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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9 * modify it under the terms of the GNU General Public License
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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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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 when
29 right clicking either within a selected region on the alignment or
30 on a selected sequence name. It may not be accessible when in
31 'Cursor Mode' (toggled with the F2 key).</em><br /> <em><strong>Mac Users:</strong> pressing CTRL whilst clicking
32 the mouse/track pad is the same as a right-click. See your
33 system's settings to configure your track-pad's corners to
34 generate right-clicks.</em>
37 <li><strong>Selection</strong>
39 <li><a name="sqreport"><strong>Sequence
41 </strong></a><em>(Since Jalview 2.8)<br>Open an <a
42 href="../io/exportseqreport.html"
43 >HTML report containing the annotation and database cross
44 references</a> normally shown in the sequence's tooltip.
46 <li><strong>Show Annotations...<br>
47 </strong><em>Choose to show (unhide) either All or a selected type
48 of annotation for the selected sequences. (Since Jalview
50 <li><strong>Hide Annotations...<br>
51 </strong><em>Choose to hide either All or a selected type of
52 annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
53 <li><a name="addrefannot"><strong>Add
54 Reference Annotations<br>
55 </strong><em>Add to the alignment window any annotations on the
56 selected sequences which have been read from reference
57 sources or calculated (for example, secondary structure
58 derived from 3D structure). (Since Jalview 2.8.2)</em></li>
59 <li><strong>Edit </strong>
61 <li><strong>Copy</strong><br> <em>Copies the
62 selected region. In the applet version, the copied
63 sequences are not available to the system clipboard.</em></li>
65 </strong><em>Cuts the selected region from the alignment. In the
66 applet version, the copied sequences are not available
67 to the system clipboard.</em></li>
68 <li><strong>Edit Sequence</strong><br> <em>Edit
69 the selected sequence(s) directly. Spaces will be
70 converted to the current gap character.</em></li>
71 <li><strong>To Upper Case</strong><em><strong><br>
72 </strong><em>Changes the case of selected region to lower
74 <li><strong>To Lower Case<br>
75 </strong><em>Changes the case of selected region to upper case.</em><strong>
77 <li><strong>Toggle Case</strong><br> <em>Switches
78 the case of all residues within the selected region.</em></li>
80 <li><strong>Output to Textbox<br>
81 </strong><em>The selection area will be output to a a text window in
82 the selected alignment format. </em></li>
84 href="../features/creatinFeatures.html"
85 >Create Sequence Feature...</a></strong><br> <em>Opens the
86 dialog box for creating sequence features over the currently
87 selected region on each selected sequence.</em></li>
88 <li><strong>Create Group<br>
89 </strong><em>This will define a new group from the current
90 selection.</em><strong> </strong></li>
91 <li><strong>Remove Group<br>
92 </strong><em>This will undefine the selected group. </em><strong>
94 <li><strong>Edit (New) Group</strong><br> <em>Group
95 Editing Menu</em> <br />Options in this menu modify the name and
96 display properties of the currently selected group, or a new
97 group defined using the current selection.
99 <li><strong>Name: <Group></strong> or <strong>Edit
100 name and description</strong><br> <em>The first entry
101 in the menu displays the name for the currently selected
102 group, if it has one. Selecting this option opens a
103 window allowing the name and description for this group
104 to be edited. Click OK to set the new name and
105 decription, and cancel to leave the existing name and
106 description unchanged.</em></li>
107 <li><strong>Group Colour<br>
108 </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
110 </em><strong> </strong></li>
111 <li><strong>Boxes<br>
112 </strong><em>If selected the background of a residue within the
113 selected group will be coloured according to the
114 assigned colour scheme.</em><strong> </strong></li>
116 </strong><em>If selected the selected group will display text. </em></li>
117 <li><strong>Colour Text<br>
118 </strong><em>If selected the selected group will display text in
119 a colour slightly darker than the background colour of
120 that residue.</em></li>
121 <li><strong>Border Colour <br>
122 </strong><em>Selecting this will display a "Colour
123 Chooser" window. Select a colour than press OK to
124 set the border colour of a group.</em></li>
125 <li><strong>Show Unconserved<br>
126 </strong><em>When this is selected, all symbols in the group
127 matching the consensus sequence at that column will be
128 rendered as a '.', highlighting mutations in the group
133 <li><strong>Sequence Id<br>
134 </strong><em>This menu is only visible if you right-click on a sequence
137 <li><a name="sqreport"><strong>Sequence
139 </strong></a><em>(Since Jalview 2.8)<br>Open an <a
140 href="../io/exportseqreport.html"
141 >HTML report containing the annotation and database cross
142 references</a> normally shown in the sequence's tooltip.
144 <li><strong>Edit Name/Description<br>
145 </strong><em>You may edit the name and description of each sequence.
146 A window will be displayed asking for a new sequence name
147 and sequence description to be entered. Press OK to accept
148 your edit. To save sequence descriptions, you must save in
149 Fasta, PIR or Jalview File format.</em></li>
150 <li><strong>Add <a href="../features/annotation.html#seqannots">Reference Annotations</a></strong><br>
151 <em>When enabled, copies any available alignment
152 annotation for this sequence to the current view.</em></li>
153 <li><strong>Set as Reference</strong> or <strong>Unmark
154 as Reference</strong><br /> Sets or unsets the reference sequence for
155 the the alignment.</li>
157 <li><strong>Represent Group With (Sequence Id)</strong><br>
158 <em>All sequences in the current selection group will be
159 hidden, apart from (Sequence Id). Any edits performed on the
160 visible representative sequence will be propagated to the
161 hidden sequences. </em></li>
162 <li><a name="sqid.popup"><strong>Link</strong><br>
163 <em>This menu item lists all links which have been set
164 up in the <a href="../features/preferences.html">Preferences</a>
165 Connections tab.<br> Since Jalview 2.4, links will
166 also be made for database cross references (where the
167 database name exactly matches the link name set up in <a
168 href="../features/preferences.html"
169 >Preferences</a>). <br>Since Jalview 2.5, links are also
170 shown for non-positional sequence features attached to the
171 sequence, and any regular-expression based URL links that
172 matched the description line.
173 </em><strong><br> </strong></li>
175 <li><strong>3D Structure Data...</strong> </strong><em>This menu is
176 visible when you right-click on a sequence name. When this
177 option is clicked, Jalview will open the <a
178 href="../features/structurechooser.html">'Structure
179 Chooser' </a>, which allows you to discover and view 3D structures
180 for the current selection. For more info, see <a
181 href="../features/viewingpdbs.html">viewing PDB structures</a>.
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>