The contig editor can be invoked by double clicking the middle mouse button, or Alt the left mouse button, in any of the displays, ie template, ruler, quality or restriction enzyme plots. The editor will start up with the editing cursor on the base that corresponds to the position clicked on in the Template Display. If more than one contig is currently being displayed the editor decides which contig to show using the following rules. If the user clicks on the Quality Plot, the contig lines or the Restriction Enzyme Display, the corresponding contigs will be shown. If the user clicks on a gap between these displays the nearest contig will be selected. If the user clicks on the template or reading lines, the editor will show the contig whose left end is to the left of and closest to the cursor.
The long blue vertical line seen in the previous figure is the position of the editing cursor within a Contig Editor. Each editor will produce its own cursor and each will be visible. Moving the editing cursor within a contig editor automatically moves its cursor within the Template Display. Similarly, clicking and dragging the editor cursor with the middle mouse button, or Alt left mouse button, within the Template Display scrolls the associated Contig Editor.
The order of the contigs can be changed within the Template Display by clicking with the middle mouse button, or Alt left mouse button, on a contig line and dragging the line to the new position. The Template Display will update automatically once the mouse button is released. The change of a dark yellow template to bright yellow is indicative that the two contigs are now in consistent positions and orientations. The order of the contigs in the gap4 database, as displayed in the contig selector, can be updated by selecting the "Update contig order" command in the Edit menu.
By clicking on any of the contig lines in the ruler a popup menu is invoked. From this, information on the contig can be obtained, the contig editor can be started, the contig can be complemented, and the templates within the contig can be highlighted (shown by changing their line width).
A list named
readings always exists. It contains the
list of readings that are highlighted in all the currently shown
template displays. See section Lists. The highlighting
mechanism used is to draw the readings as thicker, bolder, lines. The
"clear Active Readings" command from the View menu clears this list. The
"highlight reading list" command loads a new set of readings to use for
the "readings" list and then highlights these.
To interactively add and remove readings from the active list use the left mouse button. Clicking on an individual reading will toggle its state from active to non active and back again. Pressing and holding the left mouse button, and moving the mouse, will drag out a bounding box. When the button is released all readings that are contained entirely within the bounding box will be toggled.
Activating a reading (using any of the above methods) when an editor is running, will also highlight the reading within the editor. Similarly, highlighting the reading in the editor activates it within the template display and adds it to the active reading list.