o Rŀg@sPdZddlmZGdddeZGdddeZGdddZGd d d Zd S) 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) )Optionalc@eZdZdZdS)ChainExceptionz1Provision for the management of Chain exceptions.N__name__ __module__ __qualname____doc__r r C/var/www/html/myenv/lib/python3.10/site-packages/Bio/Nexus/Nodes.pyrrc@r) NodeExceptionz0Provision for the management of Node exceptions.Nrr r r r r r r c@seZdZdZdddZdefddZdeefdd Zdd d d e edefd dZ ddZ ddZ ddZ ddZddZddZdS)Chainz0Stores a list of nodes that are linked together.returnNcCsi|_d|_dS)zInitialize a node chain.N)chainidselfr r r __init__!s zChain.__init__cCs|jd7_|jS)z/Get a new id for a node in the chain (PRIVATE).rrr r r _get_id&sz Chain._get_idcCst|jS)zReturn a list of all node ids.)listrkeysrr r r all_ids+sz Chain.all_idsnodeNodeprevcCsd|dur||jvrtdt||}|||||dur+|j||||j|<|S)zAttach node to another.NzUnknown predecessor: )rrstrrset_idset_prevadd_succ)rrrrr r r add/s   z Chain.addcCs||jvr tdt||j|}|j|||j|}|D] }|j||q%|j|||j|}|||S)z=Delete node from chain and relinks successors to predecessor. Unknown ID: ) rrrget_prev remove_succget_succr!r"kill)rrprev_idsucc_idsirr r r collapse<s   zChain.collapsecCs&||jvr tdt||j|=dS)z>Kill a node from chain without caring to what it is connected.r$N)rrrrrr r r r(Js  z Chain.killcCs^||jvr tdt||j|j}|dur'|j|j|j|j|d|j|_|S)z%Disconnect node from his predecessor.r$N)rrrrsuccpopindex)rrr)r r r unlinkQs    z Chain.unlinkcCsd||jvr tdt|||jvrtdt||||j|j||j||dS)zConnect son to parent.r$N)rrrr1r.appendr!)rparentchildr r r link\s   z Chain.linkcCsH||ks ||j|vrdS|j|D] }|||r!dSqdS)z+Check if grandchild is a subnode of parent.TF)rr' is_parent_of)rr3 grandchildsnr r r r6gs zChain.is_parent_ofcCsn||jvs ||jvrtd|||r||krgS|j|D]}|||r4|g|||Sq!dS)zQReturn a list of all node_ids between two nodes (excluding start, including end).z Unknown node.N)rr r6r'trace)rstartfinishr8r r r r9rs z Chain.trace)rNN)rrrr rintrrrrr#r,r(r1r5r6r9r r r r rs    rc@sjeZdZdZdddZddZddZd d Zd d Zd dZ ddZ ddZ ddZ ddZ ddZdS)rzA single node.NcCsd|_||_d|_g|_dS)z>Represent a node with one predecessor and multiple successors.N)rdatarr.rr>r r r rs z Node.__init__cCs|jdur td||_dS)z%Set the id of a node, if not set yet.NzNode id cannot be changed.)rr r-r r r r s  z Node.set_idcC|jS)zReturn the node's id.rrr r r get_idz Node.get_idcCr@)z'Return a list of the node's successors.)r.rr r r r'rBz Node.get_succcCr@)z(Return the id of the node's predecessor.rrr r r r%rBz Node.get_prevcCs.t|tgr|j|dS|j|dS)z'Add a node id to the node's successors.N) isinstancetyper.extendr2r-r r r r"sz Node.add_succcCs|j|dS)z,Remove a node id from the node's successors.N)r.remover-r r r r&szNode.remove_succcCs t|tgs td||_dS)zSet the node's successors.z$Node successor must be of list type.N)rDrEr r.)rnew_succr r r set_succs z Node.set_succcC ||_dS)zSet the node's predecessor.NrCr-r r r r! z Node.set_prevcCr@)zReturn a node's data.r>rr r r get_datarBz Node.get_datacCrJ)zSet a node's data.NrLr?r r r set_datarKz Node.set_datar<)rrrr rr rAr'r%r"r&rIr!rMrNr r r r r}s  rN)r typingr Exceptionrr rrr r r r s  _