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

  <SECT1 ID="COMPARISON-RUN">
    <TITLE>Running a Comparison</TITLE>
    <PARA>
Before running &prog; you will need to obtain a comparison, which is usually
the result of a blastn or tblastx search of a sequence of interest against
another.  The blast output will need to be processed with <ULINK
URL="http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html"
TYPE="external">MSPcrunch</ULINK>.  &prog; can only read MSPcrunch output
created with with the <LITERAL>-d</LITERAL> flag.
    </PARA>

    <SECT2 ID="COMPARISON-FILE-FORMAT">
      <TITLE>The Comparison File Format</TITLE>
      <PARA>
Here is an example input file file generated by <LITERAL>MSPcrunch
-d</LITERAL>.
        <SYNOPSIS>
1399 97.00 940 2539 sequence1.dna 1 1596 AF140550.seq
1033 93.00 9041 10501 sequence1.dna 9420 10880 AF140550.seq
828 95.00 6823 7890 sequence1.dna 7211 8276 AF140550.seq
773 94.00 2837 3841 sequence1.dna 2338 3342 AF140550.seq
        </SYNOPSIS>
      </PARA>
      <PARA>
The columns have the following meanings (in order): score, percent identity,
match start in the query sequence, match end in the query sequence, query
sequence name, subject sequence start, subject sequence end, subject sequence
name.
      </PARA>
    </SECT2>
  </SECT1>

  <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>act</COMMAND> in the &prog; installation directory (see <XREF
LINKEND="INSTALLATION">) like this:
    </PARA>

    <PARA>
      <COMMAND>~/act/act</COMMAND>
    </PARA>

    <PARA>
If all goes well you will be presented with a small window with one menu (the
File menu).  See <XREF LINKEND="LAUNCH-WINDOW"> for a description of this
window.
    </PARA>

    <PARA>
Alternatively you start &prog; with the names of two sequence/EMBL/GENBANk
files and a file containing the comparison data eg:
    </PARA>

    <PARA>
      <COMMAND>
~/act/act subject.embl query.embl blast_output.crunch
      </COMMAND>
    </PARA>

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

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

    <PARA>
      <COMMAND>
cd ~/act
      </COMMAND>
    </PARA>

    <PARA>
      <COMMAND>
java -Dartemis.environment=UNIX Dad
      </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 act.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;.
    </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 two sequence files and a file containing the results of a
comparison.  If the files you select are successfully read a new window will
open, which shows the sequences and the comparison.  See <XREF
LINKEND="MAINWINDOW-CHAPTER"> to find out how to use the main window.  The
comparison file is described in see <XREF LINKEND="COMPARISON-FILE-FORMAT">.
        </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>
  </SECT1>
</CHAPTER>
