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Names

At the left side of the editor window is a display containing the reading names and numbers. Each line consists of its orientation ("+" or "-"), reading number, a coloured template consistency status and its name. The bottom line is always CONSENSUS. Also on the bottom line is the current edit status. This is modelled on Emacs, and consists of one of ----, -%%- and -**-, to symbolise "No unsaved edits made", "No edits made - editor is in read only mode", and "Unsaved edits made".

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.

Pressing the right mouse button on a name will popup a menu containing a variety of operations to perform for that specific reading.

Goto...
This is a cascading menu containing all other readings on the same template, including ones on other contigs. Selecting the appropriate read name will move the editor to the left-most base in that sequence. If the sequence is in another editor then either the other editor will be moved (and created if needed).
Join to...
This is only shown when a template has more than one reading in it and the readings are within separate contigs. when this is the case a cascading menu presents the list of readings in other contigs. Selecting one of these will bring up the join editor with both sequences visible (so that you will need to manually scroll to approximately the correct position in order to find the join).
Select this reading
Select this reading and all to right
Deselect this reading
Deselect this reading and all to right
Select readings on this template
Deselect readings on this template
These commands (de)select one or several readings. "Select this reading" is the most simple method and this acts in the same way as simply left clicking on a sequence name. The other modes allow the (de)selection of sequences on this template (regardless of which contig they are in) or ranges. The "and all to right" modes are designed with disassemble readings in mind. Disassembling all readings from a specific point onwards using the "Move readings to new contigs" mode is analogous to using break contig. Selecting all readings within a range may be achieved by a combination of "select this reading and all to right" and a subsequence "deselect this reading and all to right" further along the contig.
List notes
This invokes the note selector with this reading already listed (see section Selecting Notes).
Set as reference sequence
This marks the sequence as the Reference sequence (see section Reference sequences).
Set as reference trace
This marks the trace as a Reference trace for use with trace differencing (see section Reference traces).
Remove reading (this only)
Remove reading and all to right
This marks one or more readings as ready for removal by disassemble readings (see section Removing readings from the contig). You will then be prompted when you exit the editor whether you wish to disassemble the chosen readings.
Clear selection
This clears the current reading selection.

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Last generated on 25 November 2011.