Editing is performed by manipulating data at an editing cursor. This cursor appears as a solid block which can be moved using the following keys:
Left arrow or Control b Move left one base Right arrow or Control f Move right one base Up arrow or Control p Move up one base Down arrow or Control n Move down one base Control a Move editing cursor to start of used Control e Move editing cursor to end of used Meta a Move editing cursor to start of cutoff Meta e Move editing cursor to end of cutoff Meta < Move editing cursor to start of contig Meta > Move editing cursor to end of contig
The difference between the last four Control and Meta key combinations depends on whether "Reveal Cutoffs" is set. If it is then "Control a" will move to the start of the used data for this reading and "Meta a" will move to the start of the cutoff data for this reading. Otherwise they both move to the same point (the used data start). Similarly for "Control e" and "Meta e". The action of these four key presses in the consensus line is simply to move to the start or end of the entire consensus sequence.
The cursor can be placed on any data shown in the editor except for the status lines.
The editor operates in two main edit modes - Replace and Insert. Replace allows a character to be replaced by another and Insert allows characters to be inserted. Replace is the default mode. The mode can be changed by pressing the button marked "Insert". The checkbox next to the button will be set (filled by a dark colour) when the mode is "Insert". These modes have no effect on consensus editing, which is deliberately restricted. Certain actions are considered dangerous and should be used with caution. These actions require the "Superedit" toggle to be selected.
It is possible to remove a base in an individual reading using delete with superedit selected. However this will not shift any other readings and so will 'break' the alignment of the reading being edited. This is acceptable provided actions are taken to correct this, by either shifting the reading or by inserting a base elsewhere within the reading (both of which also require superedit). Note though that insertion and deletion of bases within the cutoff data will shuffle the cutoff data rather than the reading itself and hence will not break alignment. However this operation still requires use of superedit.
Typically insertion and deletion within a reading is best performed as a consensus edit. Only insertion and deletion of pads are allowed in the consensus. Typing a '*' whilst on the consensus will insert a pad between the base underneath the cursor and the base to the left of the cursor. This will insert a pad in every reading covering that consensus position, and will shift all readings that start rightwards of the cursor right one position in order to maintain alignment. Similarly, deletion will only allow removal of pads from the consensus. It will remove the pad to the left of the cursor in all readings covering that position, and will shift all readings starting to the right of the cursor left one position.
To shift a reading place the cursor at the far left end of the reading. If reveal cutoffs is set this should be the far left end of the cutoff data. Then typing space or delete will move the reading right or left respectively by one position. This operation requires superedit.
Moving pads within a reading is often a useful procedure, and the 'movement' of a pad alone will not cause breakage of alignment. For this reason it is possible to move pads around without using insert/delete and without requiring superedit. Placing the cursor over a pad in a reading and pressing "Control l" or "Control r" will move that pad left or right one base. This operation will not work with the cursor on the consensus.
Each base has its own quality value. Assembly will allow only values between 1 and 99 inclusive. It is possible to set these quality values to 0 and 100 using the '[' and ']' keys respectively. In addition to this, all new bases added also have a quality value of 100. This aids detection of edited bases. See section Searching. Quality values may also be displayed by shading the sequence background. See section Show Quality.
The cutoff data is displayed by pressing the "Reveal Cutoffs" toggle at the top of the editor. The cutoff sequence will be displayed in grey. We call the boundary between the cutoff data and the used data the cutoff positions. These positions can be shifted left or right for each end of the reading using the Meta Left-arrow and Meta Right-arrow keys respectively. As keyboards may not have a meta key, Control Left-arrow and Control Right-arrow also have the same effect. These key combinations adjust the cutoff positions by a single base at a time. They only work when the cursor is on the very first or very last "used" base, depending on which cutoff you wish to adjust.
If large changes are required the cutoffs can be "zapped" to new positions using the "<" and ">" keys. To use these position the editing cursor to the position required (which may be within the cutoff data or the used data) and press the "<" key to set the left cutoff to the base between the cursor and the base leftwards of the cursor. Similarly ">" sets the right cutoff to the base between the cursor and the base leftwards of the cursor. Note that many keyboards have "<" and ">" above the "," and "." keys. In this case you will need to press Shift in conjunction with "," and "." to perform the operations.
A brief summary of these editing operations can be seen below:
Key Location Ins/Rep Superedit Action ------------------------------------------------------------------ base/* Reading Replace both Change base base/* Reading Insert yes Insert base delete Reading both yes Delete base delete Reading start both yes Shift left space Reading start both yes Shift right Ctrl l Reading both both Move pad left Ctrl r Reading both both Move pad right [ Reading both both Set quality to 0 ] Reading both both Set quality to 100 Ctrl Left Reading both both Move cutoff left 1 base Ctrl Right Reading both both Move cutoff right 1 base < Reading both both Set left cutoff > Reading both both Set right cutoff * Consensus both both Insert pad delete Consensus both both Delete pad (not base)