Entry Edit Concepts

There are some general concepts about operating Artemis that need to be discussed before diving into the detail.

The "Entry"

An "entry" in Artemis-speak is not necessarily a complete EMBL entry. In most places in this manual when we refer to an entry we mean a file that contains just the feature table lines (the FT lines) of an EMBL entry (see the section called "Tab" Files or "Table" Files). After loading a sequence and opening an entry edit window (see the section called Open ...) it is then possible to overlay many feature tables (see the section called Read An Entry in Chapter 3). Each of these feature table files is called an entry by Artemis and it's features are kept separate from those of other entries. This meaning of the word "entry" is used by most of the items in the File menu (see the section called The File Menu in Chapter 3) and by the "Delete An Entry ..." item in the Edit menu (see the section called Delete An Entry ... in Chapter 3).

"Tab" Files or "Table" Files

An EMBL file that only contains a feature table (just FT lines, no sequence or header lines) is called a "table" file, or sometimes just a "tab" file because the often has a name like "somefile.tab".

The Active Entries

All entries in Artemis are considered to be "active" or "inactive". The overview, DNA view and feature list parts of the main window will only display features from active entries. To find out how to set the active and inactive entries see the section called The Entry Button Line in Chapter 3.

The Default Entry

Many actions (such as creating a feature or discarding an entry) require an entry to be identified as the source or destination for the action. Some actions, such as "Move Selected Features To ..." in the edit menu, will explicitly ask for an entry, but most assume that the action refers to a "default entry" that was previously set by the user.

There are two ways to set the default entry:

Feature Segments

The term "segment" in the context of a CDS feature means the same as the word "exon". We use the term "segment", because non-CDS features (such as misc_feature) can have exon-like parts too, but the term "exon" would be inappropriate in that case.

The Selection

In common with applications like word processors and graphics programs, Artemis allows the user to "select" the objects that the program will act on. The objects to act on in Artemis are features, feature segments or bases. If a feature segment is added to the selection, the feature that contains the segment is implicitly added as well. The current selection can be changed with the Select Menu (see the section called The Select Menu in Chapter 3) or using the mouse (see the section called Changing the Selection in Chapter 3 and the section called Changing the Selection in Chapter 3).

Feature Colours

Each feature displayed in Artemis can be given a colour. The available colours are set in the options file (see the section called The Options File) and are assigned to a feature by adding a /colour qualifier (see the section called Edit Selected Features in Chapter 3). Currently the colours are specified by number - for example red is colour 2, so adding /colour=2 as a feature qualifier will make that feature red. If no /colour qualifier is set for a feature a default colour is used (the default colours are also specified in the options file).