<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-DEFAULT-ENTRY-NAME">
    <TITLE>Set Name Of Default 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-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">).
  </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 and qualifier values.
    </PARA>
  </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.
    </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-NONE">
    <TITLE>None</TITLE>
    <PARA>
Reset the selection so that nothing is selected.
    </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-FEATURES-IN-RANGE">
    <TITLE>Features in Range</TITLE>
    <PARA>
Select those (and only those) features that overlap the currently selected
range of bases.
    </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.
    </PARA>
  </SECT2>
</SECT1>

<SECT1 ID="VIEWMENU">
  <TITLE>The View Menu</TITLE>
  <PARA>
    
  </PARA>

  <SECT2 ID="VIEWMENU-VIEW-SELECTED-FEATURES">
    <TITLE>View Selected Features</TITLE>
    <PARA>
Open a view window for each selected feature showing it's feature table entry.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-VIEW-SELECTION">
    <TITLE>View Selection</TITLE>
    <PARA>
Open a view window that will show the current selection.  The window is
updated as the selection changes, so it can be left open.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-SEARCH-RESULTS">
    <TITLE>Search Results</TITLE>
    <PARA>
On this sub-menu allows the user to view the results of feature searches that
are launched from the run menu in &art;<![ %artemis-only; [ (see <XREF
LINKEND="RUNMENU">)]]>.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-SHOW-CDS-GENES-PRODUCTS">
    <TITLE>Show CDS Genes And Products</TITLE>
    <PARA>
Pop up a list of the CDS showing the gene names (from the /gene qualifier) and
the product (from the /product qualifier).
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-FEATURE-FILTERS">
    <TITLE>Feature Filters</TITLE>
    <PARA>
Each of the items in this sub-menu each allow the user to view a subset of the
active features.  An example of a subset is all those feature with
<LITERAL>misc_feature</LITERAL> as a key.  The features are displayed in a new
window that contains a feature list (see <XREF LINKEND="FEATURELIST">).
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-SHOW-OVERVIEW">
    <TITLE>Show Overview</TITLE>
    <PARA>
Open a new window the will show a summary of the active entries and some
statistics about the sequence (such as the GC content).
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-SHOW-FORWARD-OVERVIEW">
    <TITLE>Show Forward Strand Overview</TITLE>
    <PARA>
Open a new window the will show a summary of the features and bases of the
forward strand.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-SHOW-REVERSE-OVERVIEW">
    <TITLE>Show Reverse Strand Overview</TITLE>
    <PARA>
Open a new window the will show a summary of the features and bases of the
reverse strand.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-VIEW-FEATURE-BASES">
    <TITLE>View Feature Bases</TITLE>
    <PARA>
Create a view window for each selected feature, which shows bases of the
feature.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-VIEW-FEATURE-BASES-FASTA">
    <TITLE>View Feature Bases As FASTA</TITLE>
    <PARA>
Create a view window for each selected feature, which shows bases of the
feature in FASTA format.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-VIEW-FEATURE-AMINO-ACIDS">
    <TITLE>View Feature Amino Acids</TITLE>
    <PARA>
Create a view window for each selected feature, which shows amino acids of the
feature.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-VIEW-FEATURE-AMINO-ACIDS-FASTA">
    <TITLE>View Feature Amino Acids As FASTA</TITLE>
    <PARA>
Create a view window for each selected feature, which shows amino acids of the
feature in FASTA format.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-SHOW-FEATURE-STATISTICS">
    <TITLE>Show Feature Statistics</TITLE>
    <PARA>
Show some statistics about each selected feature.  On the left on the feature
information window is the amino acid composition of the feature.  On the right
is the codon composition of the feature.
    </PARA>
  </SECT2>

  <SECT2 ID="VIEWMENU-SHOW-FEATURE-PLOTS">
    <TITLE>Show Feature Plots</TITLE>
    <PARA>
Open a window for each selected feature that shows a plot of the
Kyte-Doolittle Hydrophobicity [short name: <LITERAL>hydrophobicity</LITERAL>],
the Hopp-Woods Hydrophilicity [short name: <LITERAL>hydrophilicity</LITERAL>],
and an approximation of the GCG Coiled Coils algorithm [short name:
<LITERAL>coiled_coil</LITERAL>].  The graphs and plots are described in <XREF
LINKEND="GRAPHS">. (For more detail about the coiled coils algorithm see
"Predicting Coiled Coils from Protein Sequences", Science Vol. 252 page 1162.)
    </PARA>
  </SECT2>
</SECT1>

<SECT1 ID="GOTOMENU">
  <TITLE>The Goto Menu</TITLE>
  <PARA>
The items in this menu allow the user to navigate around the sequence and
features.
  </PARA>

  <SECT2 ID="GOTOMENU-NAVIGATOR">
    <TITLE>Navigator ...</TITLE>
    <PARA>
Open a new navigation window.  This window allows the user to perform five
different tasks:
      <ORDEREDLIST>
        <LISTITEM>
          <PARA>
<EMPHASIS>Scroll all the views so that a particular base is in the centre of
the display</EMPHASIS>.  To use this function, type a base position into the
box to the right of the "Goto Base:" label then press the goto button at the
bottom of the window.  The requested base will be selected and then the
overview display and the DNA display will scroll so that the base is as near
as possible to the middle of the main window.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
<EMPHASIS>Find the next feature that has a qualifier containing a particular
string</EMPHASIS>.  To use this function, type a string into the box to the
right of the "Goto Feature With This Text:" label and then press the goto
button.  &prog; will select the first feature with the given string in any of
it's qualifier values and will then scroll the display so that feature is in
view.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
<EMPHASIS>Find the next feature that has a particular key.</EMPHASIS> To use
this function, type a key into the box to the right of the "Goto Feature With
This Key:" label and then press the goto button.  &prog; will select the first
feature with the given key and will then scroll the display so that feature is
in view.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
<EMPHASIS>Find the next occurrence of a particular base pattern in the
sequence</EMPHASIS>.  To use this function, type a base pattern into the box
to the right of the "Find Base Pattern:" label and then press the goto button.
&prog; will select the first contiguous group of bases on either strand that
match the given base pattern and will then scroll the display so that those
bases are in view.
          </PARA>
          <PARA>
Any IUB base code can be used in the pattern, so for example searching for
<LITERAL>aanntt</LITERAL> will match any six bases that start with "aa" and
ends with "tt".  See <XREF LINKEND="UIB-BASE-CODES"> for a list of the
available base codes.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
<EMPHASIS>Find the next occurrence of a particular residue pattern in the
sequence</EMPHASIS>.  To use this function, type a amino acid pattern into the
box to the right of the "Goto Amino Acid String:" label and then press the
goto button. &prog; will select the first contiguous group of bases on either
strand that translate to the given amino acids and will then scroll the
display so that those bases are in view.
          </PARA>
        </LISTITEM>
      </ORDEREDLIST>
    </PARA>
    <PARA>
Note that for all the functions above except the first ("Goto Bases"), if the
"Start search at beginning" option is set or if there is nothing selected the
search will start at the beginning of the sequence.  Otherwise the search will
start at the selected base or feature.  This means that the user can step
through the matching bases or features by pressing the goto button repeatedly.
    </PARA>
  </SECT2>

  <SECT2 ID="GOTOMENU-GOTO-SELECTION-START">
    <TITLE>Start of Selection</TITLE>
    <PARA>
Scroll all the views so that the first base of the selection is as close to
the centre as possible.  If the a range of bases is selected the views will
move to the first base of the range.  If one or more features are selected,
then the first base of the first selected feature will be centred.  Otherwise,
if one or more segments (see <XREF LINKEND="CONCEPTS-SEGMENT">) is selected then the first base of the first selected segment will be centred.
    </PARA>
  </SECT2>

  <SECT2 ID="GOTOMENU-GOTO-SELECTION-END">
    <TITLE>End of Selection</TITLE>
    <PARA>
This does the same as "Goto Start of Selection", but uses the last base of the
selected range or the last base of the last selected feature or segment.
    </PARA>
  </SECT2>

  <SECT2 ID="GOTOMENU-GOTO-FEATURE-START">
    <TITLE>Feature Start</TITLE>
    <PARA>
Scroll the views to the start of the first selected feature.
    </PARA>
  </SECT2>

  <SECT2 ID="GOTOMENU-GOTO-FEATURE-END">
    <TITLE>Feature End</TITLE>
    <PARA>
Scroll the views to the end of the first selected feature.
    </PARA>
  </SECT2>

  <SECT2 ID="GOTOMENU-GOTO-START-OF-SEQ">
    <TITLE>Start of Sequence</TITLE>
    <PARA>
Scroll the views so that the start of the sequence is visible.
    </PARA>
  </SECT2>

  <SECT2 ID="GOTOMENU-GOTO-END-OF-SEQ">
    <TITLE>End of Sequence</TITLE>
    <PARA>
Scroll the views so that the end of the sequence is visible.
    </PARA>
  </SECT2>

  <SECT2 ID="GOTOMENU-GOTO-FEATURE-BASE-POSITION">
    <TITLE>Feature Base Position ...</TITLE>
    <PARA>
Ask the user for a base position within the first selected feature, then
scroll the views so that that base position is centred.
    </PARA>
  </SECT2>

  <SECT2 ID="GOTOMENU-GOTO-FEATURE-AMINO-ACID">
    <TITLE>Feature Amino Acid ...</TITLE>
    <PARA>
Ask the user for an amino acid position within the first selected feature,
then scroll the views so that that position is centred.
    </PARA>
  </SECT2>
</SECT1>

<SECT1 ID="EDITMENU">
  <TITLE>The Edit Menu</TITLE>
  <PARA>
This menu contains most of the functions that change the entries.  Note that
the changes will not be saved back to the original files until one of the save
functions in the File menu is used<![ %artemis-only; [
(see <XREF LINKEND="FILEMENU-SAVE-AN-ENTRY">)]]>.
  </PARA>

  <SECT2 ID="EDITMENU-EDIT-SELECTED-FEATURES">
    <TITLE>Edit Selected Features</TITLE>
    <PARA>
Open an edit window for each selected feature.  From the top down the edit
window has these parts
      <ORDEREDLIST>
        <LISTITEM>
          <PARA>
At the top left is a selector for choosing the key of the feature.  This
only contains a subset of the legal keys.  The subset can be changed by
changing the <LITERAL>common_keys</LITERAL> option in the options file (see
<XREF LINKEND="OPTIONS-COMMONKEYS">).
          </PARA>
          <PARA>
At the top right of the edit window is a selector for adding a qualifier.  For
example choosing <LITERAL>note</LITERAL> from the menu will insert
<LITERAL>/note=""</LITERAL> into the qualifier edit area.
          </PARA>
        </LISTITEM>

        <LISTITEM>
          <PARA>
Just below the key and qualifier selector is the location entry field.  &prog;
understands most of the EMBL location syntax, including joins, complements,
ranges with non-exact ends (eg. <LITERAL>(100.200)..&gt;350</LITERAL>) and
references to other entries
(eg. <LITERAL>join(100..200,SPB23A1:100..200)</LITERAL>).
          </PARA>
        </LISTITEM>

        <LISTITEM>
          <PARA>
Next is a row of buttons that modify the location field:
          </PARA>
          <ITEMIZEDLIST>
            <LISTITEM>
              <PARA>
The <LITERAL>Complement</LITERAL> button will complement the contents of the
location field.
              </PARA>
            </LISTITEM>
            <LISTITEM>
              <PARA>
The <LITERAL>Grab</LITERAL> button will grab the currently selected range into
the location field.
              </PARA>
            </LISTITEM>
          </ITEMIZEDLIST>
        </LISTITEM>

        <LISTITEM>
          <PARA>
The centre of the edit window contains the qualifier entry section.  The
qualifiers should be entered the in same way the appear in the feature table
part of an EMBL entry, but without the leading <LITERAL>FT</LITERAL> and
spaces.
          </PARA>
        </LISTITEM>

        <LISTITEM>
          <PARA>
The bottom of the window contains three buttons.  The <LITERAL>OK</LITERAL>
button will update the feature with the changes that have been made by the
user and will then close the edit window.  The <LITERAL>Cancel</LITERAL>
button will discard the changes and then close the window.  The
<LITERAL>Apply</LITERAL> will make the changes, but will not close the
window.  Before any changes are made the location and the qualifiers are
checked for formatting errors.  Any errors will brought to the attention of
the user through the use of annoying pop-up boxes.  No changes will be
performed until there are no errors.
          </PARA>
        </LISTITEM>
      </ORDEREDLIST>
    </PARA>
  </SECT2>

<!-- 
  <SECT2 ID="EDITMENU-RAW-EDIT-SELECTED-FEATURES">
    <TITLE>Raw Edit Selected Features</TITLE>
    <PARA>
Open an "raw" edit window for each selected feature.
    </PARA>
  </SECT2>
-->

  <SECT2 ID="EDITMENU-SUBSEQUENCE">
    <TITLE>Edit Subsequence (and Features)</TITLE>
    <PARA>
Make a copy (in a new edit window) of the selected bases and the features in
that range.  Any features that overlap the end of the range will be truncated.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-EDIT-HEADER">
    <TITLE>Edit Header Of Default Entry</TITLE>
    <PARA>
Open a edit window containing the header of the default entry.  Changes made
in the edit window will be applied immediately to the entry provided there are
no errors in the formatting of the header.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-DUPLICATE-SELECTED-FEATURES">
    <TITLE>Duplicate Selected Features</TITLE>
    <PARA>
Make a copy of each selected feature.  Each new feature will be added just
after the original in the same entry as the original. 
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-MERGE-SELECTED-FEATURES">
    <TITLE>Merge Selected Features</TITLE>
    <PARA>
Merge the selected features into one Feature.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-DELETE-SELECTED-FEATURES">
    <TITLE>Delete Selected Features</TITLE>
    <PARA>
Remove each selected feature from it's entry.
    </PARA>
  </SECT2>

  <SECT2 ID="DELETE-SELECTED-EXONS">
    <TITLE>Delete Selected Exons</TITLE>
    <PARA>
Delete the selected exons.  The last exon of a feature can't be deleted
(delete the whole feature instead).
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-MOVE-SELECTED-FEATURES">
    <TITLE>Move Selected Features To</TITLE>
    <PARA>
Move the selected features to another entry.  Choose the destination entry
from the sub-menu.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-COPY-SELECTED-FEATURES">
    <TITLE>Copy Selected Features To</TITLE>
    <PARA>
Copy the selected features to another entry.  Choose the destination entry
from the sub-menu.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-MET">
    <TITLE>Trim Selected Features To Met</TITLE>
    <PARA>
For each of the selected features this function will attempt to move the start
position to the first ATG in the feature if the feature does not already start
on a ATG codon.  If there is no ATG in the first thirty percent of the bases
of the feature the start position will be unchanged.  The search will stop at
the end of the first segment of a multi-segment feature.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-ANY">
    <TITLE>Trim Selected Features To Any</TITLE>
    <PARA>
This works in the same way as "Trim Selected Features To Met", but will
attempt to move the start position of the feature to the first TTG, ATG or GTG
in the feature if it does not already start on one of those codons.  As above
it will only search the first thirty percent of the feature bases and will
only search the first segment of a multi-segment feature.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-NEXT-MET">
    <TITLE>Trim Selected Features To Next Met</TITLE>
    <PARA>
For each of the selected features this function will attempt to move the start
position to the next ATG in the feature (the first codon is skipped).  If
there is no ATG in the first thirty percent of the bases of the feature the
start position will be unchanged.  The search will stop at the end of the
first segment of a multi-segment feature.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-NEXT-ANY">
    <TITLE>Trim Selected Features To Next Any</TITLE>
    <PARA>
This works in the same way as "Trim Selected Features To Next Met", but will
attempt to move the start position of the feature to the next TTG, ATG or GTG
in the feature (the first codon is skipped).  As above it will only search the
first thirty percent of the feature bases and will only search the first
segment of a multi-segment feature. 
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-AUTO-GENE-NAMES">
    <TITLE>Automatically Create Gene Names</TITLE>
    <PARA>
Ask for a gene name prefix (using a text requester), and then give a unique
gene name to each CDS feature in the active entries using that prefix.  For
example if there are four CDS features with locations:
"<LITERAL>1..500</LITERAL>", "<LITERAL>complement(100..600)</LITERAL>",
"<LITERAL>200..700</LITERAL>" and "<LITERAL>complement(300..800)</LITERAL>",
entering <LITERAL>SPBC16A3</LITERAL> will give the four features these names:
<LITERAL>SPBC16A3.01</LITERAL>, <LITERAL>SPBC16A3.02c</LITERAL>,
<LITERAL>SPBC16A3.03</LITERAL> and <LITERAL>SPBC16A3.04c</LITERAL>.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-FIX-STOP-CODONS">
    <TITLE>Fix Stop Codons</TITLE>
    <PARA>
Check and fix the stop codons to all the selected features.  For each feature
if the last codon is a stop codon, then all is well, nothing further is done
about the feature.  If the last codon is not a stop codon, but the very next
codon is a stop codon, then the end of the feature is moved three base
forward.  If both the last codon and the very next codon after the feature are
not stop codons, the feature is selected, an error message is displayed and
processing stops immediately.
    </PARA>
  </SECT2>


  <SECT2 ID="EDITMENU-REVERSE-AND-COMPLEMENT">
    <TITLE>Reverse And Complement</TITLE>
    <PARA>
Reverse and complement the sequence and all the features in all the entries
(active and inactive).
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-DELETE-SELECTED-BASES">
    <TITLE>Delete Selected Bases</TITLE>
    <PARA>
Deletes the selected range of bases (if any) from both strands.  The deletion
will not proceed if the selected range overlaps any features.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-ADD-BASES-AT-SELECTION">
    <TITLE>Add Bases At Selection</TITLE>
    <PARA>
Prompt the user for some bases to insert just before the selected bases.  The
deletion will not proceed if there is no selected range, but bases can be
inserted anywhere in the sequence, including inside a feature.  The same
bases, reversed and complemented, will be inserted at the corresponding place
on the opposite strand.
    </PARA>
  </SECT2>
</SECT1>

<SECT1 ID="CREATEMENU">
  <TITLE>The Create Menu</TITLE>
  <PARA>
        
  </PARA>

  <SECT2 ID="CREATEMENU-NEW-FEATURE">
    <TITLE>New Feature</TITLE>
    <PARA>
Create a new feature in the default entry with a key of "misc_feature", a
location of "1" and no qualifiers.
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-CREATE-FEATURE-FROM-BASE-RANGE">
    <TITLE>Create Feature From Base Range</TITLE>
    <PARA>
Create a new feature in the default entry with a key of "misc_feature", no
qualifiers and a location that exactly matches the selected range of bases.
If no bases are selected an error will be reported.
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-NEW-ENTRY">
    <TITLE>New Entry</TITLE>
    <PARA>
Create a new entry with no name and no features.  The new entry will become
the default entry (see <XREF LINKEND="CONCEPTS-DEFAULTENTRY">).
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-MARK-ORF">
    <TITLE>Mark Open Reading Frames ...</TITLE>
    <PARA>
Create a feature for each "large" open reading frame in the sequence.  The
default minimum size of a "large" open reading frame can be changed by
changing the <LITERAL>minimum_orf_size</LITERAL> option (see <XREF
LINKEND="OPTIONS-MIN-ORF-SIZE">).
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-MARK-EMPTY-ORFS">
    <TITLE>Mark Empty ORFs ...</TITLE>
    <PARA>
Create a feature for each open reading frame that doesn't already contain a
feature.
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-MARK-ORF-IN-RANGE">
    <TITLE>Mark Open Reading Frames In Range ...</TITLE>
    <PARA>
Create a feature for each "large" open reading frame in a range of bases.  A
range must be selected before using this command.
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-MARK-FROM-PATTERN">
    <TITLE>Mark From Pattern ...</TITLE>
    <PARA>
Open a text requester to ask the user for a base pattern, then create a
feature for each group of bases that matches that pattern.  A new entry will
be created to hold the features with the name "matches: &lt;pattern&gt;",
where &lt;pattern&gt; is the pattern that was entered be the user.  Any IUB
base code can be used in the pattern, so for example, aanntt will match any
six bases that start with "aa" and ends with "tt".
    </PARA>
    <PARA>
      <TABLE COLSEP="1" FRAME="all" ROWSEP="1" ID="UIB-BASE-CODES">
        <TITLE>IUB Base Codes</TITLE>
        <TGROUP COLS="3" CHAROFF="50">
          <COLSPEC COLNUM="1" ALIGN="left">
          <COLSPEC COLNUM="2" ALIGN="left">
          <COLSPEC COLNUM="3" ALIGN="left">
          <TBODY>
          <ROW>
            <ENTRY>R = A or G</ENTRY>
            <ENTRY>S = G or C</ENTRY>
            <ENTRY>B = C, G or T</ENTRY>
          </ROW>
          <ROW>
            <ENTRY>Y = C or T</ENTRY>
            <ENTRY>W = A or T</ENTRY>
            <ENTRY>D = A, G or T</ENTRY>
          </ROW>
          <ROW>
            <ENTRY>K = G or T</ENTRY>
            <ENTRY>N = A, C, G or T</ENTRY>
            <ENTRY>H = A, C or T</ENTRY>
          </ROW>
          <ROW>
            <ENTRY>M = A or C</ENTRY>
            <ENTRY></ENTRY>
            <ENTRY>V = A, C or G</ENTRY>
          </ROW>
          </TBODY>
        </TGROUP>
      </TABLE>
    </PARA>
   </SECT2>

  <SECT2 ID="CREATEMENU-MARK-AMBIGUITIES">
    <TITLE>Mark Ambiguities</TITLE>
    <PARA>
Create a new feature for each block of ambiguous bases.  The new features will
have a key of <LITERAL>misc_feature</LITERAL> and will created in a new entry
called "ambiguous bases".
    </PARA>
  </SECT2> 
</SECT1>

<SECT1 ID="WRITEMENU">
  <TITLE>The Write Menu</TITLE>
  <PARA>

  </PARA>

  <SECT2 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>
  </SECT2>

  <SECT2 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>
  </SECT2>

  <SECT2 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.  If the selection consists of features 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>
  </SECT2>

  <SECT2 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.  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>
  </SECT2>

  <SECT2 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.
    </PARA>
  </SECT2>

  <SECT2 ID="WRITEMENU-ALL-BASES">
    <TITLE>Write All Bases (Raw)</TITLE>
    <PARA>
Prompt for a file name, then write the sequence to that file.
    </PARA>
  </SECT2>

  <SECT2 ID="WRITEMENU-CODON-USAGE">
    <TITLE>Write Codon Usage of Selected Features</TITLE>
    <PARA>
Prompt for a file name, then write a codon usage table for the selected
features.  In the output file each codon is followed by it's occurrence count
(per thousand) and it's percentage occurrence.<![ %artemis-only; [
(See <XREF LINKEND="DISPLAYMENU-USAGE-PLOTS"> to find out how to plot a usage
graph).]]>
    </PARA>
  </SECT2>
</SECT1>
