<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
- *
+ * 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/>.
--->
+ * 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>
+ <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
+ and database cross references</a> normally shown in the sequence's
tooltip.</em></li>
+ <li><strong>Show Annotations...<br>
+ </strong><em>Choose to show (unhide) either All or
+ a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+ <li><strong>Hide Annotations...<br>
+ </strong><em>Choose to hide either All or
+ a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+ <li><a name="addrefannot"><strong>Add Reference Annotations<br>
+ </strong><em>Add to the alignment window any annotations on the selected sequences
+ which have been read from reference sources or calculated (for example,
+ secondary structure derived from 3D structure). (Since Jalview 2.8.2)</em></li>
<li><strong>Edit </strong>
<ul>
<li><strong>Copy</strong><br>
- <em>Copys the selected region. In the applet version, the copied sequences
+ <em>Copies the selected region. In the applet version, the copied sequences
are not available to the system clipboard.</em></li>
<li><strong>Cut<br>
</strong><em>Cuts the selected region from the alignment. In the applet
<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>
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,
you must save in Fasta, PIR or Jalview File format.</em></li>
- <li><em> </em></li>
+ <li><a href="sqaddrefannot"><strong>Add Reference Annotations<br></strong><em>When enabled, copies any available alignment annotation for this sequence to the current view.</em></li>
<li><strong>Represent Group With (Sequence Id)</strong><br>
<em>All sequences in the current selection group will be hidden, apart
from (Sequence Id). Any edits performed on the visible representative
<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
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>
</ul>
</li>
<li><strong>Hide Sequences</strong><br>
git://source.jalview.org / jalview.git / blobdiff