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<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.sanger.ac.uk/Software/formats/GFF/">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 is 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="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="http://www.sanger.ac.uk/Software/Artemis/stable/manual/">the
&art; manual</ULINK> for more about &art;.
</PARA>
</SECT2>
<SECT2 ID="FILEMENU-CLOSE">
<TITLE>Close</TITLE>
<PARA>
Close this window.
</PARA>
</SECT2>
</SECT1>