?I**U#,,. 5B  V,tdjjV444 5r )rNN)rrr r rintrrr!r*r4r0r;r@rBrFr r r rrsb:  'c'  cDj C    / 5r rcTeZdZdZddZdZdZdZdZdZ d Z d Z d Z d Z d Zy)r#zA single node.Nc<d|_||_d|_g|_y)z>Represent a node with one predecessor and multiple successors.N)rdatar$r8rrMs r rz Node.__init__s   r c@|j td||_y)z%Set the id of a node, if not set yet.NzNode id cannot be changed.)rrr6s r r'z Node.set_ids 77  <= =r c|jS)zReturn the node's id.rrs r get_idz Node.get_ids wwr c|jS)z'Return a list of the node's successors.)r8rs r r/z Node.get_succ yyr c|jS)z(Return the id of the node's predecessor.r$rs r r-z Node.get_prevrSr ct|tgr|jj|y|jj |y)z'Add a node id to the node's successors.N) isinstancetyper8extendr=r6s r r)z Node.add_succs4 b$r( # II  R II  R r c:|jj|y)z,Remove a node id from the node's successors.N)r8remover6s r r.zNode.remove_succs r cRt|tgs td||_y)zSet the node's successors.z$Node successor must be of list type.N)rWrXrr8)rnew_succs r set_succz Node.set_succs#(DH- FG G r c||_y)zSet the node's predecessor.NrUr6s r r(z Node.set_prevs  r c|jS)zReturn a node's data.rMrs r get_dataz Node.get_datarSr c||_y)zSet a node's data.NrarNs r set_dataz Node.set_datas  r rI)rrr r rr'rQr/r-r)r.r^r(rbrdr r r r#r#}s< ! r r#N)r typingr Exceptionrrrr#r r r rgs>