B bq@sDdZGdddeZGdddeZGdddZGdddZd 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) c@seZdZdZdS)ChainExceptionz1Provision for the management of Chain exceptions.N)__name__ __module__ __qualname____doc__rr.lib/python3.7/site-packages/Bio/Nexus/Nodes.pyrsrc@seZdZdZdS) NodeExceptionz0Provision for the management of Node exceptions.N)rrrrrrrrrsrc@sbeZdZdZddZddZddZdd d Zd d Zd dZ ddZ ddZ ddZ ddZ dS)Chainz0Stores a list of nodes that are linked together.cCsi|_d|_dS)zInitialize a node chain.N)chainid)selfrrr__init__#szChain.__init__cCs|jd7_|jS)z/Get a new id for a node in the chain (PRIVATE).)r )r rrr_get_id(sz Chain._get_idcCst|jS)zReturn a list of all node ids.)listr keys)r rrrall_ids-sz Chain.all_idsNcCsf|dk r$||jkr$tdt|n>|}|||||dk rX|j||||j|<|S)zAttach node to another.NzUnknown predecessor: )r rstrrset_idset_prevadd_succ)r nodeprevr rrradd1s   z Chain.addcCs||jkrtdt||j|}|j|||j|}x|D]}|j||qLW|j|||j|}|||S)z=Delete node from chain and relinks successors to predecessor.z Unknown ID: ) r rrget_prev remove_succget_succrrkill)r r prev_idZsucc_idsirrrrcollapse>s    zChain.collapsecCs(||jkrtdt|n|j|=dS)z>Kill a node from chain without caring to what it is connected.z Unknown ID: N)r rr)r r rrrrLs z Chain.killcCsd||jkrtdt|nD|j|j}|dk rP|j|j|j|j|d|j|_|SdS)z%Disconnect node from his predecessor.z Unknown ID: N)r rrrsuccpopindex)r r rrrrunlinkSs    z Chain.unlinkcCsh||jkrtdt|nH||jkr8tdt|n,|||j|j||j||dS)zConnect son to parent.z Unknown ID: N)r rrr%r"appendr)r parentZchildrrrlink^s   z Chain.linkcCsN||ks||j|krdSx*|j|D]}|||r.dSq.WdSdS)z+Check if grandchild is a subnode of parent.TFN)r r is_parent_of)r r'Z grandchildsnrrrr)is  zChain.is_parent_ofcCsn||jks||jkrtd|||r0||kr4gSx4|j|D]"}|||rD|g|||SqDWdS)zQReturn a list of all node_ids between two nodes (excluding start, including end).z Unknown node.N)r rr)rtrace)r startZfinishr*rrrr+ts z Chain.trace)N)rrrrrrrrr!rr%r(r)r+rrrrr s    r c@sjeZdZdZdddZddZddZd d Zd d Zd dZ ddZ ddZ ddZ ddZ ddZdS)NodezA single node.NcCsd|_||_d|_g|_dS)z>Represent a node with one predecessor and multiple successors.N)r datarr")r r.rrrrsz Node.__init__cCs|jdk rtd||_dS)z%Set the id of a node, if not set yet.NzNode id cannot be changed.)r r)r r rrrrs z Node.set_idcCs|jS)zReturn the node's id.)r )r rrrget_idsz Node.get_idcCs|jS)z'Return a list of the node's successors.)r")r rrrrsz Node.get_succcCs|jS)z(Return the id of the node's predecessor.)r)r rrrrsz Node.get_prevcCs,t|tgr|j|n |j|dS)z'Add a node id to the node's successors.N) isinstancetyper"extendr&)r r rrrrsz Node.add_succcCs|j|dS)z,Remove a node id from the node's successors.N)r"remove)r r rrrrszNode.remove_succcCs t|tgstd||_dS)zSet the node's successors.z$Node successor must be of list type.N)r0r1rr")r Znew_succrrrset_succsz Node.set_succcCs ||_dS)zSet the node's predecessor.N)r)r r rrrrsz Node.set_prevcCs|jS)zReturn a node's data.)r.)r rrrget_datasz Node.get_datacCs ||_dS)zSet a node's data.N)r.)r r.rrrset_datasz Node.set_data)N)rrrrrrr/rrrrr4rr5r6rrrrr-s r-N)r Exceptionrrr r-rrrrs_