3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ 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
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Popup Menu</title>
28 <strong>Popup Menu</strong><br> <em>This menu is visible
29 when right clicking either within a selected region on the
30 alignment, on a sequence name, and also when right-clicking a sequence feature. It may not be accessible
31 when in 'Cursor Mode' (toggled with the F2 key).</em><br /> <em><strong>Mac
32 Users:</strong> pressing CTRL whilst clicking the mouse/track pad is the
33 same as a right-click. See your system's settings to configure
34 your track-pad's corners to generate right-clicks.</em>
37 <li><strong>Selection<br/></strong>
38 <em>This menu is only visible when right-clicking a selected sequence or region of the alignment. </em>
40 <li><a name="sqreport"><strong>Sequence
42 </strong></a><em>(Since Jalview 2.8)<br>Open an <a
43 href="../io/exportseqreport.html">HTML report
44 containing the annotation and database cross references</a> normally
45 shown in the sequence's tooltip.
47 <li><strong>Show Annotations...<br>
48 </strong><em>Choose to show (unhide) either All or a selected type
49 of annotation for the selected sequences. (Since Jalview
51 <li><strong>Hide Annotations...<br>
52 </strong><em>Choose to hide either All or a selected type of
53 annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
54 <li><a name="addrefannot"><strong>Add
55 Reference Annotations<br>
56 </strong><em>Add to the alignment window any annotations on the
57 selected sequences which have been read from reference
58 sources or calculated (for example, secondary structure
59 derived from 3D structure). (Since Jalview 2.8.2)</em></li>
60 <li><strong>Edit </strong>
62 <li><strong>Copy</strong><br> <em>Copies the
63 selected region. In the applet version, the copied
64 sequences are not available to the system clipboard.</em></li>
66 </strong><em>Cuts the selected region from the alignment. In the
67 applet version, the copied sequences are not available
68 to the system clipboard.</em></li>
69 <li><strong>Edit Sequence</strong><br> <em>Edit
70 the selected sequence(s) directly. Spaces will be
71 converted to the current gap character.</em></li>
72 <li><strong>To Upper Case</strong><em><strong><br>
73 </strong><em>Changes the case of selected region to lower
75 <li><strong>To Lower Case<br>
76 </strong><em>Changes the case of selected region to upper case.</em><strong>
78 <li><strong>Toggle Case</strong><br> <em>Switches
79 the case of all residues within the selected region.</em></li>
81 <li><strong>Output to Textbox<br>
82 </strong><em>The selection area will be output to a a text window in
83 the selected alignment format. </em></li>
85 href="../features/creatinFeatures.html">Create
86 Sequence Feature...</a></strong><br> <em>Opens the dialog box
87 for creating sequence features over the currently selected
88 region on each selected sequence.</em></li>
89 <li><strong>Create Group<br>
90 </strong><em>This will define a new group from the current
91 selection.</em><strong> </strong></li>
92 <li><strong>Remove Group<br>
93 </strong><em>This will undefine the selected group. </em><strong>
95 <li><strong>Edit (New) Group</strong><br> <em>Group
96 Editing Menu</em> <br />Options in this menu modify the name and
97 display properties of the currently selected group, or a new
98 group defined using the current selection.
100 <li><strong>Name: <Group></strong> or <strong>Edit
101 name and description</strong><br> <em>The first entry
102 in the menu displays the name for the currently selected
103 group, if it has one. Selecting this option opens a
104 window allowing the name and description for this group
105 to be edited. Click OK to set the new name and
106 decription, and cancel to leave the existing name and
107 description unchanged.</em></li>
108 <li><strong>Group Colour<br>
109 </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
111 </em><strong> </strong></li>
112 <li><strong>Boxes<br>
113 </strong><em>If selected the background of a residue within the
114 selected group will be coloured according to the
115 assigned colour scheme.</em><strong> </strong></li>
117 </strong><em>If selected the selected group will display text. </em></li>
118 <li><strong>Colour Text<br>
119 </strong><em>If selected the selected group will display text in
120 a colour slightly darker than the background colour of
121 that residue.</em></li>
122 <li><strong>Border Colour <br>
123 </strong><em>Selecting this will display a "Colour
124 Chooser" window. Select a colour than press OK to
125 set the border colour of a group.</em></li>
126 <li><strong>Show Unconserved<br>
127 </strong><em>When this is selected, all symbols in the group
128 matching the consensus sequence at that column will be
129 rendered as a '.', highlighting mutations in the group
134 <li><strong>Sequence Id<br>
135 </strong><em>This menu is only visible if you right-click on a sequence
138 <li><a name="sqreport"><strong>Sequence
140 </strong></a><em>(Since Jalview 2.8)<br>Open an <a
141 href="../io/exportseqreport.html">HTML report
142 containing the annotation and database cross references</a>
143 normally shown in the sequence's tooltip.
145 <li><strong>Edit Name/Description<br>
146 </strong><em>You may edit the name and description of each sequence.
147 A window will be displayed asking for a new sequence name
148 and sequence description to be entered. Press OK to accept
149 your edit. To save sequence descriptions, you must save in
150 Fasta, PIR or Jalview File format.</em></li>
152 href="../features/annotation.html#seqannots">Reference
153 Annotations</a></strong><br> <em>When enabled, copies any
154 available alignment annotation for this sequence to the
155 current view.</em></li>
156 <li><strong>Set as Reference</strong> or <strong>Unmark
157 as Reference</strong><br /> Sets or unsets the reference sequence
158 for the the alignment.</li>
160 <li><strong>Represent Group With (Sequence Id)</strong><br>
161 <em>All sequences in the current selection group will be
162 hidden, apart from (Sequence Id). Any edits performed on the
163 visible representative sequence will be propagated to the
164 hidden sequences. </em></li>
165 <li><a name="sqid.popup"><strong>Link</strong><br>
166 <em>This menu item lists all links which have been set
167 up in the <a href="../features/preferences.html">Preferences</a>
168 Connections tab.<br> Since Jalview 2.4, links will
169 also be made for database cross references (where the
170 database name exactly matches the link name set up in <a
171 href="../features/preferences.html">Preferences</a>).
172 <br>Since Jalview 2.5, links are also shown for
173 non-positional sequence features attached to the sequence,
174 and any regular-expression based URL links that matched
175 the description line.
176 </em><strong><br> </strong></li>
178 <li><strong>3D Structure Data...</strong> </strong><em>This menu is
179 visible when you right-click on a sequence name. When this
180 option is clicked, Jalview will open the <a
181 href="../features/structurechooser.html">'Structure Chooser'
182 </a>, which allows you to discover and view 3D structures for the
183 current selection. For more info, see <a
184 href="../features/viewingpdbs.html">viewing PDB structures</a>.
186 <li><strong>VARNA 2D Structure</strong><br /> <em> If the
187 sequence or alignment has RNA structure, then <strong>VARNA
188 2D Structure</strong> entries will also be present enabling you to open
189 a linked view of the RNA structure in <a
190 href="../features/varna.html">VARNA</a>.
192 <li><a name="hideinserts"><strong>Hide Insertions</strong></a><br />
193 <em>Hides columns containing gaps in both the current
194 sequence and selected region, and reveals columns not including
195 gaps. (before 2.10.2, this option hid or revealed columns
196 according to gaps in just the current sequence)</em></li>
197 <li><strong>Hide Sequences</strong><br> <em>Hides the
198 currently selected sequences in this alignment view.</em><strong><br>
199 </strong><br/> <br/></li>
201 <li><strong><a name="featuredetails"> Feature Details</a><br /></strong>
202 <em>Each entry opens a <a
203 href="../features/seqfeaturereport.html">Sequence Feature
204 Report</a> for visible features under the mouse.<br />Only visible
205 when right-clicking a region where <a
206 href="../features/seqfeatures.html">Sequence Features</a> are