<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
<head>
<title>Popup Menu</title>
</head>
<ul>
<li><strong>Selection</strong>
<ul>
+ <li><a name="sqreport"><strong>Sequence Details ...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
+ and database cross references</a> normally shown in the sequence's
+ tooltip.</em></li>
<li><strong>Edit </strong>
<ul>
<li><strong>Copy</strong><br>
<li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>
<em>Opens the dialog box for creating sequence features over the currently
selected region on each selected sequence.</em></li>
- <li><strong>Group</strong><br>
- <em>Group Operations</em>
- <ul>
- <li><strong>Group</strong><em>This is the first entry in the
- menu, and will display the currently selected group's
- name. Selecting it displays a window allowing the name and
- description for this group to be edited. Click OK to set the
- new name and decription, and cancel to leave the existing
- name and description unchanged.</em></li>
+ <li><strong>Create Group<br>
+ </strong><em>This will define a new group from the current selection.</em><strong>
+ </strong></li>
<li><strong>Remove Group<br>
</strong><em>This will undefine the selected group. </em><strong>
</strong></li>
+ <li><strong>Edit (New) Group</strong><br>
+ <em>Group Editing Menu</em> <br />Options in this menu modify
+ the name and display properties of the currently selected group, or
+ a new group defined using the current selection.
+ <ul>
+ <li><strong>Name: <Group></strong> or <strong>Edit name and description</strong><br><em>The first entry in the
+ menu displays the name for the currently selected group, if it has one. Selecting this option opens a window allowing the name and
+ description for this group to be edited. Click OK to set the
+ new name and decription, and cancel to leave the existing
+ name and description unchanged.</em></li>
<li><strong>Group Colour<br>
</strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
of the group.</em><strong> </strong></li>
</strong><em>Selecting this will display a "Colour Chooser"
window. Select a colour than press OK to set the border colour of
a group.</em></li>
- </ul>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all symbols in the group matching the consensus sequence at that column will be rendered as a '.', highlighting mutations in the group area.
+ </em></li>
+ </ul>
</li>
+<!-- not available in 2.5 yet
+ <li><strong>Group Links<br>
+ </strong><em>This menu is only visible if there are group links available for the current selection.
+ </em>
+ <ul>
+ <li><em>ID links</em> allow you to send IDs associated with the current selection to a web server.</li>
+ <li><em>Sequence links</em> allow you to send the sequences in the currently selected region to a web server.</li>
+ <li><em>Sequence and ID links</em> allow you to send sets of IDs and sequences associated with the current selection to a web server.</li>
</ul>
+ <em>Group Links were added in Jalview 2.5</em></li>
+--> </ul>
</li>
<li><strong>Sequence Id<br>
</strong><em>This menu is only visible if you right-click on a sequence name.
</em>
<ul>
- <li><strong>Edit Name/Description<br>
+ <li><a name="sqreport"><strong>Sequence Details ...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
+ and database cross references</a> normally shown in the sequence's
+ tooltip.</em></li>
+ <li><strong>Edit Name/Description<br>
</strong><em>You may edit the name and description of each sequence. A
window will be displayed asking for a new sequence name and sequence description
to be entered. Press OK to accept your edit. To save sequence descriptions,
<em>All sequences in the current selection group will be hidden, apart
from (Sequence Id). Any edits performed on the visible representative
sequence will be propagated to the hidden sequences. </em></li>
- <li><strong>Link</strong><br>
+ <li><a name="sqid.popup"><strong>Link</strong><br>
<em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a>
Connections tab.<br>
Since Jalview 2.4, links will also be made for database cross
references (where the database name exactly matches the link name set up in <a href="../features/preferences.html">Preferences</a>).
+ <br>Since Jalview 2.5, links are also shown for non-positional sequence features attached to
+ the sequence, and any regular-expression based URL links that
+ matched the description line.
</em><strong><br>
</strong></li>
</ul>
<li><strong>From File<br>
</strong><em>Load a PDB file from local disk which will be associated
with this sequence. This file will be used if the user subsequently
- clicks on "View PDB Structure" menu item.</em></li>
+ clicks on "View Structure" menu item.</em></li>
<li><strong>Enter PDB id<br>
</strong><em>Enter the PDB id from an input window. This PDB id will
be used by the service WSDBFetch, provided by the EBI, to fetch the
- PDB file if the user subsequently clicks on "View PDB Structure"
+ PDB file if the user subsequently clicks on its "View Structure"
menu item. </em></li>
<li><strong>Discover PDB ids<br>
</strong><em>This will use the service WSDBFetch, provided by the
</li>
<li><strong>View Structure<br>
</strong><em> If the sequence has an associated PDB file added by one
- of the methods described above, Jalview will display a 3D interactive
- viewer of the file.<br>
+ of the methods described above, Jalview will open a 3D interactive
+ view of the file.<br>
These entries will only be present if the sequence has <a
- href="../features/viewingpdbs.html">associated PDB structures</a>.</em><br>
+ href="../features/viewingpdbs.html">associated PDB structures</a>.<br/>
+ If the sequence or alignment has RNA structure, then <strong>2D RNA</strong> entries will also be present enabling you to open a linked view of the RNA structure in <a href="../features/varna.html">VARNA</a>.</em><br>
+ </li>
+ <p><em>Other menu entries may also be shown if the current selection includes sequences with associated structure data:</em><br>
+ <ul>
+ <li><strong>"Structure→View all <em>N</em>
+ structures<br/>
+ </strong><em>Opens a new window containing all structures associated
+ with the current selection, superposed according to the currently selected region of the alignment.<br/>(This
+ capability was added in Jalview 2.7)</em>
+ </li>
+ <li><strong>"Structure→View all <em>N</em>
+ representative structures<br/>
+ </strong><em>Open a new window containing exactly one structure per
+ currently selected sequence.<br />
+ (The View representative structures option was introduced in
+ Jalview 2.8.1)</em></li>
+ </ul>
+ <br> <li>
+
</li>
</ul>
</li>
git://source.jalview.org / jalview.git / blobdiff