Contigs can be selected by either clicking with the left mouse button on the line representing the required contig in the contig selector window or alternatively by choosing the "List contigs" option from the "View" menu. This option invokes a "Contig Names" list box where the contig names and numbers are listed in the same order as they appear in the contig selector window. Clicking on a name within the list box is equivalent to clicking on the corresponding contig in the contig selector.
Most commands require a contig identifier (which can be the name or
number of any reading on the contig) and
Gap contains several
mechanisms for obtaining this information from users. The names or
numbers can be typed or cut and pasted into dialogue boxes (note that a
reading number must be preceded by a # character, e.g. "#102" means
reading number 102 but "102" means the reading with name 102). Also any
currently active dialogue boxes that require a contig to be selected can
be updated simply by clicking on a contig in the contig selector or clicking
on an entry in the "Contig Names" list box. For
example, if the Edit contig command is selected from the Edit menu it
will bring up a dialogue requesting the identity of the contig to edit.
If the user clicks the left mouse button on a contig in the contig
selector window, the contig editor dialogue will automatically change to
contain the name of the selected contig. Some commands, such as the
Contig Editor, can be selected from a popup menu that is activated by
clicking the right mouse button on the contig line in the Contig
Selector or clicking the right mouse button on the corresponding name within
the "Contig Names" list box. This simultaneously defines the contig to
operate on and so the command starts up without dialogue.
Several contigs can be selected at once by either clicking on each contig with the left mouse button or dragging out a selection rectangle by holding the left mouse button down. Contigs which are entirely enclosed within the rectangle will be selected. Alternatively, selecting several contigs from the "Contig Names" list box will also result in each contig being selected. Selected contigs are highlighted in bold. Selecting the same contig again will unselect it.
The currently selected contigs are also kept in a 'list' named contigs.