<SECT1 ID="FILEMENU">
  <TITLE>The File Menu</TITLE>
  <PARA>
Most of the items in this menu are used to read and write entries and parts of
entries, the exceptions are Clone and Close.
  </PARA>

  <SECT2 ID="FILEMENU-SHOW-FILEMANAGER">
    <TITLE>Show File Manager ...</TITLE>
    <PARA>
This will open the file manager, or if it is already open will bring it
to the foreground. Entries can be dragged from the file manager into
the artemis main window and dropped. When dropped the entry is then read 
in and displayed.
    </PARA>
  </SECT2>

  <SECT2 ID="FILEMENU-READ-AN-ENTRY">
    <TITLE>Read An Entry ...</TITLE>
    <PARA>
Read an entry (see <XREF LINKEND="CONCEPTS-ENTRY">), but keep it separate from
the others.  A new button will be created on the entry button line for the new
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 file formats:
    </PARA>
    <ITEMIZEDLIST>
      <LISTITEM>
        <PARA>
          <ULINK URL="http://www.ebi.ac.uk/embl/Documentation/">EMBL or GenBank feature tables</ULINK>
        </PARA>
      </LISTITEM>
      <LISTITEM>
        <PARA>
          <ULINK URL="http://www.sequenceontology.org/gff3.shtml">GFF Version 3 files</ULINK>
        </PARA>
      </LISTITEM>
      <LISTITEM>
        <PARA>
          FASTA files 
        </PARA>
      </LISTITEM>
      <LISTITEM>
        <PARA>
	  Indexed FASTA files can be read in. The files are indexed
using <ULINK URL="http://samtools.sourceforge.net/">SAMtools</ULINK>:
        </PARA>
       <SYNOPSIS>
samtools faidx ref.fasta
        </SYNOPSIS>
      </LISTITEM>
      <LISTITEM>
        <PARA>
The indexed FASTA can be used with an indexed GFF to overlay annotation on the sequence. 
To index the GFF first sort and bgzip the file and then use tabix with "-p gff" option (see the 
<ULINK URL="http://samtools.sourceforge.net/tabix.shtml">tabix manual</ULINK>):
        </PARA>
       <SYNOPSIS>
(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz; 
tabix -p gff sorted.gff.gz
        </SYNOPSIS>
        <PARA>
A drop down menu of the contigs or chromosomes sequences is provided in the Entry toolbar
to select the sequence. Using indexed FASTA and indexed GFF files improves the memory management 
and enables large genomes to be viewed. Note that as it is indexed the sequence and annotation are 
read-only and cannot be edited. When there are many contigs to select from it can be easier
to display the one of interest by typing the name into the drop down list.
        </PARA>
      </LISTITEM>
      <LISTITEM>
        <PARA>
The output of <ULINK
URL="http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/"><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 version
2.2.2</ULINK> 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-READ-ENTRY-INTO">
    <TITLE>Read Entry Into</TITLE>
    <PARA>
Read the features from an entry (see <XREF LINKEND="CONCEPTS-ENTRY">)
chosen by the user and then insert them into the entry selected by
the user.
    </PARA>
  </SECT2>

  &nextgen;

  <SECT2 ID="FILEMENU-SAVE-DEFAULT-ENTRY">
    <TITLE>Save Default Entry</TITLE>
    <PARA>
Save the default 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.
[shortcut key: S]
    </PARA>
  </SECT2>

  <SECT2 ID="FILEMENU-SAVE-AN-ENTRY">
    <TITLE>Save An Entry</TITLE>
    <PARA>
This item will do the same as "Save Default Entry" for the chosen entry.
    </PARA>
  </SECT2>

  <SECT2 ID="FILEMENU-SAVE-ENTRY-AS-MENU">
    <TITLE>Save An Entry As</TITLE>
    <PARA>
This sub-menu contains the less frequently used save functions.
    </PARA>

    <SECT3 ID="FILEMENU-SAVE-ENTRY-AS">
      <TITLE>New File</TITLE>
      <PARA>
Ask for the name of file to save the given entry to.  The name of entry (as
displayed in the entry button line) will change to the new name.
      </PARA>
    </SECT3>

    <SECT3 ID="FILEMENU-SAVE-ENTRY-AS-EMBL">
      <TITLE>EMBL Format</TITLE>
      <PARA>
This does the same as "Save An Entry As -> New File ...", but will write the
features and sequence of the entry in EMBL format.  Note that currently the
header of a GENBANK entry can't be converted to the equivalent EMBL header (it
will be discarded instead).
      </PARA>
    </SECT3>

    <SECT3 ID="FILEMENU-SAVE-ENTRY-AS-GENBANK">
      <TITLE>GENBANK Format</TITLE>
      <PARA>
This does the same as "Save An Entry As -> New File ...", but will write the
features and sequence of the entry in GENBANK format.  Note that currently the
header of a EMBL entry can't be converted to the equivalent GENBANK header (it
will be discarded instead).
      </PARA>
    </SECT3>

    <SECT3 ID="FILEMENU-SAVE-ENTRY-AS-SEQUIN">
      <TITLE>Sequin Table Format</TITLE>
      <PARA>
This saves a file in <ULINK
URL="http://www.ncbi.nlm.nih.gov/Sequin/table.html" TYPE="external">Sequin table format
</ULINK> which is used by <ULINK
URL="http://www.ncbi.nlm.nih.gov/Sequin/" TYPE="external">Sequin
</ULINK>.
     </PARA>
    </SECT3>


    <SECT3 ID="FILEMENU-SAVE-ENTRY-AS-GFF">
      <TITLE>GFF Format</TITLE>
      <PARA>
Writes the features in GFF format and sequence of the entry in FASTA format to
a file selected by the user.  Note that if you use this function on an EMBL or
GENBANK entry the header will discarded.
      </PARA>
    </SECT3>

    <SECT3 ID="FILEMENU-SAVE-EMBL-SUBMISSION">
      <TITLE>EMBL Submission Format</TITLE>
      <PARA>
This does the same as "Save An Entry As -> EMBL Format ...", but
will write an entry/tab file that contains only valid EMBL qualifiers (see
<XREF LINKEND="OPTIONS-EXTRAQUALIFIERS">) and valid EMBL keys (see <XREF
LINKEND="OPTIONS-EXTRAKEYS">).  It will also check that the start and stop
codons of each CDS are sensible, that no two features have the same key and
location and that all required EMBL qualifiers are present.
      </PARA>
    </SECT3>
  </SECT2>

  <SECT2 ID="FILEMENU-SAVE-ALL-ENTRIES">
    <TITLE>Save All Entries</TITLE>
    <PARA>
This acts like "Save Default Entry", but save all the entries.
    </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>


  <SECT2 ID="FILEMENU-CLONE-WINDOW">
    <TITLE>Clone This Window</TITLE>
    <PARA>
Make a new main window with the same contents as the current window.  All
changes in the old window will be reflected in the new window, and vice
versa.  The exception to this rule is the selection (see <XREF
LINKEND="CONCEPTS-SELECTION">), which is not shared between the
old and new window.
    </PARA>
  </SECT2>

  <SECT2 ID="FILEMENU-IMAGE-WINDOW">
    <TITLE>Save As Image Files (png/jpeg)</TITLE>
    <PARA>
Print out the contents of the current window. All or some of the
window panels can be select  for printing to an image file. 
    </PARA>
  </SECT2>

   <SECT2 ID="FILEMENU-PRINT-WINDOW">
     <TITLE>Print</TITLE>
     <PARA>
This option can be used to print the contents of the current window
to a file as PostScript or to a printer.
     </PARA>
    </SECT2>


  <SECT2 ID="FILEMENU-PRINT-PREVIEW-WINDOW">
    <TITLE>Print Preview</TITLE>
    <PARA>
This opens the print image in a preview window. This shows
what the image will look like when printed to a file.
    </PARA>
  </SECT2>


  <SECT2 ID="FILEMENU-PREFERENCES">
    <TITLE>Preferences</TITLE>
    <PARA>
This enables the user to define their own shortcut preferences.
    </PARA>
  </SECT2>



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