Editing Layout:Edition

{{DISPLAYTITLE: Editing a Layout}}

There are some actions that can be performed to edit the layouts loaded in OptFlux. 

== Dragging Fix/Unfix ==

The visualization uses a default algorithm for placing the nodes in the layouts. This algorithm (Force Directed Layout -http://en.wikipedia.org/wiki/Force-directed_graph_drawing) was changed to support fixed nodes. This means that a layout created by the user can only specify some positions of the nodes, while the others will be placed by the algorithm.

[[Image: FixUnfix.png|550px]]
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By right-clicking a node the user can specify if that node will be fixed to the position it is, or by unfixing if the layout algorithm will place it. It is also possible to fix and unfix nodes by type.

[[Image: DRAG.png|550px]]
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When the nodes are fixed, the user can also drag them to other positions. If multiple nodes are selected, then all fixed nodes withing the selected area will be dragged.

== Merge/Replicate Node ==

[[Image: MergeReplicate.png|1000px]]

Merging or replicating nodes allows the  user to specify if that chemical entity will be represented by more than one node or not.

By looking at the image above it is possible to see such an example:

<b>1</b> When a metabolite node is connected by several reactions, if the user right-clicks over a note, the right-click menu will show the option <i>Replicate Node</>;

<b>2</b> The replication will result in a node representing the same metabolite for each of the reactions;

<b>3</b> The option changes from <i>Replicate Node</i> to <i>Merge Node</i> when the node is connected with a single reaction.

<b>4</b> When the option is chosen a green edge will follow the mouse cursor. <b><i>It is only possible to merge nodes that represent the same metabolite!</i></b>

<b>5</b> The result is a single node replacing the merged ones.

== Delete Reaction ==
@@ Line 15: / Line 15: @@
 When the nodes are fixed, the user can also drag them to other positions. If multiple nodes are selected, then all fixed nodes withing the selected area will be dragged.
-== Merge/Replicate Metabolite Node ==
+== Merge/Replicate Node ==
 [[Image: MergeReplicate.png|1000px]]
@@ Line 32: / Line 32: @@
 <b>5</b> The result is a single node replacing the merged ones.
-== Merge/Replicate Reaction Node ==
-Similarly to the metabolite nodes, it is possible to merge and replicate reaction nodes.
-[[Image : C4 replicatemergerReaction.png | 750px]]
-<b>Two reaction nodes can be merged if they are connected with the exact same nodes and have the same reversibility!</b> Such an example is the image above where A is the merged reaction node and B the replicated node.
 == Delete Reaction ==
-[[Image: Remove reaction2.png]]
-It is possible to remove a reaction node by right-clicking on it, and selection the option showed in the image above. This will result in the removal of the reaction node, and removal of the nodes that were only connected to this specific reaction.