concepts.sgml

  <SECT1 ID="CONCEPTS">
    <TITLE>Concepts</TITLE>
    <PARA>
Here are some general concepts about &prog; that may make the rest of this
manual clearer.
    </PARA>

    <SECT2 ID="CONCEPTS-ENTRY">
      <TITLE>The "Entry"</TITLE>
      <PARA>
An "entry" in &prog;-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 <ULINK
URL="http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html">feature
table</ULINK> lines (the <LITERAL>FT</LITERAL> lines) of an 
EMBL/GENBANK entry (see <XREF LINKEND="CONCEPTS-TABFILE">).  After loading a
sequence and opening an entry edit window (see <XREF
LINKEND="LAUNCH-WINDOW-FILE-MENU-OPEN">) it is then possible to overlay many
feature tables 
(see <XREF LINKEND="FILEMENU-READ-AN-ENTRY">).  Each of these
feature table files is called an entry by &prog; and it's features are kept
separate from those of other entries.
      </PARA>
      <PARA>
This meaning of the word "entry" is
used by most of the items in the File menu (see <XREF LINKEND="FILEMENU">) and
by the items in the Entry menu (see <XREF LINKEND="ENTRIESMENU">).
      </PARA>
    </SECT2>

    <SECT2 ID="CONCEPTS-FEATURE">
      <TITLE>EMBL/Genbank Features</TITLE>
      <PARA>
A "feature" in an EMBL or Genbank file is a region of DNA that has been
annotated with a key/type (see <XREF LINKEND="CONCEPTS-KEY">) and zero or more
qualifiers (see <XREF LINKEND="CONCEPTS-QUALIFIERS">).  In an EMBL or Genbank
formated file the features of a piece of DNA are listed in the feature table
section (see <XREF LINKEND="CONCEPTS-TABFILE">).
      </PARA>
    </SECT2>

    <SECT2 ID="CONCEPTS-KEY">
      <TITLE>EMBL/Genbank Feature Keys</TITLE>
      <PARA>
All EMBL and Genbank features have exactly one "key" assigned to them.  The
key is the type of the feature.  Examples include <LITERAL>CDS</LITERAL> (a
<LITERAL>C</LITERAL>o<LITERAL>D</LITERAL>ing <LITERAL>S</LITERAL>equence),
<LITERAL>intron</LITERAL> and <LITERAL>misc_feature</LITERAL>
(<LITERAL>MISC</LITERAL>ellaneous <LITERAL>feature</LITERAL>).
      </PARA>
      <PARA>
The <ULINK URL="http://www.ebi.ac.uk">EBI</ULINK> has a list of <ULINK
URL="http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html">all possible feature keys</ULINK>.
      </PARA>
    </SECT2>

    <SECT2 ID="CONCEPTS-QUALIFIERS">
      <TITLE>EMBL/Genbank Feature Qualifiers</TITLE>
      <PARA>
The qualifiers of a feature in an EMBL or Genbank file are the notes and extra
information about the feature.  For example an <LITERAL>exon</LITERAL> feature
might have a <LITERAL>/gene="ratC"</LITERAL> qualifier, meaning that the exon
feature is part of a gene named <LITERAL>ratC</LITERAL>.
      </PARA>
      <PARA>
The <ULINK URL="http://www.ebi.ac.uk">EBI</ULINK> has a list of <ULINK
URL="http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html">all possible feature qualifiers</ULINK>.
      </PARA>
    </SECT2>

    <SECT2 ID="CONCEPTS-TABFILE">
      <TITLE>"Tab" Files or "Table" Files</TITLE>
      <PARA>          
An EMBL or Genbank file that only contains a feature table (just
<LITERAL>FT</LITERAL> 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".
      </PARA>
    </SECT2>

    <SECT2 ID="CONCEPTS-ACTIVEENTRY">
      <TITLE>The Active Entries</TITLE>
      <PARA>
All entries in &prog; 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 <XREF LINKEND="ENTRIESMENU">.
      </PARA>
    </SECT2>

    <SECT2 ID="CONCEPTS-DEFAULTENTRY">
      <TITLE>The Default Entry</TITLE>
      <PARA>
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.
      </PARA>
      <PARA>
The default entry can be set by using the "Set Default Entry ..." menu item in
the Entries menu (see <XREF LINKEND="ENTRIESMENU-SET-DEFAULT-ENTRY">)<![
%artemis-only; [ or by using the entry buttons (see <XREF
LINKEND="ENTRYBUTTONS">)]]>.
      </PARA>
    </SECT2>

    <SECT2 ID="CONCEPTS-SEGMENT">
      <TITLE>Feature Segments</TITLE>
      <PARA>
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.
      </PARA>
    </SECT2>

    <SECT2 ID="CONCEPTS-SELECTION">
      <TITLE>The Selection</TITLE>
      <PARA>
In common with applications like word processors and graphics programs, &prog;
allows the user to "select" the objects that the program will act on.  The
objects to act on in &prog; 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 <XREF LINKEND="SELECTMENU">) or using the mouse (see
<XREF LINKEND="VIEWS-SELECTION"><![ %artemis-only; [ and <XREF
LINKEND="FEATURELIST-SELECTION">]]>).
      </PARA>
    </SECT2>

    <SECT2 ID="CONCEPTS-COLOUR">
      <TITLE>Feature Colours</TITLE>
      <PARA>
Each feature displayed in &prog; can be given a colour.  The available colours
are set in the options file (see <XREF LINKEND="OPTIONS-CHAPT">) and are
assigned to a feature by adding a <LITERAL>/colour</LITERAL> qualifier (see
<XREF LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">).  Currently there are two
ways of specifying feature colours.  The first way uses a single number.  For
example red is colour 2, so adding <LITERAL>/colour=2</LITERAL> 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
<LITERAL>/colour=255 0 0</LITERAL> is another way to give a feature the colour
red.  If no <LITERAL>/colour</LITERAL> qualifier is set for a feature a
default colour is used (the default colours are also specified in the options
file).
      </PARA>
    </SECT2>
  </SECT1>