Visualizer

Two visualizers for hierarchical graph rewriting are available; UNYO-UNYO and Graphene.

The basic information of UNYO-UNYO (sometimes called UNYO-UNYO 3G) is given below.

UNYO-UNYO

Basic Operations

Step 1: Start - Select a program

Using UNYO-UNYO alone

1. Start up UNYO-UNYO (see UNYO-UNYO).
2. Choose "File > Open File" in the top menu bar.
3. Select LMNtal execution options.
4. Select a program which you want to open.

Using UNYO-UNYO from LaViT

1. Start up LaViT.
2. Choose "File > Open File" in the top menu bar or Write a program using the editor in the upper-left pane of the screen.
3. Select LMNtal execution options from the option tab, if you need.
4. Click the "UNYO(3G)" button in the bottom left of the screen, and UNYO-UNYO will start up.

Step 2: Show the graph of the program

1. After Step 1, the initial state of the graph is displayed.
2. Click the "Go Ahead" button at the bottom of the center panel, then a program will proceed.
   • In the text box at the left, you can specify the number of rule applicable times.(default number is 1)
   • If you select the "Until Stop" checkbox, the program proceed until it terminate, or you click the "Stop" button, or it break at the breakpoint.

Function List

1: Menu Bar

File:

• Open File(Ctrl+O): open a program file.
• Save Graph Image(Ctrl+I):
• Restart(F11):

Edit: now being developed...

Zoom(Scroll wheel, Ctrl++(;), Ctrl+-): change the scale of the graph.

View:

• Show Map(Ctrl+M): show the whole graph.
• Antialiasing:
• Monochrome Display:
• Show Full Name: show full name of atoms or membranes.
• Show Initials: show initials of atoms or membranes.
• Hide Name: hide name of atoms or membranes.
• Show Reaction Point: show reaction points of the graph.
• Show Link Number:
• Info Font Size:

2: Graph Controller

• Until Stop: make the program proceed until it terminate, or is suspended by '"Stop"' button, or break at a breakpoint.
• Go Ahead: perform one-step reduction by default. For multi-step reductions, change the number in the text box to the left.
• Stop: suspend the running program.
• Hide All: hide the contents of all cells.
• Show All: show the contents of all cells.
• Always Heating Up: always calculate the graph layout.
• Heating Up: activate the stable state nodes temporarily, and restart calculating those layout.
• Cool Down: inactivate nodes, and terminate calculating layout.
• Auto Centering: move the whole graph in the center of the Graph Panel.

3: Tab Panel

• Log: show the system log.
• Process: show the text representation of the graph and the applied rule.
• Rule: show the rules in the membrane you click.
• Option: change the graph layout algorithm.
• Shape: change the shapes of atoms.
• Breakpoint: set breakpoints.
• Search: search nodes in the Graph Panel.

4: Graph Panel

• Drag: move the selected nodes.
• Click: select a node, if it is at the point.
• Ctrl+Click: select/unselect the nodes.
• Ctrl+A: select all of the nodes.
• Shift+Drag: select/unselect the nodes in the framed rectangle by dragging.
• Space+Drag: move the graph.
• Double-Click: hide/show the contents of the double-clicked cell.
• Right-Click:
  • Hold: pin down the selected nodes.(Pinned-down entities can be moved manually but will not move automatically)
  • Release: release the pinned-down nodes.
  • Ravel Out: exert repulsive force from the center of the connected component which contains selected nodes.