menus.sgml

<SECT1 ID="ENTRIESMENU">
  <TITLE>The Entries Menu</TITLE>
  <PARA>
The items in this menu are used to change which entry is the default entry and
which entries are active (see <XREF LINKEND="CONCEPTS-ENTRY">).  At the
bottom of the menu there is a toggle button for each entry which controls
whether the entry is active or not.<![ %artemis-only; [ These toggle buttons
work in a similar way the the buttons on the entry button line (see <XREF
LINKEND="ENTRYBUTTONS">).]]>
  </PARA>
  <PARA>
Here is a description of the other menu items:
  </PARA>

  <SECT2 ID="ENTRIESMENU-SET-NAME-OF-ENTRY">
    <TITLE>Set Name Of Entry</TITLE>
    <PARA>
Set the name of an entry chosen from a sub-menu.  The name of the entry is
used as the name of the file when the entry is saved.
    </PARA>
  </SECT2>

  <SECT2 ID="ENTRIESMENU-SET-DEFAULT-ENTRY">
    <TITLE>Set Default Entry</TITLE>
    <PARA>
Set the default entry by choosing one of the entries from the sub-menu.  (See
<XREF LINKEND="CONCEPTS-DEFAULTENTRY">).
    </PARA>
  </SECT2>

  <SECT2 ID="ENTRIESMENU-REMOVE-AN-ENTRY">
    <TITLE>Remove An Entry</TITLE>
    <PARA>
Remove an entry from &prog; by choosing one of the entries from the sub-menu.
The original file that this entry came from (if any) will not be removed.
    </PARA>
  </SECT2>

  <SECT2 ID="ENTRIESMENU-REMOVE-ACTIVE-ENTRIES">
    <TITLE>Remove Active Entries</TITLE>
    <PARA>
Remove the entries that are currently active.  (See <XREF
LINKEND="CONCEPTS-ACTIVEENTRY">).
    </PARA>
  </SECT2>

  <SECT2 ID="ENTRIESMENU-DEACTIVATE-ALL">
    <TITLE>Deactivate All Entries</TITLE>
    <PARA>
Choosing this menu item will deactivate all entries.  (See <XREF
LINKEND="CONCEPTS-ACTIVEENTRY">.)
    </PARA>
  </SECT2>
</SECT1>

<SECT1 ID="SELECTMENU">
  <TITLE>The Select Menu</TITLE>
  <PARA>
The items in this menu are used to modify the current selection (see <XREF
LINKEND="CONCEPTS-SELECTION">).  &art;<![ %artemis-only; [ A short summary of
the current selection is shown at the top of the main window (see <XREF
LINKEND="MAINWINDOW-BREAKDOWN-SELECTIONSTATUS"> for details).]]>.
  </PARA>

  <SECT2 ID="SELECTMENU-FEATURE-SELECTOR">
    <TITLE>Feature Selector ...</TITLE>
    <PARA>
Open a new Feature Selector window.  This window allows the user to choose
which features to select or view based on feature keys (see <XREF
LINKEND="CONCEPTS-KEY">), qualifier values (see <XREF
LINKEND="CONCEPTS-QUALIFIERS">) and amino acid motifs.
    </PARA>
    <PARA>
The Select button will set the selection to the contain those features that
match the given key, qualifier and amino acid motif combination.
    </PARA>
    <PARA>
The View button will create a new feature list (see <XREF
LINKEND="FEATURELIST">) containing only those features that
match the given key, qualifier and amino acid motif combination.
    </PARA>
    <SCREENSHOT>
      <SCREENINFO>
The Selector window
      </SCREENINFO>
      <MEDIAOBJECT>
        <IMAGEOBJECT>
          <IMAGEDATA FORMAT="gif" FILEREF="selector.gif">
        </IMAGEOBJECT>
        <IMAGEOBJECT>
          <IMAGEDATA FORMAT="eps" FILEREF="selector.eps">
        </IMAGEOBJECT>
      </MEDIAOBJECT>
    </SCREENSHOT>
  </SECT2>

  <SECT2 ID="SELECTMENU-ALL">
    <TITLE>All</TITLE>
    <PARA>
Reset the selection so that nothing is selected then select all the features
in the active entries.  [shortcut key: A]
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-ALLBASES">
    <TITLE>All Bases</TITLE>
    <PARA>
Reset the selection so that nothing is selected then select all the bases in
the sequence.
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-ALLFEATURES-NONMATCHING-REGIONS">
    <TITLE>Select All Features in Non-matching Regions</TITLE>
    <PARA>
Select all features that have no corresponding match in ACT. This is used to
higlight regions that are different between sets of sequence. It will only take 
into account matches that have not been filtered out using the score, identity 
or length cut-off.
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-NONE">
    <TITLE>None</TITLE>
    <PARA>
Clear the selection so that nothing is selected.  [shortcut key: N]
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-BY-KEY">
    <TITLE>By Key</TITLE>
    <PARA>
Ask the user for a feature key, reset the selection so that nothing is
selected, then select all the features with the key given by the user.
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-CDS-FEATURES">
    <TITLE>CDS Features</TITLE>
    <PARA>
Reset the selection so that nothing is selected, then select all the CDS
features that do not have a /pseudo qualifier.
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-SAME-KEY">
    <TITLE>Same Key</TITLE>
    <PARA>
Select all the features that have the same key as any of the currently
selected features.
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-ORF">
    <TITLE>Open Reading Frame</TITLE>
    <PARA>
Extend the current selection of bases to cover complete open reading frames.
Selecting a single base or codon and then choosing this menu item has a
similar effect to double clicking the middle button on a base or residue (see
<XREF LINKEND="VIEWS-SELECTION"> for details).
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-OVERLAPPING-SELECTION">
    <TITLE>Features Overlapping Selection</TITLE>
    <PARA>
Select those (and only those) features that overlap the currently selected
range of bases or any of the currently selected features.  The current
selection will be discarded.
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-BASE-RANGE">
    <TITLE>Base Range ...</TITLE>
    <PARA>
Ask the user for a range of bases, then select those bases.  The range should
look something like this: <LITERAL>100-200</LITERAL>,
<LITERAL>complement(100..200)</LITERAL>, <LITERAL>100.200</LITERAL> or
<LITERAL>100..200</LITERAL>.  If the first number is larger than the
second the bases will be selected on the forward strand, otherwise they will
be selected on the reverse strand (unless there is a
<LITERAL>complement</LITERAL> around the range, in which case the sense is
reversed).
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-FEATURE-AA-RANGE">
    <TITLE>Feature AA Range ...</TITLE>
    <PARA>
Ask the user for a range of amino acids in the selected feature and select
those bases.  The range should look something like this:
<LITERAL>100-200</LITERAL>, or <LITERAL>100..200</LITERAL>.
    </PARA>
  </SECT2>

  <SECT2 ID="SELECTMENU-TOGGLE-SELECTION">
    <TITLE>Toggle Selection</TITLE>
    <PARA>
Invert the selection - after choosing this menu item the selection will
contain only those features that were not in the selection beforehand.