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The Settings Menu

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. Settings can be saved using the "Save settings" button. Settings for the following options can be changed.

Status Line

The contig editor can display several additional text lines underneath the consensus sequence. This "status" data is of textual form and can provide additional information about the data displayed above. 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 indicate: 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. Alternatively, using the "Translate using feature tables", only segments described in CDS records will be translated. The CDS records are those contained in the reference sequence. Translations 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.

Note that the data in the status line cannot be cut and pasted, modified or searched; it is not possible to move the cursor into these lines.

Trace Display

The editor trace display has two configurations specific to its own usage.

When switched on, auto-display traces will direct certain searches to automatically display relevant traces to aid in solving problems. This works in conjunction with most appropriate searches. The traces chosen to solve the "problem" will, by default, be the best trace from each strand which agrees with the consensus (which is calculated at a low consensus cutoff) and the best trace from each strand which disagrees with the consensus. This selection of traces may be adjusted by modifying the CONTIG_EDITOR.AUTO_DISPLAY_TRACES_CONF configuration variable. The default setting of this is "+ - +d -d". Each of the space separated elements in this string corresponds to a trace file to choose. If one cannot be found, then it is ignored. The order listed here is the order in which they will be displayed in the trace window. The complete list of available trace specifiers is:

Best +ve strand trace agreeing with consensus
Best +ve strand dye-primer trace agreeing with consensus
Best +ve strand dye-terminator trace agreeing with consensus
Best -ve strand trace agreeing with consensus
Best -ve strand dye-primer trace agreeing with consensus
Best -ve strand dye-terminator trace agreeing with consensus
Best trace disagreeing with consensus
Best +ve strand trace disagreeing with consensus
Best -ve strand trace disagreeing with consensus
Second best +ve strand trace agreeing with consensus
Second best +ve strand dye-primer trace agreeing with consensus
Second best +ve strand dye-terminator trace agreeing with consensus
Second best -ve strand trace agreeing with consensus
Second best -ve strand dye-primer trace agreeing with consensus
Second best -ve strand dye-terminator trace agreeing with consensus
Second best trace disagreeing with consensus
Second best +ve strand trace disagreeing with consensus
Second best -ve strand trace disagreeing with consensus

Once this is activated, whenever the user double clicks on a base in the editor sequence display, not only is the reading's trace displayed, but also its designated reference trace plus the difference between them. If its complementary reading is available, its trace and reference trace and their differences are also displayed.

(Click for full size image)

Trace differences display

As is shown in the figure below, it is also possible to set the trace difference display to use positive and negative references

(Click for full size image)

For further information about mutation detection, seesection Search for Mutations.

Consensus Algorithm

This allows selection of the consensus algorithm to use within the Contig Editor. Like the consensus and quality cutoff parameters, it is local to the specific editor being used. The main Consensus algorithm option should be used to globally change the algorithm being used.See section Consensus Algorithm.

Highlight Disagreements

This toggles between the normal sequence display (showing the current base assignments) and one in which those assignments that differ from the consensus are highlighted. It makes scanning for problems by eye much easier.

Several modes of highlighting are available: "By dots" will only display the bases that differ from the consensus, displaying all other bases as full stops. The base colours are as normal (ie reflecting tags and quality). "By foreground colour" and "By background colour" displays all base characters, but colours those that differ from the consensus. This allows easier visual scanning of the context that a difference occurs in, but it may be wise to disable the displaying of tags. Finally the "Case sensitive" toggle controls whether upper and lower case bases of the same base type should be considered differences.

Compare Strands

This toggles the consensus calculation routine between treating both strands together or independently. In the independent case any difference between the two strands is shown in the consensus as a '-'. Hence these clashes are found as problems by the "Search by problem" option.

Toggle auto-save

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 its data to disk every 50 edits. Each time an auto save is performed it is announced in the output window. Saving more frequently can still be performed manually by using "Save Contig".

Unlike "saves" made using the manual "Save Contig" command, the "Undo" button will allow the user to undo edits regardless of when the last auto save occurred.

3 Character Amino Acids

By default, the codon translation within the status line displays single character amino acid codes. Selecting "3 Character Amino Acids" will toggle the status line to display three character amino acid codes.

Group Readings by Templates

When set, this forces readings from the same template to be displayed vertically adjacent to one another. The real "X coordinate" of the reading is not changed, so this has no effect for readings from the same template that are never visible together on the screen at the same time. The purpose of the function is to provide a method for grouping batches of readings together, for example when looking for mutations. They do not need to be from the same template, but can be grouped using the template name.

Note that when this mode is in use the operation of the up and down arrow keys incorrectly affects the editing cursor. Using the mouse to position the editing cursor still works correctly.

Show Reading and Consensus Quality

When the quality cutoff value is 0 or higher and either of the "show reading quality" or "show consensus quality" toggles is set, the background for bases is shaded in a grey level dependent on their quality. There are ten levels of shading with the darkest representing poor data and the lightest representing good data. 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.

The colours used are adjustable by modifying your `.gaprc' file. The defaults are shown below.

set_def CONTIG_EDITOR.QUAL0_COLOUR     "#494949"
set_def CONTIG_EDITOR.QUAL1_COLOUR     "#696969"
set_def CONTIG_EDITOR.QUAL2_COLOUR     "#898989"
set_def CONTIG_EDITOR.QUAL3_COLOUR     "#a9a9a9"
set_def CONTIG_EDITOR.QUAL4_COLOUR     "#b9b9b9"
set_def CONTIG_EDITOR.QUAL5_COLOUR     "#c9c9c9"
set_def CONTIG_EDITOR.QUAL6_COLOUR     "#d9d9d9"
set_def CONTIG_EDITOR.QUAL7_COLOUR     "#e0e0e0"
set_def CONTIG_EDITOR.QUAL8_COLOUR     "#e8e8e8"
set_def CONTIG_EDITOR.QUAL9_COLOUR     "#f0f0f0"
set_def CONTIG_EDITOR.QUAL_IGNORE      "#ff5050"

Show edits

When set, any change between the bases displayed and the original sequence held in the trace files is shown by changing the background colour of the changed base. The detection of these edits depends on the quality values and the "original position" data. Hence the traces do not need to be present in order to detect edits. The colour of the bases reflects the type of change found. The colours are adjustable by editing the `.gaprc' file. The following table lists the colour, gaprc variable name and the meaning.

CONTIG_EDITOR.EDIT_BASE_COLOUR -- Base change or insertion

Show Unpadded Positions

The ruler at the top of the contig editor displays every tenth base number in the consensus sequence. Without "show unpadded positions" enabled any character in the consensus is counted, including padding characters. If "show unpadded positions" is enabled the ruler will only count non pad ("*") characters. Please note that this may considerably slow down the editor on large databases as the full consensus needs to be calculated in order to plot the ruler. If you just need to obtain the occasional unpadded position it is better to press the Enter key or to use the "unpadded position" search.

Set Active Tags

"Set Active Tags" allows configuration of which tag types should be displayed within the editor. Note that searches for tag annotations will only examine active tags, but searching for a specific tag type will find tags even when tags of this type are not visible. In this situation the tag will still be invisible, 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. An alternative to using this dialogue is using the Control-Q key, which toggles the display of active tags.

Set Output List

"Set output list" pops up a dialogue asking for a list name to be used when outputting reading names (see section Lists). Once an output list has been specified, pressing the middle button, or Alt left mouse 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. The list is never cleared by the editor. This allows multiple editors to append to the same list. If required, use the list menu to clear the list.

Set Default Confidences

Replacing bases or inserting new bases in the editor can assign new confidence values to those bases. The default setting is to set these confidence values to 100 which has the effect of forcing the consensus to be that base. The "Set Default Confidences" dialogue allows these default values to be changed. The allowable range of confidence values for a base is from 0 to 100 inclusive. The dialogue also allows selection of confidence -1. This tells the editor to not change the confidence value. When replacing a base this keeps the same confidence value of the base that is being replaced. When inserting a base this uses the average of the confidence value of the two surrounding bases.

Set or unset saving of undo

Storing the undo information takes up a great deal of computer memory and slows down the alignment algorithm. Particularly when using the Join Editor for very large overlaps (e.g. after copying batches of readings from one database to another), it can be useful to turn off the saving of undo information. For this reason the settings menu contains an option to turn off (or on) the saving of undo information.

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This page is maintained by staden-package. Last generated on 22 October 2002.