<body>
<p><strong>Alignment Window Menus</strong></p>
-<ul>
<li><strong>File</strong>
<ul>
<li><strong>Fetch Sequence</strong><br>
determine which <a href="../io/index.html">alignment format</a> to
save as.</em></li>
<li><strong>Output to Textbox<br>
- </strong><em>The alignment will be displayed in plain text in a new window
- which you can "Copy and Paste" using the pull down menu, or
- your standard operating system copy and paste keys. <br>
+ </strong><em>The alignment will be displayed in plain text in a new
+ window, which you can "Copy and Paste" using the pull down
+ menu, or your standard operating system copy and paste keys. The
+ output window also has a <strong>"New Window"</strong>
+ button to import the (possibly edited) text as a new alignment.<br>
Select the format of the text by selecting one of the following menu
items.</em>
<ul>
displayed below the alignment. The default setting is to display the
conservation calculation, quality calculation and consensus values as
bar charts. </em></li>
+ <li><strong>Automatic Scrolling<br>
+ </strong><em>When selected, the view will automatically scroll to display the
+ highlighted sequence position corresponding to the position under the mouse
+ pointer in a linked alignment or structure view.</em>
+ </li>
<li><strong>Show Sequence Features</strong><br>
<em>Show or hide sequence features on this alignment.</em></li>
<li><strong><a href="../features/featuresettings.html">Seqence
<em>Opens the Sequence Feature Settings dialog box to control the
colour and display of sequence features on the alignment, and
configure and retrieve features from DAS annotation servers.</em></li>
+ <li><strong>Sequence ID Tooltip</strong><em> (application only)
+ <br>This submenu's options allow the inclusion or exclusion of
+ non-positional sequence features or database cross references
+ from the tooltip shown when the mouse hovers over the sequence ID panel.</em></li>
+
<li><strong><a href="../features/overview.html">Overview
Window</a><br>
</strong><em>A scaled version of the alignment will be displayed in a
<li><strong>Scale Right</strong><br>
Show the sequence position for the last aligned residue in each row
in the right-most column of the alignment.</li>
- </em></li>
<li><strong>Show Sequence Limits<br>
</strong><em>If this box is selected the sequence name will have the start
and end position of the sequence appended to the name, in the format
will appear as blank spaces. <br>
You may set the default gap character in <a
href="../features/preferences.html">preferences</a>.</em></li>
+ <li><strong>Centre Annotation Labels<br>
+ </strong><em>Select this to center labels along an annotation row
+ relative to their associated column (default is off, i.e. left-justified).</em></li>
</ul>
- </li>
<li><strong>Colour</strong>
<ul>
<li><strong>Apply Colour To All Groups<br>
BLOSUM62 scores in the alignment. See <a
href="../calculations/pca.html">Principal Component Analysis</a>.</em> <br>
</li>
+ <li><strong>Extract Scores ... (optional)</strong><br>
+ <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
+ When selected, these numbers are parsed into sequence associated annotation which can
+ then be used to sort the alignment via the Sort by→Score menu.</em> <br>
+ </li>
<li><strong>Autocalculate Consensus</strong><br>
<em>For large alignments it can be useful to deselect
"Autocalculate Consensus" when editing. This prevents the
</ul>
</li>
<li><strong>Web Service<br>
- </strong> <em>Selecting one of the following menu items starts a remote
+ </strong>
+ <ul><li><strong>Fetch DB References</strong><br>
+ <em>This will use any of the database services that Jalview is aware
+ of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI)
+ to verify the sequence and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.</em><br>
+ </li>
+ </ul>
+ <em>Selecting one of the following menu items starts a remote
service on compute facilities at the University of Dundee. You need a
continuous network connection in order to use these services through
Jalview. </em>
git://source.jalview.org / jalview.git / blobdiff