Manual > User interface

User interface

• Window layout
• Multiple-document interface
• Automatic highlighting
• Annotate with ease
• Graphical map refresh modes

Window layout

The user interface (UI) is subdivided in four panes (sections) as shown above. The "Multi-purpose pane" is hidden when not in use, and is activated to display analysis results, option dialogs and various tools. It remains open until being closed by a click on the close button . When the multi-purpose pane shows information referring to sequence positions the sequence pane is write-protected.

If the active project is a linear sequence, the multi-purpose pane will appear on the right side of the sequence pane, and the graphical map will occupy the entire width below. When switching between viewing circular and linear sequences the user interface will reorganize accordingly.

The toolbars (Properties/Analysis/Tools) contains a subset of program functions. Additional functions are available from the top menu and context-sensitive right-click menus. These include functions like export to various formats, setting a restore point and undo changes, make reverse and complement sequences, translation of open reading frames, codon-usage compatibility analysis, manage sequence databases and application settings, etc.

A footer at the very bottom displays current cursor position, or selection range and length if a subsequence is selected in the sequence pane, and the graphical-map update-mode currently selected (see below).

Two functions make use of separate windows; "Sequence Alignment Editor" and " Text Editor". These are independent of other windows and their contents. The functions load files directly from disk with the contents last saved.

Multiple-document interface

Open and work on different projects side by side, the number is only limited by available system memory. Opened projects are contained in separate tabs in the sequence pane. When switching between tabs, the graphical map, user interface layout and running analysis are automatically updated to reflect the current active project.

Automatic highlighting

When a row in a results table or the annotation manager is clicked, or an element in a graphical map is clicked, the feature is automatically highlighted in the sequence pane. Regions, like ORFs, get a dark-yellow background colour. Points, like cut sites, get a distinct red background colour on the two bases surrounding the site.

Annotate with ease

Analysis results are easily annotated in the sequence pane/graphical map. Select the rows of interest and click the annotate button , and it's done.

Graphical map refresh modes

Choose between two different modes for how graphical maps and behind-the-scenes data are refreshed when editing project sequence using keyboard input, cut/paste or undo/redo.

The default mode at startup is 'Immediate', which means immediate refresh after every keystroke and other editing events. What you see is what you have. Visible features and behind-the-scenes data are always synchronised, and implementation of edits cannot be forgotten. A minor disadvantage is that one may see temporary map rearrangements while editing. On a slow computer refreshing may lag behind when editing very large and complex projects.

The alternative map refresh mode is 'On-demand' by pressing the ENTER key. Refreshing of maps and behind-the-scenes data is suspended until pressing ENTER. This may be useful when editing very large and complex projects on a slow computer, to have a lag-free experience. The disadvantage is that edits may be 'forgotten' if ENTER is not pressed before running other processes that cause programmatic refresh. The sequence editor must have focus when pressing the ENTER key, so it's a good habbit to click in the editor and see a blinking cursor before pressing ENTER.

Map refresh mode is set in the Options menu. When switching refresh mode, the new mode is applied to all open projects and those opened afterwards. 'Immediate' mode is the default and selected on application startup.