Using object views

An Object view is a graphical representation for structured biologial data, or Object, in UGENE.

A single object view can visualize one or several objects of different types.
For example a single view can show a sequence, annotations for the sequence, 3D model for the part of the sequence or its chromatogram simultaneously.

The type of an object is indicated by a symbol in square brackets:

Below is the list of object types supported by the current version of Unipro UGENE.

Object types:

• [a] - annotations for DNA sequence regions
• [c] - chromatogram data
• [i] - a file with an index information for a set of other, usually large files
• [m] - multiple sequence alignment
• [s] - nucleic, protein or raw sequence
• [t] - plain text
• [3d] - 3D model

To see the list of all available views for a given object select the object and activate context menu inside of the Project view window.
When menu appears select "Open view" submenu:

The picture above illustrates an option to visualize selected DNA sequence object using Sequence view - a complex and extensible object view that focuses on visualization of DNA sequence objects in combination with different kinds of related data: sequence annotations, graphs, chromatograms, sequence analysis algorithms. The content of Sequence view will be discussed in a separate chapter later.

One of the most important features supported by most of the object views is an ability to save and restore visual view state. Saving and restoring visual state of an object view enables rapid switching between diferent data regions and is similar to bookmarks used in Web browsers.

Initially every object view is created as transient. It means that its state is not saved. To enable state saving for the view select the item with a view name in "Bookmarks" part of the Project Viewer window and select "Add bookmark" option from the context menu:

For every persistent view UGENE automatically saves the state of the view when the view is closed in "Auto saved" bookmark.

Now, by activating bookmarks you can restore the original view state. For example the for a Sequence View bookmarks can store a visual position and zoom scale for a sequence region.

Unipro UGENE has limited set of built-in object views. Extensions modules or plugins can be used to adjust the exising views or to add new views to the tool.

Next page: Adding and removing plugins>>