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.
    </PARA>
  </SECT2>
</SECT1>

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

  </PARA>

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

  <SECT2 ID="VIEWMENU-VIEW-SELECTION">
    <TITLE>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>
    <PARA>
When one feature is selected the window will show the text (EMBL, GenBank or
GFF format) of the feature, the base composition, GC percentage, correlation
score (see <XREF LINKEND="GRAPHMENU-CORRELATION-SCORES">), and the bases and
translation of the sequence of the feature.
    </PARA>
    <PARA>
When two or more features are selected the window will show the text (EMBL,
GenBank or GFF format) of the features, the base composition, average GC
percentage, average correlation score, minimum/maximum GC content and
minimum/maximum correlation score of the feature sequence.
    </PARA>
    <PARA>
When a range of bases is selected the window will show the base composition,
GC content percentage and the bases and translation of the sequence of the
feature.
    </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>CDS Genes And Products</TITLE>
    <PARA>
Pop up a feature list (see <XREF LINKEND="FEATURELIST">) of the CDS showing
the gene names (from the /gene qualifier) and
the product (from the /product qualifier).  This list includes pseudo genes.
    </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 features with
<LITERAL>misc_feature</LITERAL> as a key.  The features are displayed in a new
window that contains a menu bar with possible actions to apply to the subset,
and feature list (see <XREF LINKEND="FEATURELIST">).  Most of the possible
actions will apply only to the features in the list.  For example "Show
Overview" in the View menu (see <XREF LINKEND="VIEWMENU-SHOW-OVERVIEW">) will
include statistics only on the features in the list.
    </PARA>

    <SECT3 ID="VIEWMENU-FEATURE-FILTERS-SUSPSTART">
      <TITLE>Suspicious Start Codons ...</TITLE>
      <PARA>
Show those CDS features that have a suspicious start codon.  ie. the first
codon of the feature isn't ATG (in eukaroytic mode) or ATG, GTG and TTG (in
prokaryotic mode).  This function is effected by the setting of the
"Eukaroytic Mode" option in the main options menu (see <XREF
LINKEND="LAUNCH-WINDOW-OPTIONS-EUK"> for more).
      </PARA>
    </SECT3>

    <SECT3 ID="VIEWMENU-FEATURE-FILTERS-SUSPSTOP">
      <TITLE>Suspicious Stop Codons ...</TITLE>
      <PARA>
Show those CDS features that have a suspicious stop codon.  ie. the last codon
of the feature isn't one of TAA, TAG or TGA.
      </PARA>
    </SECT3>

    <SECT3 ID="VIEWMENU-FEATURE-FILTERS-NONEMBLKEYS">
      <TITLE>Non EMBL Keys ...</TITLE>
      <PARA>
Show those features that have a key that isn't valid for EMBL/GenBank
entries.
      </PARA>
    </SECT3>

    <SECT3 ID="VIEWMENU-FEATURE-FILTERS-">
      <TITLE>Duplicated Features ...</TITLE>
      <PARA>
Show those features that are duplicated (ie. features that have the same key
and location as another feature).  These sort of duplicates aren't allowed by
the EMBL database.
      </PARA>
    </SECT3>

    <SECT3 ID="VIEWMENU-FEATURE-FILTERS-OVERLAPPING">
      <TITLE>Overlapping CDS Features ...</TITLE>
      <PARA>
Show those CDS features that overlap another CDS feature (on either strand).
      </PARA>
    </SECT3>

    <SECT3 ID="VIEWMENU-FEATURE-FILTERS-REQQUAL">
      <TITLE>Features Missing Required Qualifiers ...</TITLE>
      <PARA>
Show those features that are missing a qualifier that is required by the EMBL
database.
      </PARA>
    </SECT3>

    <SECT3 ID="VIEWMENU-FEATURE-FILTERS-BYKEY">
      <TITLE>Filter By Key ...</TITLE>
      <PARA>
Show those features that have a key chosen by the user.
      </PARA>
    </SECT3>

    <SECT3 ID="VIEWMENU-FEATURE-FILTERS-SELECTED">
      <TITLE>Selected Features ...</TITLE>
      <PARA>
Show the currently selected features in a new feature list.  The contents of
the list will remain the same even if selection subsequently changes.  This is
useful for bookmarking a collection of features for later use.
      </PARA>
    </SECT3>
  </SECT2>

  <SECT2 ID="VIEWMENU-SHOW-OVERVIEW">
    <TITLE>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).
[shortcut key: O]
    </PARA>

    <SECT3 ID="VIEWMENU-SHOW-OVERVIEW-SEQSTATS">
      <TITLE>Sequence Statistics</TITLE>
      <PARA>
The overview window show the following statistics about the sequence:
        <ITEMIZEDLIST>
          <LISTITEM>
            <PARA>
Number of bases.
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
GC percentage.
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
The number of each nucleotide in the sequence.
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
GC percentage of non-ambiguous bases - ie. the GC content percentage ignoring
bases other than A,T,C and G.  This should be the same as the "GC percentage"
above.
            </PARA>
          </LISTITEM>
        </ITEMIZEDLIST>
      </PARA>
    </SECT3>

    <SECT3 ID="VIEWMENU-SHOW-OVERVIEW-FEATURESTATS">
      <TITLE>Feature Statistics</TITLE>
      <PARA>
The overview window also shows the following statistics about the features in
the active entries (if there are any features).  Note that the "genes" are the
non-pseudo CDS features.
        <ITEMIZEDLIST>
          <LISTITEM>
            <PARA>
Number of features in the active entries (see <XREF
LINKEND="CONCEPTS-ACTIVEENTRY">).
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
Gene density - the average number of non-pseudo CDS features per 1000 bases.
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
Average gene length - the average length of non-pseudo CDS features (not
including introns).
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
Number of non-spliced genes.
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
Number of spliced genes.
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
Number of pseudo genes (ie. CDS features with a /pseudo qualifier).
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
Protein coding (CDS) features.
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
Protein coding (CDS) bases.
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
Protein coding percentage - ie. the number of coding bases excluding introns.
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
Coding percentage (including introns).
            </PARA>
          </LISTITEM>

          <LISTITEM>
            <PARA>
A summary of the number of features of each key (type) and their colours.
            </PARA>
          </LISTITEM>
        </ITEMIZEDLIST>
      </PARA>
    </SECT3>
  </SECT2>

  <SECT2 ID="VIEWMENU-SHOW-FORWARD-OVERVIEW">
    <TITLE>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>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>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>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>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>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>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>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>].  (For more detail about the coiled coils
algorithm see "Predicting Coiled Coils from Protein Sequences", Science
Vol. 252 page 1162.) [shortcut key: W]
    </PARA>
    <PARA>
Some general information about graphs and plots in &prog; can be found in <XREF
LINKEND="GRAPHS">.  Configuration options for graphs are described in <XREF
LINKEND="OPTIONS-PLOTS">.
    </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.  [shortcut key: G]
    </PARA>
    <PARA>
This window allows the user to perform five
different tasks:
      <ORDEREDLIST>
        <LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-BASE">
          <FORMALPARA>
            <TITLE>
Scroll all the views so that a particular base is in the centre of
the display
            </TITLE>
            <PARA>
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>
          </FORMALPARA>
        </LISTITEM>
        <LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-GENENAME">
          <FORMALPARA>
            <TITLE>
Find the next feature that has the given gene name
            </TITLE>
            <PARA>
To use this function, type a gene name into the box to the right of the "Goto
Feature With This Gene Name:" label and then press the goto button.
&prog; will select the first feature with the given text in any of it's
qualifiers and will then scroll the display so that feature is in view.
            </PARA>
          </FORMALPARA>
        </LISTITEM>
        <LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-TEXT">
          <FORMALPARA>
            <TITLE>
Find the next feature that has a qualifier containing a particular string
            </TITLE>
            <PARA>
To use this function, type a string into the box to the right of the "Goto
Feature With This Qualifier Value:" label and then press the goto button.
&prog; will select the first feature with the given string in any of it's
qualifier values (see <XREF LINKEND="CONCEPTS-QUALIFIERS">) and will then
scroll the display so that feature is in view.
            </PARA>
          </FORMALPARA>
        </LISTITEM>
        <LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-KEY">
          <FORMALPARA>
            <TITLE>
Find the next feature that has a particular key
            </TITLE>
            <PARA>
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>
          </FORMALPARA>
        </LISTITEM>
        <LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-DNA-PATTERN">
          <FORMALPARA>
            <TITLE>
Find the next occurrence of a particular base pattern in the sequence
            </TITLE>
            <PARA>
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.
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="IUB-BASE-CODES"> for a list of the
available base codes.
            </PARA>
          </FORMALPARA>
        </LISTITEM>
        <LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-AA-PATTERN">
          <FORMALPARA>
            <TITLE>
Find the next occurrence of a particular residue pattern in the sequence
            </TITLE>
            <PARA>
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.  The letter 'X' can be used as an
ambiguity code, hence 'AAXXXDD' will match 'AALRTDD' or 'AATTTDD' etc.
            </PARA>
          </FORMALPARA>
        </LISTITEM>
      </ORDEREDLIST>
    </PARA>
    <PARA>
Note that for all the functions above except the first ("Goto Base"), 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>
    <PARA>
If the "Ignore Case" toggle is on (which is the default) Artemis will
ignore the difference between upper and lower case letters when searching for
a gene name, a qualifier value or a feature key.
    </PARA>
    <PARA>
The "Allow Substring Matches" toggle affects <XREF
LINKEND="GOTOMENU-NAVIGATOR-GOTO-GENENAME"> and <XREF
LINKEND="GOTOMENU-NAVIGATOR-GOTO-TEXT">.  If on &prog; will search for
qualifier values that contain the given characters.  For example searching for
the genename CDC will find CDC1, CDC2, ABCDC etc.  If the toggle is off &prog;
will only find exact matches, so searching for the gene CDC will only find
features that have <LITERAL>/gene="CDC"</LITERAL> not
<LITERAL>/gene="CDC11"</LITERAL>.
    </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.
[shortcut key: control-left]
    </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.
[shortcut key: control-right]
    </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.
[shortcut key: control-up]
    </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.
[shortcut key: control-down]
    </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-UNDO">
    <TITLE>Undo</TITLE>
    <PARA>
This function will undo the last change that was made using the Edit or Create
menus.  Up to 20 changes can be undone. This menu item is only enabled when 
there is something to undo. This limit can be changed in the
options file (see <XREF LINKEND="OPTIONS-UNDO-LEVELS">).  [shortcut key: U]
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-REDO">
    <TITLE>Redo</TITLE>
    <PARA>
This function will redo the last undo operation.
    </PARA>
  </SECT2>


  <SECT2 ID="EDITMENU-EDIT-SELECTED-FEATURES">
    <TITLE>Selected Features in Editor</TITLE>
    <PARA>
Open an edit window for each selected feature.  [shortcut key: E]
    </PARA>
    <SCREENSHOT>
      <SCREENINFO>
The feature edit window
      </SCREENINFO>
      <MEDIAOBJECT>
        <IMAGEOBJECT>
          <IMAGEDATA FORMAT="gif" FILEREF="feature_edit.gif">
        </IMAGEOBJECT>
        <IMAGEOBJECT>
          <IMAGEDATA FORMAT="eps" FILEREF="feature_edit.eps">
        </IMAGEOBJECT>
      </MEDIAOBJECT>
    </SCREENSHOT>
    <PARA>
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>
Below the location is a row of buttons:
          </PARA>
          <ITEMIZEDLIST>
            <LISTITEM>
              <PARA>
The <LITERAL>Complement</LITERAL> button will complement the contents of the
location field.
              </PARA>
            </LISTITEM>
            <LISTITEM>
              <PARA>
The <LITERAL>Grab Range</LITERAL> button will grab the currently selected
range into the location field.
              </PARA>
            </LISTITEM>
            <LISTITEM>
              <PARA>
The <LITERAL>Remove Range</LITERAL> button will remove the selected bases from
the location string.  This is normally used to create an intron in a feature.
              </PARA>
            </LISTITEM>
            <LISTITEM>
              <PARA>
Pressing the <LITERAL>Goto Feature</LITERAL> button has the same effect as the
"Start of Selection" item in the "Goto" menu.  (See <XREF
LINKEND="GOTOMENU-GOTO-SELECTION-START"> for more).
              </PARA>
            </LISTITEM>
            <LISTITEM>
              <PARA>
The <LITERAL>Select Feature</LITERAL> button selects this feature (in the same
way as clicking on the feature in one of the views).
              </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 all errors have been fixed.
          </PARA>
        </LISTITEM>
      </ORDEREDLIST>
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-SUBSEQUENCE">
    <TITLE>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-FINDANDREPLACE">
    <TITLE>Find Or Replace Qualifier Text</TITLE>
    <PARA>
    This opens a search window with options to find or replace qualifier
    text. The search can be restricted to features with a given key and/or 
    it can be restricted to a given qualifier name.
    </PARA>
    <PARA>
    Boolean operators (and/or) can be used in the search. Clicking on the
    <LITERAL>Show Boolean Search Options</LITERAL> displays 4 options. 

    <ORDEREDLIST>
      <LISTITEM>
      <PARA>
      The <LITERAL>Use boolean operators (and, or, & |)</LITERAL> means that
      it uses any of these operators that are in the <LITERAL>Find</LITERAL> text field.
      </PARA>
      </LISTITEM>
      <LISTITEM>
      <PARA>
      The <LITERAL>Match any string (i.e. x OR y)</LITERAL> means that the words in
      the <LITERAL>Find</LITERAL> text field will be separated by an OR
      condition. So that it finds those features with qulaifiers that contain any of the 
      words.
      </PARA>
      </LISTITEM>
      <LISTITEM>
      <PARA>
      The <LITERAL>Match all string (i.e. x AND y)</LITERAL> means that the words in
      the <LITERAL>Find</LITERAL> text field will be separated by an AND
      condition. So that it finds those features with qulaifiers that contain all of the
      words.
      </PARA>
      </LISTITEM>
      <LISTITEM>
      <PARA>
      The <LITERAL>No boolean search</LITERAL> option is the default. This
      means it searches for those features with qualifiers that contain the complete
      text from the <LITERAL>Find</LITERAL> text field.
      </PARA>
      </LISTITEM>
    </ORDEREDLIST>
    </PARA>
    <PARA>
    In addition selecting the Duplicate Qualifiers tab provides options to
    search for or delete duplicate qualifiers.
    </PARA>
  </SECT2>


  <SECT2 ID="QUALIFIERS">
  <TITLE>Qualifier(s) of Selected Feature</TITLE>
  <SECT3 ID="EDITMENU-CHANGE-QUALIFIERS">
    <TITLE>Change ...</TITLE>
    <PARA>
This function allows the user to add or change qualifiers on all the selected
features in one operation.  The main part of the window acts like the
qualifier editing field of the feature edit window (see <XREF
LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">).
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-REMOVE-QUALIFIERS">
    <TITLE>Remove ...</TITLE>
    <PARA>
This function allows the user to remove all qualifiers with a particular name
from all the selected features.
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-CONVERT-QUALIFIERS">
    <TITLE>Convert ...</TITLE>
    <PARA>
This function allows the user to convert all qualifiers of a particular type
to another qualifier for all the selected features.
    </PARA>
  </SECT3>
  </SECT2>

  <SECT2 ID="EDITMENU-SELECTED-FEATURES">
  <TITLE>Selected Feature(s)</TITLE>
  <SECT3 ID="EDITMENU-DUPLICATE-SELECTED-FEATURES">
    <TITLE>Duplicate</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.  [shortcut key: D]
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-MERGE-SELECTED-FEATURES">
    <TITLE>Merge</TITLE>
    <PARA>
Create a new feature that contains all the exons and qualifiers of the
selected features.  The selected features must all have the same key.
[shortcut key: M]
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-UNMERGE-SELECTED-FEATURE">
    <TITLE>Unmerge</TITLE>
    <PARA>
If the selection contains exactly two exons and those exons are adjacent in
the same feature, split the feature into two pieces between the exons.  The
original feature is truncated and a new feature is created.  The qualifiers of
the old feature are copied to new feature.
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-UNMERGE-ALL-SEGMENTS">
    <TITLE>Unmerge All Segments</TITLE>
    <PARA>
All exons in a feature are unmerged.
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-DELETE-SELECTED-FEATURES">
    <TITLE>Delete</TITLE>
    <PARA>