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 or on a selected sequence name. It may not be accessible
31 when in 'Cursor Mode' (toggled with the F2 key).</em>
34 <li><strong>Selection</strong>
36 <li><a name="sqreport"><strong>Sequence
38 </strong></a><em>(Since Jalview 2.8)<br>Open an <a
39 href="../io/exportseqreport.html"
40 >HTML report containing the annotation and database cross
41 references</a> normally shown in the sequence's tooltip.
43 <li><strong>Show Annotations...<br>
44 </strong><em>Choose to show (unhide) either All or a selected type
45 of annotation for the selected sequences. (Since Jalview
47 <li><strong>Hide Annotations...<br>
48 </strong><em>Choose to hide either All or a selected type of
49 annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
50 <li><a name="addrefannot"><strong>Add
51 Reference Annotations<br>
52 </strong><em>Add to the alignment window any annotations on the
53 selected sequences which have been read from reference
54 sources or calculated (for example, secondary structure
55 derived from 3D structure). (Since Jalview 2.8.2)</em></li>
56 <li><strong>Edit </strong>
58 <li><strong>Copy</strong><br> <em>Copies the
59 selected region. In the applet version, the copied
60 sequences are not available to the system clipboard.</em></li>
62 </strong><em>Cuts the selected region from the alignment. In the
63 applet version, the copied sequences are not available
64 to the system clipboard.</em></li>
65 <li><strong>Edit Sequence</strong><br> <em>Edit
66 the selected sequence(s) directly. Spaces will be
67 converted to the current gap character.</em></li>
68 <li><strong>To Upper Case</strong><em><strong><br>
69 </strong><em>Changes the case of selected region to lower
71 <li><strong>To Lower Case<br>
72 </strong><em>Changes the case of selected region to upper case.</em><strong>
74 <li><strong>Toggle Case</strong><br> <em>Switches
75 the case of all residues within the selected region.</em></li>
77 <li><strong>Output to Textbox<br>
78 </strong><em>The selection area will be output to a a text window in
79 the selected alignment format. </em></li>
81 href="../features/creatinFeatures.html"
82 >Create Sequence Feature...</a></strong><br> <em>Opens the
83 dialog box for creating sequence features over the currently
84 selected region on each selected sequence.</em></li>
85 <li><strong>Create Group<br>
86 </strong><em>This will define a new group from the current
87 selection.</em><strong> </strong></li>
88 <li><strong>Remove Group<br>
89 </strong><em>This will undefine the selected group. </em><strong>
91 <li><strong>Edit (New) Group</strong><br> <em>Group
92 Editing Menu</em> <br />Options in this menu modify the name and
93 display properties of the currently selected group, or a new
94 group defined using the current selection.
96 <li><strong>Name: <Group></strong> or <strong>Edit
97 name and description</strong><br> <em>The first entry
98 in the menu displays the name for the currently selected
99 group, if it has one. Selecting this option opens a
100 window allowing the name and description for this group
101 to be edited. Click OK to set the new name and
102 decription, and cancel to leave the existing name and
103 description unchanged.</em></li>
104 <li><strong>Group Colour<br>
105 </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
107 </em><strong> </strong></li>
108 <li><strong>Boxes<br>
109 </strong><em>If selected the background of a residue within the
110 selected group will be coloured according to the
111 assigned colour scheme.</em><strong> </strong></li>
113 </strong><em>If selected the selected group will display text. </em></li>
114 <li><strong>Colour Text<br>
115 </strong><em>If selected the selected group will display text in
116 a colour slightly darker than the background colour of
117 that residue.</em></li>
118 <li><strong>Border Colour <br>
119 </strong><em>Selecting this will display a "Colour
120 Chooser" window. Select a colour than press OK to
121 set the border colour of a group.</em></li>
122 <li><strong>Show Unconserved<br>
123 </strong><em>When this is selected, all symbols in the group
124 matching the consensus sequence at that column will be
125 rendered as a '.', highlighting mutations in the group
130 <li><strong>Sequence Id<br>
131 </strong><em>This menu is only visible if you right-click on a sequence
134 <li><a name="sqreport"><strong>Sequence
136 </strong></a><em>(Since Jalview 2.8)<br>Open an <a
137 href="../io/exportseqreport.html"
138 >HTML report containing the annotation and database cross
139 references</a> normally shown in the sequence's tooltip.
141 <li><strong>Edit Name/Description<br>
142 </strong><em>You may edit the name and description of each sequence.
143 A window will be displayed asking for a new sequence name
144 and sequence description to be entered. Press OK to accept
145 your edit. To save sequence descriptions, you must save in
146 Fasta, PIR or Jalview File format.</em></li>
147 <li><a href="sqaddrefannot"><strong>Add
148 Reference Annotations<br>
149 </strong><em>When enabled, copies any available alignment
150 annotation for this sequence to the current view.</em></li>
151 <li><strong>Set as Reference</strong> or <strong>Unmark
152 as Reference</strong><br /> Sets or unsets the reference sequence for
153 the the alignment.</li>
155 <li><strong>Represent Group With (Sequence Id)</strong><br>
156 <em>All sequences in the current selection group will be
157 hidden, apart from (Sequence Id). Any edits performed on the
158 visible representative sequence will be propagated to the
159 hidden sequences. </em></li>
160 <li><a name="sqid.popup"><strong>Link</strong><br>
161 <em>This menu item lists all links which have been set
162 up in the <a href="../features/preferences.html">Preferences</a>
163 Connections tab.<br> Since Jalview 2.4, links will
164 also be made for database cross references (where the
165 database name exactly matches the link name set up in <a
166 href="../features/preferences.html"
167 >Preferences</a>). <br>Since Jalview 2.5, links are also
168 shown for non-positional sequence features attached to the
169 sequence, and any regular-expression based URL links that
170 matched the description line.
171 </em><strong><br> </strong></li>
173 <li><strong>3D Structure Data...</strong> </strong><em>This menu is
174 visible when you right-click on a sequence name. When this
175 option is clicked, Jalview will open a <a
176 href="../features/structurechooser.html"
177 >'Structure Chooser' </a> dialogue with options to select the
178 structure which will eventually be opened in a 3D interactive
179 view.<br> These entries will only be present if the
180 sequence has <a href="../features/viewingpdbs.html">associated
183 <li><strong>VARNA 2D Structure</strong><br />
184 <em> If the sequence or alignment has RNA structure, then <strong>VARNA
185 2D Structure</strong> entries will also be present enabling you to open
186 a linked view of the RNA structure in <a
187 href="../features/varna.html"
190 <li><a name="hideinserts"><strong>Hide Insertions</strong></a><br />
191 <em>Hides columns containing gaps in the current sequence or
192 selected region, and reveals columns not including gaps.</em>
193 <li><strong>Hide Sequences</strong><br> <em>Hides the
194 currently selected sequences in this alignment view.</em><strong><br>