Gap4 has a main window from which all the main options are selected from menus. When a database is open it also has a Contig Selector which will transform into a Contig Comparator whenever needed. In addition many of the gap4 functions, such as the Contig Editor or the Template Display will create their own windows when they are activated. All the graphical displays and the Contig Editor can be scrolled in register. The base of the graphical display windows usually contains an Information Line for showing short textual data about results or items touched by the mouse cursor. Gap4 is best operated using a three button mouse, but alternative keybindings are available. Full details of the user interface are described elsewhere (see section User Interface), and here we give an introduction based around a series of screenshots.
The main window (shown below) contains an Output window for textual results, an Error window for error messages, and a series of menus arranged along the top. The contents of the two text windows can be searched, edited and saved. Each set of results is preceded by a header containing the time and date when it was generated.
Some of the text will be underlined and shaded differently. These are hyperlinks which perform an operation when clicked (with the left mouse button) on, typically invoking a graphical display such as the contig editor. Clicking on these with the right mouse button will bring up a menu of additional operations. At present only a few commands (Show Relationships and the Search functions) produce hypertext, but if there is sufficient interest this may be expanded on.
![[picture]](interface.output.unix.gif.html)
(Click for full size image)
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Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_5.html