MS Trees

MS Trees are stored in the user_preferences table of the entero (system) database, type being ms_tree or ms_sa_tree (stand alone MS tree not linked with a workspace). The data column contains the following json

• data_file The location of the file containing json data in the following format

  • scheme_genes obsolete - A list of all the loci used for the scheme (can be retrieved from the scheme)

  • scheme The name (description) of the scheme

  • isolates A list of the metadata for each strain. Each item in the list consists of a dictionary of key/value pairs, with ‘StrainID’ being the strain id in the database and ID being the node ID that the strain is associated with e.g. {“StrainID”:5641,”ID”:”ST454”,”Name”:”bug1”,”Country”:”Germany”,’’’’’}

  • links A list of the links in the tree, each item is a dictionary with:-

    • source The index (in the identifiers) of the source of the link

    • target The index of the link target

    • distance The relative length of the link

  • identifiers a list of all the node identifiers. Each item is another list of all the STs in the node (due to missing data, a node can occasionally consist of more than one ST) e.g. [[“ST3453”,”ST232”],[“ST454”],[“ST23”],…..]

  • metadata_options A dictionary of categories to field name:labels e.g {“Metadata{“city”:City”,…},”Custom Fields:{“field_a”:”Field A”}}

  • current_metadata The name of the metadata last displayed in the tree

• layout_file The location of the file containing the layout information of the tree

  • node_positions A dictionary of node id to an array of x,y co-ordinates e.g {“ST232”:[762,232],”ST233”:[22,33],…}

  • nodes_links Extra information about the nodes/links:

    • max_link_scale

    • base_node_size

    • size_power

    • scale

    • translate

• parent The id of the parent workspace (if applicable)

• complete ‘true’ if the tree has been calculated