options.sgml

<CHAPTER ID="OPTIONS-CHAPT">
  <TITLE>&prog; Configuration Options</TITLE>

  <SECT1 ID="OPTIONS-INTRO">
    <TITLE>The Options File</TITLE>
    <PARA>
When started on &prog; will potentially look in 5 different places for files
to examine for configuration information.  &prog; reads from the locations in
order, so the user can override the default options.  Note that on Macintosh
and Windows systems the "current directory" mentioned below is the directory
where the &prog; application has been installed.
    </PARA>

    <PARA>
This is the search order:
      <ITEMIZEDLIST>
        <LISTITEM>
          <PARA>
The standard &prog; options are read first.  On UNIX this file is in the file
<LITERAL>etc/options</LITERAL> in the &prog; distribution directory.  Changing
that file will change the options settings for all users.  On Macintosh and
Windows system the standard options are stored in the &prog; application
itself and can't be changed (easily).
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
If the user has specified an options file on the command line with the
<LITERAL>-options</LITERAL> argument, it will be read next.  (UNIX only - see
<XREF LINKEND="UNIXARGS"> for more).
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
If there is a file called <LITERAL>diani.ini</LITERAL> in the current
directory it will be read.  This is for backwards compatibility.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
If there is a file called <LITERAL>options</LITERAL>,
<LITERAL>options.txt</LITERAL> or <LITERAL>options.text</LITERAL> in the
current directory it will be read.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
If there is a file in the user's home directory called
<LITERAL>.artemis_options</LITERAL> it will be read.
          </PARA>
        </LISTITEM>
      </ITEMIZEDLIST>
    </PARA>
  </SECT1>

  <SECT1 ID="OPTIONS-DESCRIPTIONS">
    <TITLE>&prog; Option Descriptions</TITLE>
    <PARA>
This section describes the possible options for &prog;.
    </PARA>

    <SECT2 ID="OPTIONS-FONTSIZE">
      <TITLE><LITERAL>font_size</LITERAL></TITLE>
      <PARA>
This option will set the font size for all the &prog; windows.  [default: 14]
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-FONTNAME">
      <TITLE><LITERAL>font_name</LITERAL></TITLE>
      <PARA>
This option is used to choose the font for all the &prog; windows.  The font
must be fixed-width.  [default: "Monospaced"]
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-BASE-PLOT-HEIGHT">
      <TITLE><LITERAL>base_plot_height</LITERAL></TITLE>
      <PARA>
The height (in pixels) of each of the base plots.  [default: 150]
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-FEATURE-PLOT-HEIGHT">
      <TITLE><LITERAL>feature_plot_height</LITERAL></TITLE>
      <PARA>
The height (in pixels) of each of the feature plots.  [default: 160]
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-DRAWFEATUREBORDERS">
      <TITLE><LITERAL>draw_feature_borders</LITERAL></TITLE>
      <PARA>
If set to yes, borders will be drawn around each feature and each exon.  if
set to no, borders will only be drawn around the selected features.  This can
also be set in the views popup menu (see <XREF
LINKEND="VIEWS-POPUPMENU-TOGGLES-FEATURE-BORDERS">).  [default: "yes"]
      <PARA>
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-SHOWFORWARDLINES">
       <TITLE><LITERAL>show_forward_lines</LITERAL></TITLE>
       <PARA>
If set to yes, the forward frame lines are shown by default. This can
also be set in the views popup menu.  [default: "yes"]
       <PARA>
       </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-SHOWREVERSELINES">
       <TITLE><LITERAL>show_reverse_lines</LITERAL></TITLE>
       <PARA>
	  If set to yes, the reverse frame lines are shown by default. This can
	  also be set in the views popup menu.  [default: "yes"]
       <PARA>
       </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-DRAWFEATUREARROWS">
      <TITLE><LITERAL>draw_feature_arrows</LITERAL></TITLE>
      <PARA>
If set to yes, a direction arrow will be drawn around at the end of each
feature.  if set to no, no arrows will be drawn.  This can also be set in the
views popup menu (see <XREF LINKEND="VIEWS-POPUPMENU-TOGGLES-FEATURE-ARROWS">).
[default: "yes"] 
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-OVERVIEW-FEATURE-LABELS">
      <TITLE><LITERAL>overview_feature_labels</LITERAL></TITLE>
      <PARA>
If this option is no then the feature labels in the overview (see <XREF
LINKEND="MAINWINDOW-OVERVIEW">) will be off at
startup.  [default: "yes"] 
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-OVERVIEW-ONE-LINE-PER-ENTRY">
      <TITLE><LITERAL>overview_one_line_per_entry</LITERAL></TITLE>
      <PARA>
If this option is set yes then the overview (see <XREF
LINKEND="MAINWINDOW-OVERVIEW">) will start in one line per entry mode. 
[default: "no"] 
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-SHOW-LIST">
      <TITLE><LITERAL>show_list</LITERAL></TITLE>
      <PARA>
If set to yes then the feature list (see <XREF LINKEND="FEATURELIST">) will be
shown on startup.  [default: "yes"] 
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-SHOW-BASE-VIEW">
      <TITLE><LITERAL>show_base_view</LITERAL></TITLE>
      <PARA>
If set to yes then the DNA base view (see <XREF LINKEND="VIEWS">) will be
shown on startup.  [default: "yes"]
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-FEATURES-ON-FRAME-LINES">
      <TITLE><LITERAL>features_on_frame_lines</LITERAL></TITLE>
      <PARA>
If set to yes then the "All Features On Frame Lines" option will be set to
yes on startup.  (See <XREF LINKEND="VIEWS-POPUPMENU-TOGGLES-FRAMEFEATURES">)
[default: "no"]
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-FRAME-LINE-FEATURES">
      <TITLE><LITERAL>frame_line_features</LITERAL></TITLE>
      <PARA>
This is a list of the feature keys that should be shown by default on the
frame lines. e.g.
        <SYNOPSIS>
frame_line_features =  \
  CDS \
  polypeptide
        </SYNOPSIS>
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-FEATURE-LABELS">
      <TITLE><LITERAL>feature_labels</LITERAL></TITLE>
      <PARA>
If set to yes then the feature labels will be shown on startup.  
(See <XREF LINKEND="VIEWS-POPUPMENU-TOGGLES-FRAMEFEATURES">)
[default: "yes"]
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-ONE-LINE-PER-ENTRY">
      <TITLE><LITERAL>one_line_per_entry</LITERAL></TITLE>
      <PARA>
If set to yes then the "One Line Per Entry" option will be set to
yes on startup.  (See <XREF LINKEND="VIEWS-POPUPMENU-TOGGLES-FRAMEFEATURES">)
[default: "no"]
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-GENETICCODES">
      <TITLE><LITERAL>genetic_codes</LITERAL></TITLE>
      <PARA>
This option gives the list of names of the available genetic code tables.
For each name in the list there is a translation_table_NUMBER entry (see
below) where NUMBER is its location in the genetic_codes list. Similarly
the start codons are defined as start_codons_NUMBER for each code.
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-TRANSLATION-TABLE">
      <TITLE><LITERAL>translation_table_1</LITERAL></TITLE>
      <PARA>
The translation_table option is used to lookup codon translations.  The
table must have exactly 64 entries, and there is one entry for each codon.
      </PARA>
      <PARA>
The entries should appear in this order:
        <SYNOPSIS>
  TTT TTC TTA TTG
  TCT TCC ...
  ...
        </SYNOPSIS>
      </PARA>
      <PARA>
This is the default setting for this option is the Standard Code:
        <SYNOPSIS>
translation_table_1 = \
     f f l l \
     s s s s \
     y y * * \
     c c * w \
             \
     l l l l \
     p p p p \
     h h q q \
     r r r r \
             \
     i i i m \
     t t t t \
     n n k k \
     s s r r \
             \
     v v v v \
     a a a a \
     d d e e \
     g g g g
        </SYNOPSIS>
      </PARA>
      <PARA>
The other translation table entries are defined by giving the differences
to the Standard Code. These are given as the bases that make up the codon
immediately followed by the translation (e.g. atam, so that 'ata' codes
for 'm').
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-EXTRAKEYS">
      <TITLE><LITERAL>extra_keys</LITERAL></TITLE>
      <PARA>
This contains a list of keys (separated by spaces) that are allowed in
addition to those specified by EMBL.  The official EMBL keys are listed in the
<LITERAL>feature_keys</LITERAL> file in the &prog; code directory.
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-EXTRAQUALIFIERS">
      <TITLE><LITERAL>extra_qualifiers</LITERAL></TITLE>
      <PARA>
This contains a list of qualifiers (and their associated type) that are
allowed in addition to those specified by EMBL.  The official EMBL qualifiers
and qualifier types are listed and described in the
<LITERAL>qualifier_types</LITERAL> file in the &prog; code directory.
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-COMMONKEYS">
      <TITLE><LITERAL>common_keys</LITERAL></TITLE>
      <PARA>
This is a list of the keys that should be shown by default in the feature edit
window.  (see <XREF LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">).
      </PARA>
      <PARA>
The default setting for this option is:
        <SYNOPSIS>
common_keys = \
    allele attenuator CDS conflict exon intron LTR misc_feature misc_RNA mRNA \
    mutation polyA_signal polyA_site promoter protein_bind RBS repeat_region \
    repeat_unit rRNA scRNA snRNA source stem_loop STS TATA_signal terminator \
    tRNA unsure variation -10_signal -35_signal CDS_motif gene \
    BLASTN_HIT CDS_BEFORE CDS_AFTER BLASTCDS
        </SYNOPSIS>
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-HYPERLINKS">
      <TITLE><LITERAL>hyperlinks</LITERAL></TITLE>
      <PARA>
This is a list of databases and their URL's for Artemis to provide
hyperlinks in the Feature Editor (see <XREF LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">).
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-UNDO-LEVELS">
      <TITLE><LITERAL>undo_levels</LITERAL></TITLE>
      <PARA>
The number of levels of undo to save or 0 to disable undo.  More undo
levels will require more memory.  [default: 20]
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-MIN-ORF-SIZE">
      <TITLE><LITERAL>minimum_orf_size</LITERAL></TITLE>
      <PARA>
This option is used to set the minimum size (in amino acid residues) of a
"large" open reading frame, which controls which ORFS are marked by the "Mark
Open Reading Frames" menu item (see <XREF LINKEND="CREATEMENU-MARK-ORF">).
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-DIRECTEDIT">
      <TITLE><LITERAL>direct_edit</LITERAL></TITLE>
      <PARA>
Set the default value for the direct edit option.  A value of "yes" will turn
direct edit on by default.  See <XREF
LINKEND="LAUNCH-WINDOW-OPTIONS-DIRECT-EDIT">
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-FEATURE-DNA-PROGRAMS">
      <TITLE><LITERAL>feature_dna_programs</LITERAL></TITLE>
      <PARA>
This is a list of the possible external programs that can be run on the bases
of a feature.  Each pair in the list is a program name and a default database
to use for that program.  For each program name there must be a corresponding
shell script called "run_something".  eg. run_blastn.  See <XREF
LINKEND="RUNMENU-CONFIGURATION"> for more information.
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-FEATURE-PROTEIN-PROGRAMS">
      <TITLE><LITERAL>feature_protein_programs</LITERAL></TITLE>
      <PARA>
This is a list of the possible external programs that can be run on the
translation of a feature.  Each pair in the list is a program name and a
default database to use for that program.  For each program name there must be
a corresponding shell script called "run_something".  eg. run_blastp for
blastp or run_fasta for fasta.  See <XREF LINKEND="RUNMENU-CONFIGURATION"> for
more information.
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-NCBI-DNA-PROGRAMS">
      <TITLE><LITERAL>ncbi_dna_search</LITERAL></TITLE>
      <PARA>
This lists the NCBI web-BLAST applications that the bases of a selected feature can
be sent to. See <XREF LINKEND="RUNMENU">.
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-NCBI-PROTEIN-PROGRAMS">
      <TITLE><LITERAL>ncbi_protein_search</LITERAL></TITLE>
      <PARA>
This lists the NCBI web-BLAST applications that the translation of a selected feature can
be sent to. See <XREF LINKEND="RUNMENU">.
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-COLOUR">
      <TITLE>Setting Colours</TITLE>
      <PARA>
The feature colours (see <XREF LINKEND="CONCEPTS-COLOUR">) used by &prog; can
be changed using the options file.  By default there are 18 possible colours
(numbered 0 to 17), but any number can be used.  The option names for the
colours are <LITERAL>colour_0</LITERAL>, <LITERAL>colour_1</LITERAL>, etc.
The value of each of these qualifiers should be the three numbers separated by
spaces.  The numbers correspond to red, green and blue respectively and each
number is an intensity from 0 to 255.  As an example, to change colour 2 to
white put this line in the options file:
        <SYNOPSIS>
colour_2 = 255 255 255
        </SYNOPSIS>
Here is a list of the default colour numbers:
        <SYNOPSIS>
0  white          (RGB values: 255 255 255)
1  dark grey      (RGB values: 100 100 100)
2  red            (RGB values: 255   0   0)
3  green          (RGB values:   0 255   0)
4  blue           (RGB values:   0   0 255)
5  cyan           (RGB values:   0 255 255)
6  magenta        (RGB values: 255   0 255)
7  yellow         (RGB values: 255 255   0)
8  pale green     (RGB values: 152 251 152)
9  light sky blue (RGB values: 135 206 250)
10 orange         (RGB values: 255 165   0)
11 brown          (RGB values: 200 150 100)
12 pale pink      (RGB values: 255 200 200)
13 light grey     (RGB values: 170 170 170)
14 black          (RGB values:   0   0   0)
15 mid red:       (RGB values: 255  63  63)
16 light red      (RGB values: 255 127 127)
17 pink           (RGB values: 255 191 191)
        </SYNOPSIS>
      </PARA>
    </SECT2>
    <SECT2 ID="OPTIONS-PLOTS">
      <TITLE>Options For Plots and Graphs</TITLE>
      <PARA>
Each graph type has three option settings associated with it: the default
minimum window size, default maximum window size and the default window size.
The option names have the following form:
<LITERAL>[short_name]_default_min_window</LITERAL>,
<LITERAL>[short_name]_default_max_window</LITERAL> and
<LITERAL>[short_name]_default_window</LITERAL> (respectively).
<LITERAL>[short_name]</LITERAL> should be replaced with the short name of the
graph.  (The available short names are documented in <XREF
LINKEND="GRAPHMENU"> and
<XREF LINKEND="VIEWMENU-SHOW-FEATURE-PLOTS">).
      </PARA>
      <PARA>
As an example the short name of the GC content graph is gc_content so to set
the initial minimum window size to 100, the maximum to 1000 and the initial
window size to 150 use these setting:
        <SYNOPSIS>
gc_content_default_min_window = 100
gc_content_default_max_window = 1000
gc_content_default_window_size = 150
        </SYNOPSIS>
      </PARA>
      <PARA>
See also <XREF LINKEND="GRAPHS">.
      </PARA>
    </SECT2>

    <SECT2 ID="OPTIONS-CHADO">
      <TITLE>Options For A Chado Database</TITLE>

    <SECT3 ID="OPTIONS-CHADO-EXON-MODEL">
       <TITLE><LITERAL>chado_exon_model</LITERAL></TITLE>
       <PARA>
       This is the feature key used when chado exons are joined and displayed in &prog;.
       For example: <SYNOPSIS>chado_exon_model=CDS</SYNOPSIS> 
       [default: "exon-model"] 
       </PARA>
    </SECT3>

    <SECT3 ID="OPTIONS-CHADO-TRANSCRIPT">
        <TITLE><LITERAL>chado_transcript</LITERAL></TITLE>
	<PARA>
	This is the feature key used when chado transcripts are created in a gene 
	model. [default: "mRNA"] 
	</PARA>
    </SECT3>

    <SECT3 ID="OPTIONS-CHADO-SERVERS">
      <TITLE><LITERAL>chado_servers</LITERAL></TITLE>
      <PARA>
      This can be used to provide a list of available databases. For example:
      <SYNOPSIS>chado_servers = \
        test localhost:5432/test?userName \
	genedb_ro db.genedb.org:5432/snapshot?genedb_ro
      </SYNOPSIS>
      </PARA>
    </SECT3>

    </SECT2>
  </SECT1>

  <SECT1 ID="OPTIONS-FILE">
    <TITLE>Options File Format</TITLE>
    <PARA>
The option files it should contain settings that look like this:

      <SYNOPSIS>
option_name = option_value
      </SYNOPSIS>

If the value of an options is too long to fit on one line it can be split over
several lines by ending each line with a backslash like this:

      <SYNOPSIS>
option_name = option_value another_option_value \
    a_third_option_value a_forth_option_value
      </SYNOPSIS>
    </PARA>

    <SECT2 ID="OPTIONS-EXAMPLE">
      <TITLE>An Example Options File</TITLE>
      <PARA>
Here is an example options file:
      </PARA>
      <SYNOPSIS>
# this line is a comment

font_size = 14

minimum_orf_size = 100

common_keys = \
    allele attenuator CDS conflict exon intron LTR misc_feature misc_RNA mRNA \
    mutation polyA_signal polyA_site promoter protein_bind RBS repeat_region \
    repeat_unit rRNA scRNA snRNA source stem_loop STS TATA_signal terminator \
    tRNA unsure variation -10_signal -35_signal CDS_motif gene
      </SYNOPSIS>
    </SECT2>
  </SECT1>
</CHAPTER>