ReactionLayouter Documentation

ReactionLayouter Documentation

The ReactionLayouter GUI contains three widgets with which the user can interact. The menu bar allows the user to load and save files as well as to set some global options. The graph panel shows the network graph of a loaded file or enables the user to create his/her own graph. The user can change the apperance of the graph via a menu which appears on clicking the right mouse button. The action panel contains different possibilities to create, delete, move or edit nodes and edges in the graph.

Create a graph layout

  1. Start: java org.eml.simulation.ReactionLayouter
  2. Load an ascii or SBML file.
  3. If needed: join all nodes with more than one occurence.
  4. If needed: set your layout options.
  5. Apply layout algorithm.(layout examples)
  6. If needed: save the layout in an SBML file.

Menu

The main menu at the top of the ReactionLayouter window contains four submenus.

Snapshot of submenu File

File menu item Description
New Graph Creates an empty graph panel.
Load ASCII reaction file Choosing this menuentry brings up a file manager, so that the user can choose ascii file. (ascii file format)
Load SVG graph Choosing this menuentry brings up a file manager, so that the user can choose a svg graph file.
Save SVG graph Choosing this menuentry brings up a file manager, so that the user can save the current graph in the svg format.
Load SBML file Clicking here brings up a file manager, with which the user can select a SBML file to load.
Save SBML file Choosing this menuentry brings up a file manager, so that the user can save the current graph in the SBML format with layout information, but that does not work for new created graphs.
Load serialized graph Choosing this menuentry brings up a file manager, so that the user can choose a file to load (Java serialization protocol see).
Save serialized graph Clicking here brings up a file manager, with which the user can save the current graph.
Exit Exit ReactionLayouter.



Snapshot of submenu View

Settings menu item Description
View compounds as ... Here you can select the representation style of compunds.
  • circles: Compound representation as circle
  • labels: main: Compound representation as label side: Compound representation as label
Send to animator tool Send this graph to the animator tool SimWiz.



Snapshot of submenu Graph Layout

Settings menu item Description
Join all nodes with identical names Joins all occurences of a node with the same name to one single node.
Set layout algorithm options Set options to adopt the layout algorithm to the user needs.
Apply layout algorithm Starts the layout process.
Change list of side compounds Add or delete side compounds from a predefined list.



Snapshot of submenu Utils

Settings menu item Description
Check for double node names Invokes a dialog box with the name of all nodes which occur at least two times in the graph. By clicking on a name the corresponding nodes are highlighted in the graph.
Modify size of image plane Resize the image plane.
Write png image Save the current network graph as png image file.



Graph Panel

The menu for this panel can be opened via a right mouse click.

Snapshot of popup menu in the graph panel

Settings menu item Description
Zoom in Zoom into the graph by a predefined zoom factor.
Zoom out Zoom into the graph by a predefined zoom factor.
Zoom free Set your own zoom factor.
Fit into panel Fit the graph into the size of the panel.
Set size of all nodes Set the size of the nodes in the circle representation.
Set size of all pseudonodes Set the diameter of the pseudonodes.
Set size of all node name font Set the font size of compounds in label representation.



Action Panel

The panel enables the user to create a new or to change the current network graph.
  1. Choose type of selection (Node, Edge, Reaction).
  2. Mark selection in the graph panel type by using the left mouse button.
  3. Choose action.

Snapshot of the action panel

Katja Wegner
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