2 <head><title>Key Strokes</title></head>
4 <p><strong>Key Strokes</strong></p>
6 Jalview has two distinct modes of keyboard operation - in 'Normal'
7 mode, single keystrokes (including those shown next to menu items)
8 provide short cuts to common commands. In <a
9 href="features/cursorMode.html">'Cursor'</a> mode (enabled by
10 <em>F2</em>), some of these are disabled and more complex 'Compound
11 Keystrokes' can be entered to perform precise navigation, selection
12 and editing operations.
16 <td><strong>Key</strong></td>
17 <td><strong>Which Mode</strong></td>
18 <td><strong>Action</strong></td>
21 <td><strong>Escape</strong></td><td>Both</td>
22 <td>The Panic button.</td></tr>
24 <tr><td><strong> Escape</strong></td>
26 <td>Clears the current selection region, highlighted columns and highlghted
30 <td><strong>Escape</strong></td>
32 <td>As in normal mode, but also cancels any partially entered commands</td></tr>
34 <td><strong><em>F1</em></strong></td>
36 <td>Show Help Documentation</td></tr>
38 <td><strong><em>F2</em></strong></td>
40 <td>Toggle Cursor mode on / off</td>
43 <td><strong>Control 'Z'</strong></td>
45 <td>Undoes the last sequence edit</td>
48 <td><strong>Control 'Y'</strong></td>
50 <td>Redo the last sequence edit undone.</td>
53 <td><strong>Up Arrow</strong></td>
55 <td>Moves selected sequence(s) up the alignment</td></tr>
57 <td><strong>Down Arrow</strong></td>
59 <td>Moves selected sequence(s) down the alignment.</td></tr>
60 <tr><td><strong>Cursor Keys<br>
61 (Arrow Keys)</strong></td>
63 <td>Move cursor around alignment</td>
65 <tr><td><strong>Page Up</strong></td><td>Both</td><td>Scroll up the alignment view</td></tr>
66 <tr><td><strong>Page Down</strong></td><td>Both</td><td>Scroll down the alignment view</td></tr>
68 <td><strong>Control 'A'</strong></td>
70 <td>Selects all sequences in the alignment</td>
73 <td><strong>Control 'I'</strong></td>
76 <td>Invert sequence selection.
80 <td><strong>Control Alt 'I'</strong></td>
83 <td>Invert column selection.
87 <td><strong>Control 'C'</strong></td>
89 <td>Copies the selected region into the clipboard as a Fasta format file<br>
90 <em>nb. not available in applet, as no clipboard is available</em></td>
93 <td><strong>Control 'V'</strong></td>
96 Paste the contents of the clipboard to the current alignment
97 window. (Alignment Window->Edit->Paste->Add to this Alignment)<br>
98 <em>nb. if the paste is from a Jalview alignment, any sequence and alignment
99 annotations will also be copied over.</em></td></tr>
101 <td><strong>Control Shift 'V'</strong></td>
103 <td>Paste the contents of the clipboard to a new alignment
104 window. (Alignment Window->Edit->Paste->To New Alignment)</td>
107 <td><strong>Control 'X'</strong></td>
109 <td>Cuts the (fully) selected sequences from the alignment.
110 <!-- not yet in this version
111 This will not happen if only some
112 columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->
116 <td><strong>Control 'F'</strong></td>
118 <td>Launches the search window</td>
121 <td><strong>H</strong></td>
123 <td>Hides / Reveals selected columns and sequences</td>
126 <td><strong>Control 'H'</strong></td>
128 <td>Hides / Reveals selected columns</td>
131 <td><strong>Shift 'H'</strong></td>
133 <td>Hides / Reveals selected sequences</td>
136 <td><strong>Control 'O'</strong></td>
138 <td>Input new alignment from file</td>
141 <td><strong>Control 'S'</strong></td>
143 <td>Save alignment with current filename and format</td>
146 <td><strong>Control Shift 'S'</strong></td>
148 <td>Save alignment as a new file or with a different format</td>
151 <td><strong>Control 'P'</strong></td>
153 <td>Opens the print dialog box to print the current view</td>
156 <td><strong>Control 'W'</strong></td>
158 <td>Closes the current view or the current alignment</td>
161 <td><strong>Backspace</strong></td>
163 <td>Delete the currently selected rows or columns from the alignment.</td>
166 <td><strong>Control 'L'</strong></td>
168 <td>Remove columns to left of left-most column marker.</td>
171 <td><strong>Control 'R'</strong></td>
173 <td>Remove columns to right of right-most column marker.</td>
176 <td><strong>Control 'E'</strong></td>
178 <td>Remove gapped columns</td>
181 <td><strong>Control Shift 'E'</strong></td>
183 <td>Remove all gaps</td>
186 <td><strong>Control 'D'</strong></td>
188 <td>Open the 'Remove redundancy' Dialog box.</td>
192 <td><strong></strong></td>
199 <p>The compound commands available in the Cursor mode are summarised
200 below. Single letter commands can be prefixed by digits to specify a repetition
201 number, and some more complex commands take one or more numeric
202 parameters (prefixing the command key and separated by commas).</p>
203 <table border=1><tr><td><strong>Compound
204 Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>
205 <tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a
206 numeric parameter (<strong><em>p</em></strong>) or repetition number for a cursor movement or edit
208 <tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or
209 more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>) for a command.</td></tr>
210 <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>
211 <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>
212 <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>
213 <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>
214 <tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>
215 <tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>
216 <tr><td><strong><em>[p]</em><br>Space</strong></td><td>Cursor</td><td>Inserts
217 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>
218 <tr><td><strong><em>[p]</em><br>Delete<br></strong></td><td>Cursor</td><td>Removes
219 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>
220 <tr><td><strong><em>[p]</em><br>Backspace<br></strong></td><td>Cursor</td><td>Removes
221 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>