file_menu.sgml

<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/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 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 is 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>

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