The 2DViewer is another software component associated with the CellUniverse of the CELLmicrocosmos CellExplorer. It is especially important to generate and edit tours. Der 2DViewer provides a number of different layouts to visualize the tours in two dimensions as well as several modi supporting the navigation.
The first drop down menu lists different layouts which can be used to change the two-dimensional representation of the tour. These settings apply only to the visualization in the 2DViewer. They do not affect properties of the tour, such as the duration or the sequence.
Right of the layout menu a two buttons are placed: "+" and "-" Zeichen, which can be used to zoom in or zoom out.
Moreover, it is possible to change the zoom factor by using the mouse whell in the 2DViewer.
The second drop down menu shows the different edit modes used in
conjunction with the 2DViewer. Those can
be used to change the tour as well as changing the visual
representation of the tour in the 2DViewer.
As soon as tour points were generated by using the right click menu
in the CellUniverse or the CellEditor, the tour points are visualized in
the 2DViewer.
The right mouse
button toggles a popup menu which provides options to jump or focus
to selected nodes or to change the navigation mode in the CellUniverse. This popup menu will also be
shown in the following modi.
This modus is a simplified visualization of the networks or tours in the 2DViewer. By pressing the right mouse button and moving the mouse, the view can be shifted, and the mouse wheel changes the zoom factor. Performing a double click onto a TourPoint centers the CellUniverse at the center of the associated (cell) component.
By holding the left mouse button, picked nodes can be dragged. This mode can be used if the standard layouts do not meet the expectations. After all nodes were dragged to their final positions, the new layout can be saved by pressing the Save button.
This mode is needed to create new pathways or to change an existing one. By left clicking onto a free position in the 2DViewer, an dialog appears which enables the user to define the name of a new mode. Moreover, the type has to be declared: enzymes or compounds. (Note that enzymes can be localized by using the PathwayIntegration, whereas compounds are always placed in relation to their neighboring enzymes.) By right clicking onto an enzyme or compound node, the regular popup menu appears extended by the editing entries; Rename, for changing node names, and Delete, for deleting a node.
This mode is important to edit the tour using the 2DViewer. By using the tour list at the right border of the 2DViewer, the sequential order of the TourPoints can be adjusted via drag'n'drop.
To start a tour, the button on the right side of the bottom row in the 2DViewer can be used, or by right clicking e.g. into the CellUniverse and selecting Start Tour.