3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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/>.
20 <title>Popup Menu</title>
24 <p><strong>Popup Menu</strong><br>
25 <em>This menu is visible when right clicking either within a
26 selected region on the alignment or on a selected sequence name. It may
27 not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
29 <li><strong>Selection</strong>
31 <li><strong>Edit </strong>
33 <li><strong>Copy</strong><br>
34 <em>Copys the selected region. In the applet version, the copied sequences
35 are not available to the system clipboard.</em></li>
37 </strong><em>Cuts the selected region from the alignment. In the applet
38 version, the copied sequences are not available to the system clipboard.</em></li>
39 <li><strong>Edit Sequence</strong><br>
40 <em>Edit the selected sequence(s) directly. Spaces will be converted
41 to the current gap character.</em></li>
42 <li><strong>To Upper Case</strong><em><strong><br>
43 </strong><em>Changes the case of selected region to lower case.</em>
45 <li><strong>To Lower Case<br>
46 </strong><em>Changes the case of selected region to upper case.</em><strong>
48 <li><strong>Toggle Case</strong><br>
49 <em>Switches the case of all residues within the selected region.</em></li>
52 <li><strong>Output to Textbox<br>
53 </strong><em>The selection area will be output to a a text window in the
54 selected alignment format. </em></li>
55 <li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>
56 <em>Opens the dialog box for creating sequence features over the currently
57 selected region on each selected sequence.</em></li>
58 <li><strong>Group</strong><br>
59 <em>Group Operations</em>
61 <li><strong>Group</strong><em>This is the first entry in the
62 menu, and will display the currently selected group's
63 name. Selecting it displays a window allowing the name and
64 description for this group to be edited. Click OK to set the
65 new name and decription, and cancel to leave the existing
66 name and description unchanged.</em></li>
67 <li><strong>Remove Group<br>
68 </strong><em>This will undefine the selected group. </em><strong>
70 <li><strong>Group Colour<br>
71 </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
72 of the group.</em><strong> </strong></li>
74 </strong><em>If selected the background of a residue within the selected
75 group will be coloured according to the assigned colour scheme.</em><strong>
78 </strong><em>If selected the selected group will display text. </em></li>
79 <li><strong>Colour Text<br>
80 </strong><em>If selected the selected group will display text in a
81 colour slightly darker than the background colour of that residue.</em></li>
82 <li><strong>Border Colour <br>
83 </strong><em>Selecting this will display a "Colour Chooser"
84 window. Select a colour than press OK to set the border colour of
86 <li><strong>Show Unconserved<br>
87 </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.
91 <!-- not available in 2.5 yet
92 <li><strong>Group Links<br>
93 </strong><em>This menu is only visible if there are group links available for the current selection.
96 <li><em>ID links</em> allow you to send IDs associated with the current selection to a web server.</li>
97 <li><em>Sequence links</em> allow you to send the sequences in the currently selected region to a web server.</li>
98 <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>
100 <em>Group Links were added in Jalview 2.5</em></li>
103 <li><strong>Sequence Id<br>
104 </strong><em>This menu is only visible if you right-click on a sequence name.
107 <li><strong>Edit Name/Description<br>
108 </strong><em>You may edit the name and description of each sequence. A
109 window will be displayed asking for a new sequence name and sequence description
110 to be entered. Press OK to accept your edit. To save sequence descriptions,
111 you must save in Fasta, PIR or Jalview File format.</em></li>
113 <li><strong>Represent Group With (Sequence Id)</strong><br>
114 <em>All sequences in the current selection group will be hidden, apart
115 from (Sequence Id). Any edits performed on the visible representative
116 sequence will be propagated to the hidden sequences. </em></li>
117 <li><a name="sqid.popup"><strong>Link</strong><br>
118 <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a>
120 Since Jalview 2.4, links will also be made for database cross
121 references (where the database name exactly matches the link name set up in <a href="../features/preferences.html">Preferences</a>).
122 <br>Since Jalview 2.5, links are also shown for non-positional sequence features attached to
123 the sequence, and any regular-expression based URL links that
124 matched the description line.
129 <li><strong>Structure</strong>
130 </strong><em>This menu is only visible if you right-click on a sequence name.
133 <li><strong>Associate Structure with Sequence</strong>
135 <li><strong>From File<br>
136 </strong><em>Load a PDB file from local disk which will be associated
137 with this sequence. This file will be used if the user subsequently
138 clicks on "View PDB Structure" menu item.</em></li>
139 <li><strong>Enter PDB id<br>
140 </strong><em>Enter the PDB id from an input window. This PDB id will
141 be used by the service WSDBFetch, provided by the EBI, to fetch the
142 PDB file if the user subsequently clicks on "View PDB Structure"
143 menu item. </em></li>
144 <li><strong>Discover PDB ids<br>
145 </strong><em>This will use the service WSDBFetch, provided by the
146 EBI, to retrieve all PDB ids associated with the sequences in the
147 alignment if the sequences have valid Uniprot names or accession ids.
151 <li><strong>View Structure<br>
152 </strong><em> If the sequence has an associated PDB file added by one
153 of the methods described above, Jalview will display a 3D interactive
154 viewer of the file.<br>
155 These entries will only be present if the sequence has <a
156 href="../features/viewingpdbs.html">associated PDB structures</a>.</em><br>
160 <li><strong>Hide Sequences</strong><br>
161 <em>Hides the currently selected sequences in this alignment view.</em><strong><br>