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.
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11 * of the License, or (at your option) any later version.
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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.
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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 alignment
30 or on a selected sequence name. It may not be accessible when in
31 'Cursor Mode' (toggled with the F2 key).</em>
34 <li><strong>Selection</strong>
36 <li><a name="sqreport"><strong>Sequence Details...<br>
37 </strong></a><em>(Since Jalview 2.8)<br>Open an <a
38 href="../io/exportseqreport.html">HTML report containing the
39 annotation and database cross references</a> normally shown in
40 the sequence's tooltip.
42 <li><strong>Show Annotations...<br>
43 </strong><em>Choose to show (unhide) either All or a selected type of
44 annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
45 <li><strong>Hide Annotations...<br>
46 </strong><em>Choose to hide either All or a selected type of annotation
47 for the selected sequences. (Since Jalview 2.8.2)</em></li>
48 <li><a name="addrefannot"><strong>Add Reference
50 </strong><em>Add to the alignment window any annotations on the
51 selected sequences which have been read from reference sources or
52 calculated (for example, secondary structure derived from 3D
53 structure). (Since Jalview 2.8.2)</em></li>
54 <li><strong>Edit </strong>
56 <li><strong>Copy</strong><br> <em>Copies the
57 selected region. In the applet version, the copied sequences are
58 not available to the system clipboard.</em></li>
60 </strong><em>Cuts the selected region from the alignment. In the
61 applet version, the copied sequences are not available to the
62 system clipboard.</em></li>
63 <li><strong>Edit Sequence</strong><br> <em>Edit the
64 selected sequence(s) directly. Spaces will be converted to the
65 current gap character.</em></li>
66 <li><strong>To Upper Case</strong><em><strong><br>
67 </strong><em>Changes the case of selected region to lower case.</em> </em></li>
68 <li><strong>To Lower Case<br>
69 </strong><em>Changes the case of selected region to upper case.</em><strong>
71 <li><strong>Toggle Case</strong><br> <em>Switches
72 the case of all residues within the selected region.</em></li>
74 <li><strong>Output to Textbox<br>
75 </strong><em>The selection area will be output to a a text window in the
76 selected alignment format. </em></li>
77 <li><strong><a href="../features/creatinFeatures.html">Create
78 Sequence Feature...</a></strong><br> <em>Opens the dialog box for
79 creating sequence features over the currently selected region on
80 each selected sequence.</em></li>
81 <li><strong>Create Group<br>
82 </strong><em>This will define a new group from the current selection.</em><strong>
84 <li><strong>Remove Group<br>
85 </strong><em>This will undefine the selected group. </em><strong> </strong></li>
86 <li><strong>Edit (New) Group</strong><br> <em>Group
87 Editing Menu</em> <br />Options in this menu modify the name and
88 display properties of the currently selected group, or a new group
89 defined using the current selection.
91 <li><strong>Name: <Group></strong> or <strong>Edit
92 name and description</strong><br> <em>The first entry in the
93 menu displays the name for the currently selected group, if it
94 has one. Selecting this option opens a window allowing the name
95 and description for this group to be edited. Click OK to set the
96 new name and decription, and cancel to leave the existing name
97 and description unchanged.</em></li>
98 <li><strong>Group Colour<br>
99 </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
101 </em><strong> </strong></li>
102 <li><strong>Boxes<br>
103 </strong><em>If selected the background of a residue within the
104 selected group will be coloured according to the assigned colour
105 scheme.</em><strong> </strong></li>
107 </strong><em>If selected the selected group will display text. </em></li>
108 <li><strong>Colour Text<br>
109 </strong><em>If selected the selected group will display text in a
110 colour slightly darker than the background colour of that
112 <li><strong>Border Colour <br>
113 </strong><em>Selecting this will display a "Colour Chooser"
114 window. Select a colour than press OK to set the border colour
115 of a group.</em></li>
116 <li><strong>Show Unconserved<br>
117 </strong><em>When this is selected, all symbols in the group matching
118 the consensus sequence at that column will be rendered as a '.',
119 highlighting mutations in the group area. </em></li>
123 <li><strong>Sequence Id<br>
124 </strong><em>This menu is only visible if you right-click on a sequence
127 <li><a name="sqreport"><strong>Sequence Details
129 </strong></a><em>(Since Jalview 2.8)<br>Open an <a
130 href="../io/exportseqreport.html">HTML report containing the
131 annotation and database cross references</a> normally shown in the
134 <li><strong>Edit Name/Description<br>
135 </strong><em>You may edit the name and description of each sequence. A
136 window will be displayed asking for a new sequence name and
137 sequence description to be entered. Press OK to accept your edit.
138 To save sequence descriptions, you must save in Fasta, PIR or
139 Jalview File format.</em></li>
140 <li><a href="sqaddrefannot"><strong>Add Reference
142 </strong><em>When enabled, copies any available alignment annotation
143 for this sequence to the current view.</em></li>
144 <li><strong>Represent Group With (Sequence Id)</strong><br>
145 <em>All sequences in the current selection group will be
146 hidden, apart from (Sequence Id). Any edits performed on the
147 visible representative sequence will be propagated to the hidden
148 sequences. </em></li>
149 <li><a name="sqid.popup"><strong>Link</strong><br> <em>This
150 menu item lists all links which have been set up in the <a
151 href="../features/preferences.html">Preferences</a> Connections
152 tab.<br> Since Jalview 2.4, links will also be made for
153 database cross references (where the database name exactly
154 matches the link name set up in <a
155 href="../features/preferences.html">Preferences</a>). <br>Since
156 Jalview 2.5, links are also shown for non-positional sequence
157 features attached to the sequence, and any regular-expression
158 based URL links that matched the description line.
159 </em><strong><br> </strong></li>
161 <li><strong>View Structure</strong> </strong><em>This menu is only
162 visible if you right-click on a sequence name. If the
163 sequence has an associated PDB file(s), Jalview will open a 'Structure Chooser'
164 dialogue with options to select the structure which will eventually be opened in
165 a 3D interactive view.<br> These entries will only be present if the sequence
166 has <a href="../features/viewingpdbs.html">associated PDB
167 structures</a>.<br /> If the sequence or alignment has RNA structure,
168 then <strong>2D RNA</strong> entries will also be present enabling
169 you to open a linked view of the RNA structure in <a
170 href="../features/varna.html">VARNA</a>.
175 <em>Other menu entries may also be shown if the current
176 selection includes sequences with associated structure data:</em><br>
178 <li><strong>Associate Structure with Sequence</strong>
180 <li><strong>From File<br>
181 </strong><em>Load a PDB file from local disk which will be associated
182 with this sequence. This file will be used if the user subsequently
183 clicks on "View Structure" menu item.</em></li>
184 <li><strong>Enter PDB id<br>
185 </strong><em>Enter the PDB id from an input window. This PDB id will
186 be used by the service WSDBFetch, provided by the EBI, to fetch the
187 PDB file if the user subsequently clicks on its "View Structure"
188 menu item. </em></li>
189 <li><strong>Discover PDB ids<br>
190 </strong><em>This will use the service WSDBFetch, provided by the
191 EBI, to retrieve all PDB ids associated with the sequences in the
192 alignment if the sequences have valid Uniprot names or accession ids.
198 <li><strong>Structure→View all <em>N</em>
200 </strong><em>Opens a new window containing all structures associated
201 with the current selection, superposed according to the currently
202 selected region of the alignment.<br />(This capability was
203 added in Jalview 2.7)
205 <li><strong>Structure→View all <em>N</em>
206 representative structures<br />
207 </strong><em>Open a new window containing exactly one structure per
208 currently selected sequence.<br /> (The View representative
209 structures option was introduced in Jalview 2.8.1)
214 <li><strong>Hide Sequences</strong><br> <em>Hides the
215 currently selected sequences in this alignment view.</em><strong><br>