<CHAPTER ID="START">
  <TITLE>Starting &prog;</TITLE>

  <SECT1 ID="RUNNINGUNIX"> 
    <TITLE>Running &prog; on UNIX Systems</TITLE>
    <PARA>
On Unix the easiest way to run the program is to run the script called
<COMMAND>art</COMMAND> in the &prog; installation directory (see <XREF
LINKEND="INSTALLATION">) like this:
    </PARA>

    <PARA>
      <COMMAND>~/artemis/art</COMMAND>
    </PARA>

    <PARA>
If all goes well you will be presented with a small window with two
menus.  See <XREF LINKEND="LAUNCH-WINDOW"> to find out what to do next.
    </PARA>

    <PARA>
Alternatively you start &prog; with the name of a sequence file or embl file
eg:
    </PARA>

    <PARA>
      <COMMAND>~/artemis/art ~/artemis/etc/c1215.embl</COMMAND>
    </PARA>

    <PARA>
See <XREF LINKEND="UNIXARGS"> for a list of the other possible arguments.
    </PARA>

    <PARA>
Here is an alternative way to run &prog; if the <COMMAND>art</COMMAND> script
doesn't work for you:
    </PARA>

    <PARA>
      <COMMAND>
cd ~/artemis
      </COMMAND>
    </PARA>

    <PARA>
      <COMMAND>
java -Dartemis.environment=UNIX Diana
      </COMMAND>
    </PARA>
  </SECT1>

&unixargs;

  <SECT1 ID="RUNNINGPC"> 
    <TITLE>Running &prog; on Windows Systems</TITLE>
    <PARA>
On systems with Java 1.2 (aka Java 2) installed &prog; can be started by double
clicking on the artemis.jar icon.
    </PARA>
  </SECT1>

  <SECT1 ID="RUNNINGMAC"> 
    <TITLE>Running &prog; on Macintosh Systems</TITLE>
    <PARA>
On Macintosh machines &prog; can be started by double clicking on the ACT
icon.
    </PARA>
  </SECT1>

  <SECT1 ID="LAUNCH-WINDOW">
    <TITLE>The &prog; Launch Window</TITLE>
    <PARA>
This is the first window that opens when you start &prog;.  The menus at the
top of this window allow you to read a new sequence or embl entry.
    </PARA>
    <SECT2 ID="LAUNCH-WINDOW-FILE-MENU">
      <TITLE>The File Menu</TITLE>
      <SECT3 ID="LAUNCH-WINDOW-FILE-MENU-OPEN">
        <TITLE>Open ...</TITLE>
        <PARA>
If you select this menu item a file requester will be displayed which allows
you to open a flat file containing an entry.  If the file you select is
successfully read a new window will open, which shows the sequence and
features for the entry.  See <XREF LINKEND="MAINWINDOW-CHAPTER"> to find out
how to use the main window.
        </PARA>
      </SECT3>

      <SECT3 ID="LAUNCH-WINDOW-FILE-MENU-READ-FROM-EBI">
        <TITLE>Read from EBI ...</TITLE>
        <PARA>
The functions will ask the user for an accession number and then will attempt
to read it directly from the <ULINK URL="http://www.ebi.ac.uk"
TYPE="external">EBI</ULINK> using <ULINK
URL="http://corba.ebi.ac.uk/index.html" TYPE="external">CORBA</ULINK>.  If all
goes well you will be presented with an view/edit window (see <XREF
LINKEND="MAINWINDOW-CHAPTER">).
        </PARA>
        <PARA>
Please note that this feature is still experimental and may not be available
on all platforms.  In particular, it doesn't work correctly on machines that
have Java 1.2 installed.  Solaris and Microsoft Windows machines the most are
likely to have Java 1.2 and hence are most likely to have problems.
        </PARA>
      </SECT3>

      <SECT3 ID="LAUNCH-WINDOW-FILE-MENU-QUIT">
        <TITLE>Quit</TITLE>
        <PARA>
This menu item will close all windows and then exit the program
        </PARA>
      </SECT3>
    </SECT2>

    <SECT2 ID="LAUNCH-WINDOW-OPTIONS">
      <TITLE>The Options Menu</TITLE>
      <SECT3>
        <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.  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-SHOW-LOG">
        <TITLE>Show Log Window</TITLE>
        <PARA>
Show the log of informational messages from Artemis.  Currently the log window
is only used on UNIX systems to show the output of external programs.  This
menu item is only available when running Artemis on UNIX or GNU/Linux systems.
        </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 Artemis on UNIX or GNU/Linux systems.
        </PARA>
      </SECT3>
    </SECT2>
  </SECT1>
</CHAPTER>
