Hierarchical View

This feature provides a useful overview of an entire dataset. The Hierarchical View uses the :DEFAULT-SUBCLASS and :DEFAULT-INSTANCES relationship to show inheritance hierarchies for a dataset. It is also linked with the display in the Main View. Below we see a default view as the tool is first opened. In this example, the Wines example from the Protégé domain, we see the root node, and its immediate children. To see all the nodes in the domain, select the root node and choose Expand All (warning: time-consuming on large datasets). Nodes showing an inverted triangle indicates that it has hidden children. Colour coding is taken from the main view panel and can be configured with the Node filter.

Double-clicking on a node displays its corresponding node in the main view. That node is enlargened to reflect this. The hierarchical view can also be useful to show multiple inheritance in complex graphs; using the tooltips, hover over the nodes that have multiple incoming links, and the tooltips will show the complete inheritance tree.

NOTE: a node in the main Shrimp view represents certain information, but with multiple parents, there can be many nodes on the main view that represent the same data. For example, filtering a specific node will cause all nodes that represent the same data to be filtered.

Display Modes

There are three display modes for this view. They are the navigation mode, filtered mode, and search results view. These are three different options for how the display changes on the screen.

Change the current mode by clicking the appropriate radio button at the bottom of the panel, as shown below.

Navigation mode highlights the node selected on the hierarchical view screen by enlarging it, so that you can always determine what node you are viewing or editing in the main view.
Filtered mode highlights by enlarging in the hierarchical view those nodes you have filtered from the nested view.
Search Results mode will highlight the nodes for which you have performed a successful search. Note that this is not affected by any searches done in Protege forms (such as Classes or Instances panels), or other parent applications.

Navigation of the Hierarchical View

This mode is used to browse the view. There are several controls that affect the navigation. Those listed are defaults, but these are configurable for your preferences and needs (e.g. a Macintosh system) using the Tools > Options > User Controls menu.

[Menu] Navigate > Home : This command takes the user to the extent of all visible nodes. This is useful when the display expands beyond the scope of the current window size, or when enlarging the window.
[Mouse] Middle-click - this zooms the user in on the mouse location, as long as it is on a node.
[Mouse] Shift-Middle-Click - zooms back out on mouse location.
[Keyboard] +/- keys - Zooms in and out
[Keyboard] Arrow keys - Pan the view in all four directions.

Editing Hierarchical View

[Menu] Edit > Select Inverse - Deselects the currently selected nodes, and selects any unselected nodes.
[Context Menu] Collapse - Collapses the currently selected node into an inverted triangle shape. Collapsing a node means that, much like folders in a file manager, the contents of the node are hidden but present. Collapsing a node is useful in large graphs when you want to abstract the detailed content to focus on the higher level concepts. For example, implementation classes could be collapsed into the parent package node.
[Context Menu] Expand - On the selected nodes, if a node has not previously been expanded, its immediate children are shown. If a node has been collapsed and then is expanded, all the descendents of this node that were "collapsed" are shown again.
[Context Menu] Expand All - Expands all the children of the current node. If performed on the root node, shows all the nodes.
[Context Menu] Prune - As seen below, this action edits the tree so that only the selected node and any descendents are retained. All other nodes are hidden, and the new root node takes the shape of a diamond. This view is useful to zero in on an area of interest. You cannot prune more than once; to do this, first unprune the tree and then re-prune on the node of interest. Note that pruning is different than filtering. Filters apply only to the display in the Main View. Pruning applies only to the Hierarchical View.
[Context Menu] Unprune - Essentially undoes the prune operation. No node need be selected for this operation.

Changing Layouts

Under the Layout menu, there are two layout algorithms which can be selected for the Hierarchical view, Radial Layout, and Tree Layout. These algorithms are applied to all nodes shown on the view. This means that those nodes which are filtered or collapsed, i.e. not visible, are not calculated in the layout routine.