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>Key Strokes</title>
27 <strong>Key Strokes</strong>
30 Jalview has two distinct modes of keyboard operation - in 'Normal'
31 mode, single keystrokes (including those shown next to menu items)
32 provide short cuts to common commands. In <a
33 href="features/cursorMode.html">'Cursor'</a> mode (enabled by
34 <em>F2</em>), some of these are disabled and more complex 'Compound
35 Keystrokes' can be entered to perform precise navigation, selection
36 and editing operations.
40 <td><strong>Key</strong></td>
41 <td><strong>Which Mode</strong></td>
42 <td><strong>Action</strong></td>
45 <td><strong>Escape</strong></td><td>Both</td>
46 <td>The Panic button.</td></tr>
49 <td><strong> Escape</strong></td>
51 <td>Clears the current selection region, highlighted columns
52 and highlghted residues.</td>
55 <td><strong>Escape</strong></td>
57 <td>As in normal mode, but also cancels any partially entered
61 <td><strong><em>F1</em></strong></td>
63 <td>Show Help Documentation</td>
66 <td><strong><em>F2</em></strong></td>
68 <td>Toggle Cursor mode on / off</td>
71 <td><strong>Control 'Z'</strong></td>
73 <td>Undoes the last sequence edit</td>
76 <td><strong>Control 'Y'</strong></td>
78 <td>Redo the last sequence edit undone.</td>
81 <td><strong>Up Arrow</strong></td>
83 <td>Moves selected sequence(s) up the alignment.<br />In
84 Cursor mode press Alt key to move selection or sequence under
89 <td><strong>Down Arrow</strong></td>
91 <td>Moves selected sequence(s) down the alignment.<br />In
92 Cursor mode press Alt key to move selection or sequence under
97 <td><strong>Left Arrow</strong></td>
99 <td>Slides selected sequence(s) left. Press Alt key to slide
103 <td><strong>Right Arrow</strong></td>
105 <td>Slides selected sequence(s) right. Press Alt key to slide
109 <td><strong>Cursor Keys<br> (Arrow Keys)
112 <td>Move cursor around alignment.<br /> Press SHIFT to move
113 cursor from an aligned region to next gap, or to the next
114 aligned region when at a gap.
118 <td><strong>Page Up</strong></td>
120 <td>Scroll up the alignment view</td>
123 <td><strong>Page Down</strong></td>
125 <td>Scroll down the alignment view</td>
128 <td><strong>Control 'A'</strong></td>
130 <td>Selects all sequences in the alignment</td>
133 <td><strong>Control 'I'</strong></td>
135 <td>Invert sequence selection.</td>
138 <td><strong>Control Alt 'I'</strong></td>
140 <td>Invert column selection.</td>
143 <td><strong>Control 'C'</strong></td>
145 <td>Copies the selected region into the clipboard as a Fasta
146 format file<br> <em>nb. not available in applet, as no
147 clipboard is available</em>
151 <td><strong>Control 'V'</strong></td>
153 <td>Paste the contents of the clipboard to the current
154 alignment window. (Alignment Window->Edit->Paste->Add to this
155 Alignment)<br> <em>nb. if the paste is from a Jalview
156 alignment, any sequence and alignment annotations will also be
161 <td><strong>Control Shift 'V'</strong></td>
163 <td>Paste the contents of the clipboard to a new alignment
164 window. (Alignment Window->Edit->Paste->To New Alignment)</td>
167 <td><strong>Control 'X'</strong></td>
169 <td>Cuts the (fully) selected sequences from the alignment. <!-- not yet in this version
170 This will not happen if only some
171 columns are selected, you should use the <a href="features/hiddenRegions.html">Hide Regions feature</a> instead.-->
175 <td><strong>Control 'F'</strong></td>
177 <td>Launches the search window</td>
179 <tr><td><strong>B</strong></td>
181 <td>Add highlighted columns to current column selection</td>
183 <tr><td><strong>Alt 'B'</strong></td>
185 <td>Add all but the currently highlighted columns to current selection</td>
187 <tr><td><strong>Control 'B'</strong></td>
189 <td>Toggle the column selection marks for the currently highlighted
190 columns (or all others if Alt is also pressed)</td>
193 <td><strong>H</strong></td>
195 <td>Hides / Reveals selected columns and sequences</td>
198 <td><strong>Control 'H'</strong></td>
200 <td>Hides / Reveals selected columns</td>
203 <td><strong>Shift 'H'</strong></td>
205 <td>Hides / Reveals selected sequences</td>
208 <td><strong>Control + Shift 'H'</strong></td>
210 <td>Hides everything but the current selection</td>
213 <td><strong>Control 'O'</strong></td>
215 <td>Input new alignment from file</td>
218 <td><strong>Control 'S'</strong></td>
220 <td>Save alignment with current filename and format</td>
223 <td><strong>Control Shift 'S'</strong></td>
225 <td>Save alignment as a new file or with a different format</td>
228 <td><strong>Control 'P'</strong></td>
230 <td>Opens the print dialog box to print the current view</td>
233 <td><strong>Control 'W'</strong></td>
235 <td>Closes the current view or the current alignment</td>
238 <td><strong>Backspace</strong></td>
240 <td>Delete the currently selected rows or columns from the
244 <td><strong>Control 'L'</strong></td>
246 <td>Remove columns to left of left-most column marker.</td>
249 <td><strong>Control 'R'</strong></td>
251 <td>Remove columns to right of right-most column marker.</td>
254 <td><strong>Control 'E'</strong></td>
256 <td>Remove gapped columns</td>
259 <td><strong>Control Shift 'E'</strong></td>
261 <td>Remove all gaps</td>
264 <td><strong>Control 'D'</strong></td>
266 <td>Open the 'Remove redundancy' Dialog box.</td>
269 <td><strong></strong></td>
274 <p>The compound commands available in the Cursor mode are
275 summarised below. Single letter commands can be prefixed by digits
276 to specify a repetition number, and some more complex commands take
277 one or more numeric parameters (prefixing the command key and
278 separated by commas).</p>
281 <td><strong>Compound Command</strong></td>
283 <td>Action (and parameter description)</td>
286 <td><strong>0-9</strong></td>
288 <td>Begin entering a numeric parameter (<strong><em>p</em></strong>)
289 or repetition number for a cursor movement or edit command.
293 <td><strong>,</strong></td>
295 <td>Separates one or more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>)
300 <td><strong><strong><em>p1</em></strong>,<strong><em>p2</em></strong><br>Return</strong></td>
302 <td>Move cursor to a particular column (<strong><em>p1</em></strong>)
303 and row (<strong><em>p2</em></strong>) in the alignment.<br>
304 <em>e.g. '5,6<Return>' moves the cursor to the 5th
305 column in the 6th sequence.</em></td>
308 <td><strong><em>p</em>S</strong></td>
310 <td>Jump to the <strong><em>p</em></strong>'th sequence in
315 <td><strong><em>p</em>P</strong></td>
317 <td>Jump to <em><strong>p</strong></em>'th amino acid in
322 <td><strong><em>p</em>C</strong></td>
324 <td>Jump to <em><strong>p</strong></em>'th column in the
329 <td><strong>Q</strong></td>
331 <td>Marks the top left corner of the selection area</td>
334 <td><strong>M</strong></td>
336 <td>Marks the bottom right corner of the selection area</td>
339 <td><strong><em>[p]</em><br>Space</strong></td>
341 <td>Inserts one (or optionally <strong><em>p</em></strong>)
342 gaps at the current position.<br> <em>Hold down
343 Control or Shift to insert gaps over a sequence group</em></td>
346 <td><strong><em>[p]</em><br>Delete<br></strong></td>
348 <td>Removes one (or optionally <strong><em>p</em></strong>)
349 gaps at the cursor position.<br> <em>Hold down Control
350 or Shift to insert gaps over a sequence group</em></td>
353 <td><strong><em>[p]</em><br>Backspace<br></strong></td>
355 <td>Removes one (or optionally <strong><em>p</em></strong>)
356 gaps at the cursor position.<br> <em>Hold down Control
357 or Shift to insert gaps over a sequence group</em></td>