Most of the buttons of the user interface are linked to tooltips (a.k.a. short explanation of the button function). These tooltips appear after leaving the mouse cursor for a few seconds over the button. Values in tables can also be displayed in tooltips, which may be useful when table cells are too small to display large values.
Bookmarks are used as locations of interest, which can be loaded/saved from/to a file.
A new tab "Bookmarks" has been created next to "Filter.." and "History" tabs.
It contains icons to load, save, add or delete bookmarks.
The format is a simple tab-separated text file (without header), with one bookmark per line (see exemple below).
First column contains chromosome ID, second column contains start position, third column contains end position, fourth column contains a description (without blank spaces).
| 1 | 245678 | 356777 | description_first_bookmark |
| X | 3780000 | 5000873 | description_second_bookmark |
| ... | ... | ... | ... |
The main display is made of four components, from top to bottom: chromosomes, current chromosome, default tracks -gene and DNA- and finally user tracks. These components are each separated by a divider, which should display two arrows on its left. Clicking on these arrows allow to fold/unfold the components. The divider can also be dragged, so that components may reach an appropriate size.
When double-clicking on an entry in a table (either a gene, location or bookmark), window coordinates of this entry are modified to take into account a certain amount of nucleotides on both left and right sides. This amount can be adjusted in the "Browse with mouse" tab, below the tracks. This amount does not apply when selecting directly a region with the mouse.
Some tracks can be resized vertically. In that case, at least one of the top/bottom margins is colored in grey.
To resize this track, simply move the mouse cursor over the grey margin, press left mouse button and
drag margin until track has the right size.
To resize several tracks at once, simply select as many tracks as required in the track management panel,
then resize one of these tracks as explained above.
To quickly navigate to a track without scrolling, double-click on its name in the track management panel.
While selecting a region on a track, pressing CTRL before releasing mouse button will not zoom to that location (useful to only display coordinates and window size).
Track operations and properties (such as colors or groups) are gathered in a dialog window which can be displayed by clicking on the "Track properties" button in the track managment panel toolbar. Since several track types can co-exist at the same time in the viewer, and that each type can have different properties, one track of a specific type must be selected to enable the track properties button.
Key combinations allow multiple selection or deselection of track operations.
To change color of all tracks in a group in a single step, change color of the first track of the group, then choose Color by -> Group.
Drag and drop is supported on several areas of the viewer. Each area will only react to the specific type of drop for which it was made.