Here are some general concepts about Artemis that may make the rest of this manual clearer.
An "entry" in Artemis-speak is not necessarily a complete EMBL or GENBANK 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/GENBANK 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 ... in Chapter 2) 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 items in the Entry menu (see the section called The Entries Menu in Chapter 3).
A "feature" in an EMBL or Genbank file is a region of DNA that has been annotated with a key/type (see the section called EMBL/Genbank Feature Keys) and zero or more qualifiers (see the section called EMBL/Genbank Feature Qualifiers). In an EMBL or Genbank formated file the features of a piece of DNA are listed in the feature table section (see the section called "Tab" Files or "Table" Files).
All EMBL and Genbank features have exactly one "key" assigned to them. The key is the type of the feature. Examples include CDS (a CoDing Sequence), intron and misc_feature (MISCellaneous feature).
The qualifiers of a feature in an EMBL or Genbank file are the notes and extra information about the feature. For example an exon feature might have a /gene="ratC" qualifier, meaning that the exon feature is part of a gene named ratC.
An EMBL or Genbank 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".
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 Entries Menu in Chapter 3.
Many actions (such as creating features) 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 some assume that the action refers to a "default entry" that was previously set by the user.
The default entry can be set by using the "Set Default Entry ..." menu item in the Entries menu (see the section called Set Default Entry in Chapter 3) or by using the entry buttons (see the section called The Entry Button Line in Chapter 3).
The term "segment" in the context of a CDS feature means "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.
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 from a View Window in Chapter 3 and the section called Changing the Selection from the Feature List in Chapter 3).
Each feature displayed in Artemis can be given a colour. The available colours are set in the options file (see Chapter 5) and are assigned to a feature by adding a /colour qualifier (see the section called Edit Selected Features in Chapter 3). Currently there are two ways of specifying feature colours. The first way uses a single number. For example red is colour 2, so adding /colour=2 as a feature qualifier will make that feature red. The second way is to specify the red, green and blue components of the colour. Each of the components can take values from 0 to 255, with 255 being the most intense. For example /colour=255 0 0 is another way to give a feature the colour 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).