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| SubsystemDiagram |
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A subsystem diagram is a visual rendering of the components of a subsystem, similar in feel to the KEGG maps. SEED supports the addition of new diagrams by users.
This document discusses how to do that.
Diagrams for a subsystem are stored in the directory FIGdisk/FIG/Data/SubsystemDiagrams/<subsystemname>.
Multiple diagrams can be created for a subsystem; each diagram is stored in a subdirectory of the directory mentioned above.
An individual diagram directory contains two files. First is the image itself, stored as diagram.png in the PNG format.
The other is called area_table, which is a text file defining the areas to be highlighted.
Each line in area_table is a tab-separated triple (area_id, keyword, value). area_id is a string uniquely identifying an area on the diagram.
The keywords we support are the following:
role: This declares that the given area has the given role. The value is the name of the role as used in the subsystem.
abbrev: The abbreviation used for this role.
compound: Declares that the given area represents a compound.
link: Declares that the given area has the given hyperlink.
shape: The shape that the area is to be rendered as. This can be one of the following:
rect:x1,y1,x2,y2: A rectangle from (x1, y1) to (x2, y2).
circle:x,y,r: A circle at (x, y) of radius r.
Once a diagram directory has been created, it is installed into the SEED by running the following commands:
make_maps_from_subs init_maps load_kegg load_local_maps
The first command reformats the diagram into the format expected by the local map rendering subsystem. The rest of the commands reload the maps from the flat files.
