<SECT1 ID="FILEMENU">
  <TITLE>The File Menu</TITLE>
  <PARA>
  </PARA>

  <SECT2 ID="FILEMENU-READ-AN-ENTRY">
    <TITLE>Read An Entry ...</TITLE>
    <PARA>
Read an entry for this sequence, but keep it separate from the others.  See
<XREF LINKEND="CONCEPTS-ENTRY"> to see what we mean when we say "entry".  The
new entry will be marked as active (see <XREF LINKEND="CONCEPTS-ACTIVEENTRY">)
and will be the new default entry (see <XREF
LINKEND="CONCEPTS-DEFAULTENTRY">).
    </PARA>
    <PARA>
This function only reads the feature section of the input file - the sequence
(if any) is ignored.
    </PARA>
    <PARA>
&prog; can read these feature files formats:
    </PARA>
    <ITEMIZEDLIST>
      <LISTITEM>
        <PARA>
          <ULINK URL="http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html">EMBL or GenBank feature tables</ULINK>
        </PARA>
      </LISTITEM>
      <LISTITEM>
        <PARA>
          <ULINK URL="http://www.sequenceontology.org/resources/gff3.html">GFF files</ULINK>
        </PARA>
      </LISTITEM>
      <LISTITEM>
        <PARA>
The output of <ULINK
URL="http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html"><COMMAND>MSPcrunch</COMMAND></ULINK>.
<COMMAND>MSPcrunch</COMMAND> must be run with the <COMMAND>-x</COMMAND> or
<COMMAND>-d</COMMAND> flags.
        </PARA>
      </LISTITEM>
      <LISTITEM>
        <PARA>
The output of <ULINK URL="http://www.ncbi.nlm.nih.gov/BLAST/">blastall</ULINK>
version 2.2.2 or better.  <COMMAND>blastall</COMMAND> must be run with the
<COMMAND>-m 8</COMMAND> flag which generates one line of information per HSP.
Note that currently &prog; displays each Blast HSP as a separate feature
rather than displaying each BLAST hit as a feature.
        </PARA>
      </LISTITEM>
    </ITEMIZEDLIST>
  </SECT2>

  <SECT2 ID="FILEMENU-SAVE-ENTRY">
    <TITLE>Save Entry</TITLE>
    <PARA>
Save the entry to the file it came from, unless the entry has been
given a new name, in which case the entry is saved to a file with that name.
If the entry has no name, &prog; will prompt the user for a new name.
    </PARA>
  </SECT2>

  <SECT2 ID="FILEMENU-SAVE-ALL">
    <TITLE>Save All</TITLE>
    <PARA>
Save all the entries that have been loaded on top of this sequence.
    </PARA>
  </SECT2>


  <SECT2 ID="WRITEMENU">
    <TITLE>Write</TITLE>
    <PARA>

    </PARA>

    <SECT3 ID="WRITEMENU-AMINO-ACIDS-OF-SELECTED-FEATURES">
      <TITLE>Amino Acids Of Selected Features</TITLE>
      <PARA>
Prompt for a file name and then write the translation of the bases of the
selected features to that file.  The file is written in FASTA format.
      </PARA>
    </SECT3>

    <SECT3 ID="WRITEMENU-PIR-DATABASE-OF-SELECTED-FEATURES">
      <TITLE>PIR Database Of Selected Features</TITLE>
      <PARA>
Prompt for a file name and then write the translation of the bases of the
selected features to that file.  The file is written in PIR format (similar to
FASTA, but with a * as the last line of each record).
      </PARA>
    </SECT3>

    <SECT3 ID="WRITEMENU-BASES-OF-SELECTION">
      <TITLE>Bases Of Selection</TITLE>
      <PARA>
Prompt for a file name and then write the bases of the selection to that
file in the selected format.  If the selection consists of features (rather
than a base range) then the bases of each feature
will be written to the file as a separate record.  If the selection is a range
of bases, then those bases will be written.
      </PARA>
    </SECT3>

    <SECT3 ID="WRITEMENU-UPSTREAM-BASES-OF-SELECTION">
      <TITLE>Upstream Bases Of Selection</TITLE>
      <PARA>
Prompt for a number and a file name, then write that many bases upstream of
each selected feature to the file in the selected format.  For example if the
selected feature has a
location of "<LITERAL>100..200</LITERAL>", then asking for 50 upstream will
write the bases in the range 50 to 99.  Writing upstream bases of a feature on
the complementary strand will work in the expected way.
      </PARA>
    </SECT3>

    <SECT3 ID="WRITEMENU-DOWNSTREAM-BASES-OF-SELECTION">
      <TITLE>Downstream Bases Of Selection</TITLE>
      <PARA>
Prompt for a number and a file name, then write that many bases downstream of
each selected feature to the file in the selected format.
      </PARA>
    </SECT3>

    <SECT3 ID="WRITEMENU-ALL-BASES">
      <TITLE>All Bases</TITLE>
      <PARA>
Prompt for a file name, then write the complete sequence to that file in the
selected format.
      </PARA>
    </SECT3>

    <SECT3 ID="WRITEMENU-CODON-USAGE">
      <TITLE>Codon Usage of Selected Features</TITLE>
      <PARA>
Prompt for a file name, then write a codon usage table for the selected
features.  The file in written in the same format as the data at <ULINK
URL="http://www.kazusa.or.jp/codon/" TYPE="external">Kazusa codon usage
database site</ULINK>.  In the output file each codon is followed by it's
occurrence count (per thousand) and it's percentage occurrence.  (See <XREF
LINKEND="GRAPHMENU-USAGE-PLOTS"> to find out how to plot a usage graph).
      </PARA>
    </SECT3>
  </SECT2>

  &nextgen;

  <SECT2 ID="FILEMENU-EDIT-IN-ARTEMIS">
    <TITLE>Edit In Artemis ...</TITLE>
    <PARA>
Open an &art; edit window for this sequence and features.  All changes
made in the &art; window will be immediately visible in the &prog; window and
vice versa.
    </PARA>
    <PARA>
See <ULINK URL="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/artemis.pdf">the
&art; manual</ULINK> for more about &art;.
    </PARA>
  </SECT2>

  <SECT2 ID="FILEMENU-CLOSE">
    <TITLE>Close</TITLE>
    <PARA>
Close this window.
    </PARA>
  </SECT2>
</SECT1>
