options_menu.sgml

<SECT2 ID="LAUNCH-WINDOW-OPTIONS">
  <TITLE>The Options Menu</TITLE>
  <SECT3 ID="LAUNCH-WINDOW-OPTIONS-REREAD">
    <TITLE>Re-read Options</TITLE>
    <PARA>
Choosing this menu item will discard the current options settings and then
re-read the options file.  Note that changing the font size in the file and
then selecting this menu item will only change the font size for new windows,
not existing windows.  Currently some options are unaffected by this menu
item.  See <XREF LINKEND="OPTIONS-FILE"> for more information about options.
    </PARA>
  </SECT3>
  
  <SECT3 ID="LAUNCH-WINDOW-OPTIONS-DIRECT-EDIT">
    <TITLE>Enable Direct Editing</TITLE>
    <PARA>
This menu item will toggle "direct editing" option.  It is off be default
because it can have surprising results unless the user is expecting it.  See
<XREF LINKEND="VIEWS-DIRECTEDIT"> for more detail about this.
    </PARA>
  </SECT3>
  
  <SECT3 ID="LAUNCH-WINDOW-OPTIONS-EUK">
    <TITLE>Genetic Code Tables</TITLE>
    <PARA>
These options make all the 
<ULINK
URL="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes">
NCBI Genetic Codes</ULINK> available. The default setting is the
Standard Code. This setting effects the display of start codons (see <XREF
LINKEND="VIEWS-POPUPMENU-TOGGLES-STARTCODONS">) and the "Suspicious Start
Codons ..." feature filter (see <XREF
LINKEND="VIEWMENU-FEATURE-FILTERS-SUSPSTART">).
    </PARA>
  </SECT3>
 
  <SECT3 ID="LAUNCH-WINDOW-OPTIONS-SSHSEARCHES">
    <TITLE>Send Searches Via SSH</TITLE>
    <PARA>
This is an advanced option for sites that have set up the ability to
submit searches via SSH to another machine.
    </PARA>
  </SECT3>

  <SECT3 ID="BLACK-BELT-MODE">
  <TITLE>Black Belt Mode</TITLE>
    <PARA>
This is an advanced option that can be used to turn off warning message. This
options is displayed if the java property (black_belt_mode) is specified on 
opening up &prog;, i.e. art -Dblack_belt_mode=yes.
    </PARA>
  </SECT3>
 
  <SECT3 ID="LAUNCH-WINDOW-OPTIONS-HIGHLIGHTACTIVE">
    <TITLE>Highlight Active Entry</TITLE>
    <PARA>
When this option is on and the "One Line Per Entry" is on (see <XREF
LINKEND="VIEWS-POPUPMENU-ONE-LINE-PER-ENTRY">) the line that the active entry
is on will be highlighted in yellow.
    </PARA>
  </SECT3>
  
  <SECT3 ID="LAUNCH-WINDOW-OPTIONS-SHOW-LOG">
    <TITLE>Show Log Window</TITLE>
    <PARA>
Show the log of informational messages from &prog;.  Currently the log window
is only used on UNIX and GNU/Linux systems to show the output of external
programs.  This menu item is only available when running &prog; on UNIX or
GNU/Linux systems. The logging is controlled by <ULINK
URL="http://logging.apache.org/log4j/1.2/index.html">log4j</ULINK>. The
log4j.properties file (etc/log4j.properties in the source distribution) sets
the level of logging. This can be used to send the logging information to
other places such as a file.
    </PARA>
  </SECT3>
  
  <SECT3 ID="LAUNCH-WINDOW-OPTIONS-HIDE-LOG">
    <TITLE>Hide Log Window</TITLE>
    <PARA>
Hide the log of informational messages.  This menu item is only available when
running &prog; on UNIX or GNU/Linux systems.
    </PARA>
  </SECT3>
</SECT2>