At the left side of the editor window is a display containing the
reading names and numbers. Each line consists of its number (negative
numbers represent complemented readings) and its name. The bottom line
CONSENSUS. Also on the bottom line is the current edit
status. This is modelled on
Emacs, and consists of one of
-**-, to symbolise "No unsaved edits made", "No edits
made - editor is in read only mode", and "Unsaved edits made".
Pressing the right mouse button on a name will popup a menu containing
operations to perform for that specific reading. These include Remove
Reading (see section Remove Reading),
Set as reference sequence (see section Reference sequences),
Set as reference trace (see section Reference traces),
and List Notes (see section Selecting Notes). Similar menus
exist for the
CONSENSUS name and for any editor status lines displayed.
The maximum length of a reading name is 40 characters. Additionally there
are 7 characters taken up with the direction and number of a reading. By
default the names display only shows 23 characters (enough to show 16 letters
of a reading name). A horizontal scrollbar just above the reading names can be
used to scroll the reading names. Note that the numbers and orientation are
always visible. To change the width of the editor names display set the
CONTIG_EDITOR.NAMES_WIDTH setting in your `.gaprc'. For example:
set_def CONTIG_EDITOR.NAMES_WIDTH 23
The foreground colour for the text reveals whether the trace for this reading is shown - a grey foreground indicates that the trace is visible. The background colour represents a user highlight and the disassembly mode. The default background colour is light grey (the same colour as the general editor background). Clicking the left mouse button on a reading name toggles the background of the name component of number-name pair to black. This is particularly useful for keeping track of an individual reading whilst scrolling the editor. As the editor scrolls an individual reading will move up and down the editor display. By highlighting this reading it becomes easy to track. The number component of the number-name pair is used to highlight readings that are to be disassembled. See section Disassemble Readings. In this case the background is dark grey.
If the template display is in use, highlighting a reading name in the editor will select this reading in the template display (by marking it as bold). Similarly selecting a reading in the template display (left mouse button) will highlight the reading in the contig editor. Additionally the contig editor cursor is visible within the template display allowing the position of the editor to be controllable from the template display and connected plots (such as the quality plot). See section Template Display.
The readings contained within the "readings" list are automatically highlighted when the editor starts. Toggling the highlighted names in the editor updates the "readings" list accordingly.See section Special List Names.
Once an output list for the editor has been set, pressing the middle mouse button, or Alt left mouse button, on the names display has the same effect as the using the left button, except that it adds (and never removes) the reading name to the specified list. See section Set Output List. This is similar to using the left mouse button to add names to the "readings" list, except that it allows for multiple lists to be built up.