3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
4 * Copyright (C) 2014 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <title>Popup Menu</title>
25 <p><strong>Popup Menu</strong><br>
26 <em>This menu is visible when right clicking either within a
27 selected region on the alignment or on a selected sequence name. It may
28 not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
30 <li><strong>Selection</strong>
32 <li><a name="sqreport"><strong>Sequence Details ...<br>
33 </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
34 and database cross references</a> normally shown in the sequence's
36 <li><strong>Edit </strong>
38 <li><strong>Copy</strong><br>
39 <em>Copys the selected region. In the applet version, the copied sequences
40 are not available to the system clipboard.</em></li>
42 </strong><em>Cuts the selected region from the alignment. In the applet
43 version, the copied sequences are not available to the system clipboard.</em></li>
44 <li><strong>Edit Sequence</strong><br>
45 <em>Edit the selected sequence(s) directly. Spaces will be converted
46 to the current gap character.</em></li>
47 <li><strong>To Upper Case</strong><em><strong><br>
48 </strong><em>Changes the case of selected region to lower case.</em>
50 <li><strong>To Lower Case<br>
51 </strong><em>Changes the case of selected region to upper case.</em><strong>
53 <li><strong>Toggle Case</strong><br>
54 <em>Switches the case of all residues within the selected region.</em></li>
57 <li><strong>Output to Textbox<br>
58 </strong><em>The selection area will be output to a a text window in the
59 selected alignment format. </em></li>
60 <li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>
61 <em>Opens the dialog box for creating sequence features over the currently
62 selected region on each selected sequence.</em></li>
63 <li><strong>Create Group<br>
64 </strong><em>This will define a new group from the current selection.</em><strong>
66 <li><strong>Remove Group<br>
67 </strong><em>This will undefine the selected group. </em><strong>
69 <li><strong>Edit (New) Group</strong><br>
70 <em>Group Editing Menu</em> <br />Options in this menu modify
71 the name and display properties of the currently selected group, or
72 a new group defined using the current selection.
74 <li><strong>Name: <Group></strong> or <strong>Edit name and description</strong><br><em>The first entry in the
75 menu displays the name for the currently selected group, if it has one. Selecting this option opens a window allowing the name and
76 description for this group to be edited. Click OK to set the
77 new name and decription, and cancel to leave the existing
78 name and description unchanged.</em></li>
79 <li><strong>Group Colour<br>
80 </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
81 of the group.</em><strong> </strong></li>
83 </strong><em>If selected the background of a residue within the selected
84 group will be coloured according to the assigned colour scheme.</em><strong>
87 </strong><em>If selected the selected group will display text. </em></li>
88 <li><strong>Colour Text<br>
89 </strong><em>If selected the selected group will display text in a
90 colour slightly darker than the background colour of that residue.</em></li>
91 <li><strong>Border Colour <br>
92 </strong><em>Selecting this will display a "Colour Chooser"
93 window. Select a colour than press OK to set the border colour of
95 <li><strong>Show Unconserved<br>
96 </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.
100 <!-- not available in 2.5 yet
101 <li><strong>Group Links<br>
102 </strong><em>This menu is only visible if there are group links available for the current selection.
105 <li><em>ID links</em> allow you to send IDs associated with the current selection to a web server.</li>
106 <li><em>Sequence links</em> allow you to send the sequences in the currently selected region to a web server.</li>
107 <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>
109 <em>Group Links were added in Jalview 2.5</em></li>
112 <li><strong>Sequence Id<br>
113 </strong><em>This menu is only visible if you right-click on a sequence name.
116 <li><a name="sqreport"><strong>Sequence Details ...<br>
117 </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
118 and database cross references</a> normally shown in the sequence's
120 <li><strong>Edit Name/Description<br>
121 </strong><em>You may edit the name and description of each sequence. A
122 window will be displayed asking for a new sequence name and sequence description
123 to be entered. Press OK to accept your edit. To save sequence descriptions,
124 you must save in Fasta, PIR or Jalview File format.</em></li>
126 <li><strong>Represent Group With (Sequence Id)</strong><br>
127 <em>All sequences in the current selection group will be hidden, apart
128 from (Sequence Id). Any edits performed on the visible representative
129 sequence will be propagated to the hidden sequences. </em></li>
130 <li><a name="sqid.popup"><strong>Link</strong><br>
131 <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a>
133 Since Jalview 2.4, links will also be made for database cross
134 references (where the database name exactly matches the link name set up in <a href="../features/preferences.html">Preferences</a>).
135 <br>Since Jalview 2.5, links are also shown for non-positional sequence features attached to
136 the sequence, and any regular-expression based URL links that
137 matched the description line.
142 <li><strong>Structure</strong>
143 </strong><em>This menu is only visible if you right-click on a sequence name.
146 <li><strong>Associate Structure with Sequence</strong>
148 <li><strong>From File<br>
149 </strong><em>Load a PDB file from local disk which will be associated
150 with this sequence. This file will be used if the user subsequently
151 clicks on "View Structure" menu item.</em></li>
152 <li><strong>Enter PDB id<br>
153 </strong><em>Enter the PDB id from an input window. This PDB id will
154 be used by the service WSDBFetch, provided by the EBI, to fetch the
155 PDB file if the user subsequently clicks on its "View Structure"
156 menu item. </em></li>
157 <li><strong>Discover PDB ids<br>
158 </strong><em>This will use the service WSDBFetch, provided by the
159 EBI, to retrieve all PDB ids associated with the sequences in the
160 alignment if the sequences have valid Uniprot names or accession ids.
164 <li><strong>View Structure<br>
165 </strong><em> If the sequence has an associated PDB file added by one
166 of the methods described above, Jalview will open a 3D interactive
167 view of the file.<br>
168 These entries will only be present if the sequence has <a
169 href="../features/viewingpdbs.html">associated PDB structures</a>.<br/>
170 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>
172 <p><em>Other menu entries may also be shown if the current selection includes sequences with associated structure data:</em><br>
174 <li><strong>"Structure→View all <em>N</em>
176 </strong><em>Opens a new window containing all structures associated
177 with the current selection, superposed according to the currently selected region of the alignment.<br/>(This
178 capability was added in Jalview 2.7)</em>
180 <li><strong>"Structure→View all <em>N</em>
181 representative structures<br/>
182 </strong><em>Open a new window containing exactly one structure per
183 currently selected sequence.<br />
184 (The View representative structures option was introduced in
185 Jalview 2.8.1)</em></li>
192 <li><strong>Hide Sequences</strong><br>
193 <em>Hides the currently selected sequences in this alignment view.</em><strong><br>