瞤dk!ddlmZddlmZddlmZddlmZddlmZddlm Z m Z dd lm Z dd l m Z d d gZGd d e ZeZdS))absolute_import)print_function)stderr)clustvalidation)_translate_nodes)TreeNode ArrayTable)numpy)range ClusterNode ClusterTreec eZdZdZdZdZdZdZdZdZ dZ e ee Z e ee Z e ee Ze ee Ze e e Zd d ejfd Zd Zd ZdZdZdZddZddZdZd S)ra Creates a new Cluster Tree object, which is a collection of ClusterNode instances connected in a hierarchical way, and representing a clustering result. a newick file or string can be passed as the first argument. An ArrayTable file or instance can be passed as a second argument. Examples: t1 = Tree() # creates an empty tree t2 = Tree( '(A:1,(B:1,(C:1,D:1):0.5):0.5);' ) t3 = Tree( '/home/user/myNewickFile.txt' ) c td)Nz'This attribute can not be manually set.) ValueErrorselfvalues ;lib/python3.11/site-packages/ete3/clustering/clustertree.py_set_forbiddenzClusterNode._set_forbiddenAsBCCCcF|j||jSN) _silhouetteget_silhouette_intracluster_distrs r _get_intrazClusterNode._get_intraD&   #    ! ! !&&rcF|j||jSr)rr_intercluster_distrs r _get_interzClusterNode._get_interIr rcF|j||jSr)rrrs r _get_silhzClusterNode._get_silhNs&   #    ! ! !rcF|j||jSr)_profile_calculate_avg_profilers r _get_profzClusterNode._get_profSs$ =  ' ' ) ) )}rcF|j||jSr) _std_profiler(rs r_get_stdzClusterNode._get_stdXs&   $  ' ' ) ) )  rc||_dSr)r'rs r _set_profilezClusterNode._set_profile]s  r)fgetfsetNctj||d|_d|_d|_d|_d|_d|_|j d|j d|j d|j d|j d|r| ||r| |dSdS)Nintercluster_distintracluster_dist silhouetteprofile deviation) r __init___fdistrr"rr'r+featuresaddlink_to_arraytableset_distance_function)rnewick text_arrayfdists rr7zClusterNode.__init__fs $''' "&"&   -... -... ,''' )$$$ +&&&  0  # #J / / /  .  & &u - - - - - . .rcJdt|zS)NzClusterTree node (%s))hex__hash__rs r__repr__zClusterNode.__repr__s&DMMOO(<(<<z2ClusterNode.link_to_arraytable..s[JJJq$)LOJJ u~a7H7HJJJJJrrz7[%d] leaf names could not be mapped to the matrix rows.)fileN)typer r lenrKmin _matrix_minmax _matrix_maxrE arraytableis_leafnamerowNamesget_row_vectorr'r nancolNamesappendprintr)rarraytblmissing_leaves matrix_valuesrGrPs @rr;zClusterNode.link_to_arraytablest >>Z ' 'EEx((EJJJJE#el*;*;$<$<JJJ  .. .. ) )A ALyy{{ )qv77"11!&99  )#i[U^)<)<< %%a((( ~  q ON##$*0 2 2 2 2 rc#pK|D]}|dVdS)z\ Returns an iterator over all the profiles associated to the leaves under this node.rN) iter_leaves get_profile)rls riter_leaf_profileszClusterNode.iter_leaf_profilessI!!## % %A--//!$ $ $ $ $ % %rc>d|DS)zW Returns the list of all the profiles associated to the leaves under this node.cBg|]}|dS)r)rg)rMrhs rrQz1ClusterNode.get_leaf_profiles..s%???q "???r)rfrs rget_leaf_profileszClusterNode.get_leaf_profiless%@?D,<,<,>,>????rc||j}tj||\|_|_|_|j|j|jfS)a Calculates the node's silhouette value by using a given distance function. By default, euclidean distance is used. It also calculates the deviation profile, mean profile, and inter/intra-cluster distances. It sets the following features into the analyzed node: - node.intracluster - node.intercluster - node.silhouete intracluster distances a(i) are calculated as the Centroid Diameter intercluster distances b(i) are calculated as the Centroid linkage distance ** Rousseeuw, P.J. (1987) Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math., 20, 53-65. )r8rget_silhouette_widthrrr")rr?s rrzClusterNode.get_silhouettesO* =KE  0 = = K$143J!8$:QQQrcR||j}t|g|R}tj|g|RS)zR Calculates the Dunn index for the given set of descendant nodes. )r8r rget_dunn_index)rclustersr?nodess rget_dunnzClusterNode.get_dunns> =KE 1111-e>>JhIL999Gh^<<rsN'&&&&&%%%%%%,,,,,,######## - (GQGQGQGQGQ(GQGQGQZ r