<SECT1 ID="DISPLAYMENU">
  <TITLE>The Display Menu</TITLE>
  <PARA>
The buttons in this menu are (mostly) toggles controlling which parts of the
&prog; display are visible.  "Show Entry Buttons", "Show Base View" and "Show
Feature List" default to on/active, while the others default to off/inactive.
Some general information about the graphs can be found in <XREF
LINKEND="GRAPHS">.
  </PARA>

  <SECT2 ID="DISPLAYMENU-SHOW-ENTRY-BUTTONS">
    <TITLE>Show Entry Buttons</TITLE>
    <PARA>
This toggle controls whether the entry button line is visible.  (see <XREF
LINKEND="ENTRYBUTTONS">).  [Default: on]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-SHOW-BASE-VIEW">
    <TITLE>Show Base View</TITLE>
    <PARA>
This toggle controls whether the base view is visible.  (see <XREF
LINKEND="VIEWS">).  [Default: on]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-SHOW-FEATURE-LIST">
    <TITLE>Show Feature List</TITLE>
    <PARA>
This toggle controls whether the feature view is visible.  (see <XREF
LINKEND="FEATURELIST">).
[Default: on]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-HIDE-ALL-GRAPHS">
    <TITLE>Hide All Graphs</TITLE>
    <PARA>
This item will turn off all the visible graphs.
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-USAGE-PLOTS">
    <TITLE>Add Usage Plots ...</TITLE>
    <PARA>
This menu item prompts the user for the name of a file which should contain
codon usage data in the same format as the data at <ULINK
URL="http://www.kazusa.or.jp/codon/" TYPE="external">this web
site</ULINK>.  If Artemis successfully loads the codon usage file two new
plots will be added to the display menu and will be immediately visible.  One
plot shows the codon scores (in a sliding window) for each of the forward
reading frames and the other shows the same thing for the reverse reading
frames. [short name: <LITERAL>gc_content</LITERAL>]
    </PARA>

    <PARA>
Here is an example usage file:
      <SYNOPSIS>
UUU 32.2( 48423)  UCU 30.5( 45913)  UAU 21.8( 32829)  UGU  8.9( 13371)
UUC 13.0( 19519)  UCC 12.1( 18149)  UAC 11.8( 17721)  UGC  5.6(  8372)
UUA 26.0( 39138)  UCA 17.9( 26850)  UAA  1.3(  1944)  UGA  0.5(   733)
UUG 24.0( 36134)  UCG  8.0( 12055)  UAG  0.5(   705)  UGG 10.9( 16364)

CUU 25.3( 38015)  CCU 21.9( 32964)  CAU 16.3( 24577)  CGU 16.3( 24495)
CUC  7.3( 10922)  CCC  8.4( 12619)  CAC  6.4(  9653)  CGC  6.2(  9316)
CUA  8.6( 12957)  CCA 12.7( 19075)  CAA 27.3( 41066)  CGA  7.9( 11896)
CUG  6.3(  9503)  CCG  4.6(  6910)  CAG 10.9( 16457)  CGG  3.0(  4487)

AUU 35.0( 52636)  ACU 22.9( 34419)  AAU 33.9( 51009)  AGU 14.7( 22108)
AUC 12.6( 19000)  ACC 10.9( 16378)  AAC 17.9( 26895)  AGC  9.2( 13905)
AUA 13.1( 19726)  ACA 13.9( 20898)  AAA 39.3( 59079)  AGA 11.1( 16742)
AUG 20.9( 31376)  ACG  6.5(  9744)  AAG 25.2( 37825)  AGG  5.1(  7615)

GUU 29.3( 44015)  GCU 30.2( 45397)  GAU 38.1( 57240)  GGU 22.0( 33101)
GUC 11.0( 16497)  GCC 11.6( 17518)  GAC 15.8( 23749)  GGC  8.5( 12717)
GUA 12.3( 18451)  GCA 15.7( 23649)  GAA 44.3( 66550)  GGA 15.7( 23623)
GUG  8.3( 12422)  GCG  5.3(  8011)  GAG 21.3( 31979)  GGG  4.3(  6497)
      </SYNOPSIS>
    </PARA>
  </SECT2>

&display-common;

</SECT1>
