The purpose of this menu is to configure the operation of the contig editor, including the consensus calculation, the active tags and the status lines. The following options are available.
The contig editor can display several additional lines underneath the consensus sequence. These are of textual format and provide additional information about the data displayed above. The data in the status line may neither be cut and pasted, modified or searched; it is not possible to move the cursor into these lines. Currently, there are two forms of status line available. These are "Strands" and "Translate Frame". Both status line types update automatically as edits are made that change the consensus.
The status line menu is accessed by cascading off the settings menu. It contains the following.
"Show Strands" creates a single line consisting of the +, -, = and ! characters. These stand for positive strand only, negative strand only, both strands (in agreement) and both strands (in disagreement) respectively.
The frame translation status lines provide translations in each of the six available reading frames. This data can be displayed in either the single character or the three character amino acid codes.
Pressing the right mouse button on the 'name' segment of the status line (on the left hand side) pops up a menu. The commands available may depend on the type of the status line chosen, however currently it will always only contain the "Remove" command. This, as expected, removes the status line from the display. To remove all status lines use the "Remove all" command from the "Status Line" cascading menu.
This toggles between the normal sequence display showing the current base assignments and one in which only those assignments that differ from the consensus are shown. This makes scanning for problems by eye much easier.
This toggles the consensus calculation routine between treating both strands together or independently. In the independent case any differences between the two strands is shown in the consensus as a '-'. Hence these clashes are found as problems by the "Search by problem" code.
When switched on, auto-display traces will direct the "Next Problem" button to automatically display only the traces that are likely to be of interest for resolving the problem found. This will consist of the best trace from each strand and the best trace that disagrees with a consensus taken at 1% cutoff.
Selecting auto-save toggles the auto save feature. Initially this is turned off each time the contig editor is invoked. Once toggled the adjacent checkbox will be set to indicate the feature is enabled and the contig will be saved. From that point onwards the contig editor will write it's data to disk every 50 edits. Each time an auto save is performed notice is given in the output window. Saving more frequently can still be performed manually by using "Save Contig".
The "Undo" button will allow the user to undo edits regardless of when the last auto save occurred. Note that the same is not true regarding the manual "Save Contig" method.
The codon translation within the status line by default displays single character amino acid codes. Selecting the "3 Character Amino Acids" setting will toggle the status line to display three character amino acid codes.
When the quality cutoff value is 0 or higher and the show quality toggle is set, the background for bases is shaded in a grey level dependent on the quality. There are ten levels of shading with the darkest representing poor data and the lightest representing good data. The quality cutoff is taken as a base value to compare quality against. So with the quality cutoff set to 50, all bases with a quality of less than fifty are shown with a red foreground and a dark grey background, bases with quality just above 50 will have the darkest grey background, and bases with a quality of 100 will have the lightest background. When tags are present the background colour is that of the tag rather than the quality.
"Set Active Tags" allows configuration of which tag types should be displayed within the editor. When a tag is not displayed the search for annotation function will not find it. However searching for a specific tag type, even when tags of this type are not visible, will still find them. In this situation the tag will still not be visible, but as usual the tag location will be underlined. This option is particularly useful for exploring cases where a section of sequence has many overlapping tags. In the future we hope to solve this problem in a more satisfactory way.
"Set output list" pops up a dialogue asking for a list name to be used when outputting reading names. Once an output list has been specified, pressing the middle button on a reading name will add the name to the end of list. Note that selecting the same name more than once will add the name to the list more than once.