3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
4 * Copyright (C) 2014 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 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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 <head><title>Key Strokes</title></head>
22 <p><strong>Key Strokes</strong></p>
24 Jalview has two distinct modes of keyboard operation - in 'Normal'
25 mode, single keystrokes (including those shown next to menu items)
26 provide short cuts to common commands. In <a
27 href="features/cursorMode.html">'Cursor'</a> mode (enabled by
28 <em>F2</em>), some of these are disabled and more complex 'Compound
29 Keystrokes' can be entered to perform precise navigation, selection
30 and editing operations.
34 <td><strong>Key</strong></td>
35 <td><strong>Which Mode</strong></td>
36 <td><strong>Action</strong></td>
39 <td><strong>Escape</strong></td><td>Both</td>
40 <td>The Panic button.</td></tr>
43 <td><strong> Escape</strong></td>
45 <td>Clears the current selection region, highlighted columns and highlghted
49 <td><strong>Escape</strong></td>
51 <td>As in normal mode, but also cancels any partially entered commands</td>
54 <td><strong><em>F1</em></strong></td>
56 <td>Show Help Documentation</td>
59 <td><strong><em>F2</em></strong></td>
61 <td>Toggle Cursor mode on / off</td>
64 <td><strong>Control 'Z'</strong></td>
66 <td>Undoes the last sequence edit</td>
69 <td><strong>Control 'Y'</strong></td>
71 <td>Redo the last sequence edit undone.</td>
74 <td><strong>Up Arrow</strong></td>
76 <td>Moves selected sequence(s) up the alignment</td>
79 <td><strong>Down Arrow</strong></td>
81 <td>Moves selected sequence(s) down the alignment.</td>
84 <td><strong>Left Arrow</strong></td>
86 <td>Slides selected sequence(s) left. Press Alt key to slide in cursor mode</td>
89 <td><strong>Right Arrow</strong></td>
91 <td>Slides selected sequence(s) right. Press Alt key to slide in cursor mode</td>
94 <td><strong>Cursor Keys<br>
95 (Arrow Keys)</strong></td>
97 <td>Move cursor around alignment</td>
100 <td><strong>Page Up</strong></td>
102 <td>Scroll up the alignment view</td>
105 <td><strong>Page Down</strong></td>
107 <td>Scroll down the alignment view</td>
110 <td><strong>Control 'A'</strong></td>
112 <td>Selects all sequences in the alignment</td>
115 <td><strong>Control 'I'</strong></td>
117 <td>Invert sequence selection. </td>
120 <td><strong>Control Alt 'I'</strong></td>
122 <td>Invert column selection. </td>
125 <td><strong>Control 'C'</strong></td>
127 <td>Copies the selected region into the clipboard as a Fasta format file<br>
128 <em>nb. not available in applet, as no clipboard is available</em></td>
131 <td><strong>Control 'V'</strong></td>
133 <td> Paste the contents of the clipboard to the current alignment window.
134 (Alignment Window->Edit->Paste->Add to this Alignment)<br> <em>nb. if the
135 paste is from a Jalview alignment, any sequence and alignment annotations
136 will also be copied over.</em></td>
139 <td><strong>Control Shift 'V'</strong></td>
141 <td>Paste the contents of the clipboard to a new alignment window. (Alignment
142 Window->Edit->Paste->To New Alignment)</td>
145 <td><strong>Control 'X'</strong></td>
147 <td>Cuts the (fully) selected sequences from the alignment.
148 <!-- not yet in this version
149 This will not happen if only some
150 columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->
154 <td><strong>Control 'F'</strong></td>
156 <td>Launches the search window</td>
159 <td><strong>H</strong></td>
161 <td>Hides / Reveals selected columns and sequences</td>
164 <td><strong>Control 'H'</strong></td>
166 <td>Hides / Reveals selected columns</td>
169 <td><strong>Shift 'H'</strong></td>
171 <td>Hides / Reveals selected sequences</td>
174 <td><strong>Control + Shift 'H'</strong></td>
176 <td>Hides everything but the current selection</td>
179 <td><strong>Control 'O'</strong></td>
181 <td>Input new alignment from file</td>
184 <td><strong>Control 'S'</strong></td>
186 <td>Save alignment with current filename and format</td>
189 <td><strong>Control Shift 'S'</strong></td>
191 <td>Save alignment as a new file or with a different format</td>
194 <td><strong>Control 'P'</strong></td>
196 <td>Opens the print dialog box to print the current view</td>
199 <td><strong>Control 'W'</strong></td>
201 <td>Closes the current view or the current alignment</td>
204 <td><strong>Backspace</strong></td>
206 <td>Delete the currently selected rows or columns from the alignment.</td>
209 <td><strong>Control 'L'</strong></td>
211 <td>Remove columns to left of left-most column marker.</td>
214 <td><strong>Control 'R'</strong></td>
216 <td>Remove columns to right of right-most column marker.</td>
219 <td><strong>Control 'E'</strong></td>
221 <td>Remove gapped columns</td>
224 <td><strong>Control Shift 'E'</strong></td>
226 <td>Remove all gaps</td>
229 <td><strong>Control 'D'</strong></td>
231 <td>Open the 'Remove redundancy' Dialog box.</td>
234 <td><strong></strong></td>
239 <p>The compound commands available in the Cursor mode are summarised
240 below. Single letter commands can be prefixed by digits to specify a repetition
241 number, and some more complex commands take one or more numeric
242 parameters (prefixing the command key and separated by commas).</p>
243 <table border=1><tr><td><strong>Compound
244 Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>
245 <tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a
246 numeric parameter (<strong><em>p</em></strong>) or repetition number for a cursor movement or edit
248 <tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or
249 more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>) for a command.</td></tr>
250 <tr><td><strong><strong><em>p1</em></strong>,<strong><em>p2</em></strong><br>Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (<strong><em>p1</em></strong>) and row (<strong><em>p2</em></strong>) in the alignment.<br><em>e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>
251 <tr><td><strong><em>p</em>S</strong></td><td>Cursor</td><td>Jump to the <strong><em>p</em></strong>'th sequence in the alignment.</td></tr>
252 <tr><td><strong><em>p</em>P</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th amino acid in current sequence.</td></tr>
253 <tr><td><strong><em>p</em>C</strong></td><td>Cursor</td><td>Jump to <em><strong>p</strong></em>'th column in the alignment.</td></tr>
254 <tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>
255 <tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>
256 <tr><td><strong><em>[p]</em><br>Space</strong></td><td>Cursor</td><td>Inserts
257 one (or optionally <strong><em>p</em></strong>) gaps at the current position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>
258 <tr><td><strong><em>[p]</em><br>Delete<br></strong></td><td>Cursor</td><td>Removes
259 one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>
260 <tr><td><strong><em>[p]</em><br>Backspace<br></strong></td><td>Cursor</td><td>Removes
261 one (or optionally <strong><em>p</em></strong>) gaps at the cursor position.<br><em>Hold down Control or Shift to insert gaps over a sequence group</em></td></tr></table>