The contig editor displays only one segment of the entire contig, although several contig editors can be in use at once. Below the sequence is a scrollbar and below that a "jog" control. The scrollbar behaves as expected, allowing rapid positioning anywhere within the contig using the middle mouse button or left-clicking and dragging the slider. However with extremely long contigs (for example 100Mb) it can become tricky to move by the desired amount. Each pixel on the scrollbar may represent 100Kb worth of data, so dragging the scrollbar is only approximate positioning. Equally so clicking in the trough to move a screen-full at a time can be too small. This is where the jog-control can be of use.
By default this is always centred. Clicking and dragging this left or right starts to scroll the editor, at a speed proportional to how far away from the centre the jog is dragged. Releasing the mouse button stops automatically scrolling and recentres the jog control.
The final, more precise, manner of positioning the editor view is with the text entry box in the bottom left corner. Type in any coordinate here and press return to jump straight to that location. Note however that Gap5's coordinates are currently always in padded form; that is to say that a gap in the consensus caused by an insertion in one of the aligned sequences is still counted as a base position.
For particularly deep displays the vertical scrollbar on the right edge of the window will also be useful. While scrolling in X, the editor attempts to keep the same sequences visible on screen. To do this it may automatically adjust the Y scrollbar for you due to changing layout of sequences. (By default the top-most sequence is always the sequence that starts furthest left and the bottom most is the sequence starting furthest right.)
If you have a mouse wheel, this may also be used for small scrolling. By itself it scrolls in Y one sequence at a time. With the Control key held down it scrolls in larger increments. Using the Shift key in conjunction with the mouse wheel scrolls in X instead, with Shift+Control to scroll in larger increments.
The displayed portion of the contig is separate from the current location of the editing cursor. This is displayed as a black rectangle with typically a light coloured letter inside it. Any editing keys operate on the base underneath this or to the base immediately preceding it for Delete. We cover the topic of editing later (see section Editing), however moving the editing cursor is also another way of scrolling the editor.
Finally the Page Up and Page Down keys scroll the editor left or right by 90% of current screen width. Used with Shift the moves in increments of 1Kb, with Control in increments of 10Kb and with both Shift and Control in increments of 100Kb. The Home and End keys jump to the start or end of the current item underneath the editing curosr - either a sequence or the consensus.