-<html>\r
-<head><title>Key Strokes</title></head>\r
-<body>\r
-<p><strong>Key Strokes</strong></p>\r
-<p>\r
-Jalview responds a number of key strokes, and has two distinct modes of\r
-keyboard operation. The <em>F2</em> key switches between 'Normal' and\r
-<a href="features/cursorMode.html">'Cursor'</a> mode operation.\r
-</p>\r
-<table border="1">\r
-<tr>\r
-<td><strong>Key</strong></td><td><strong>Which Mode</strong></td><td><strong>Action</strong></td>\r
-</tr>\r
-<!--<tr>\r
-<td><strong>Escape</strong></td><td>Both</td>\r
-<td>The Panic button.</td></tr>\r
-<tr> -->\r
-<td><strong>\r
-Escape</strong></td><td>Normal</td>\r
-<td>Clears the current selection region,\r
-highlighted columns and highlghted residues.\r
-</td></tr><tr>\r
-<td><strong>Escape</strong></td><td>Cursor</td>\r
-As in normal mode, but also cancels any partially entered commands</td>\r
-</tr>\r
-<tr>\r
-<td><strong><em>F1</em></strong></td><td>Both</td>Show Help Documentation</td></tr>\r
-<tr>\r
-<td><strong><em>F2</em></strong></td><td></td><td>Toggle Cursor mode on / off</td>\r
-</tr>\r
-<tr>\r
-<td><strong>Control 'Z'</strong></td><td>Both</td><td>Undoes the last sequence edit</td>\r
-</tr>\r
-<tr>\r
-<td><strong>Up Arrow</strong></td><td>Normal</td>Moves selected sequence(s) up the\r
-alignment</td></tr>\r
-<tr>\r
-<td><strong>Down Arrow</strong></td><td>Normal</td>Moves selected sequence(s) down the\r
-alignment.</td></tr>\r
-<tr><strong>Cursor Keys<br>(Arrow Keys)</strong></td><td>Cursor</td><td>Move cursor around alignment</td>\r
-</tr>\r
-<tr>\r
-<td><strong>Control 'A'</strong></td><td>Both</td><td>Selects all sequences in the alignment</td>\r
-</tr>\r
-<tr>\r
-<td><strong>Control 'C'</strong></td><td>Both</td><td>Copies the selected region into\r
-the clipboard as a Fasta format file<br><em>nb. not available in applet, as no clipboard is available</em></td>\r
-</tr>\r
-<tr><td><strong>Control 'V'</strong></td><td>Both</td>Pastes the contents of the clipboard\r
-to a new \r
- alignment window. (same as the Alignment Window menu Edit->Paste\r
- command)<br><em>nb. if the paste is from a Jalview alignment, any\r
- sequence and alignment annotations will also be copied over.</em></td>\r
-</tr>\r
-<tr>\r
-<td><strong>Control 'X'</strong></td><td>Both</td><td>Cuts the (fully) selected\r
-sequences from the alignment.<!-- not yet in this version \r
-This will not happen if only some\r
-columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.--></td>\r
-</tr>\r
-<tr>\r
-<td><strong>Control 'F'</strong></td><td>Both</td><td>Launches the search\r
-window</td></tr>\r
-<tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a numeric parameter [p] for a cursor movement or edit command</td></tr>\r
-<tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or more numeric parameters ([p1],[p2]) for a command.</td></tr>\r
-<tr><td><strong>[p1],[p2]Return</strong></td><td>Cursor</td><td>Move cursor to a particular column (p1) and row (p2) in the alignment.<br><em>e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.</em></td></tr>\r
-<tr><td><strong>[p1]S</strong></td><td>Cursor</td><td>Jump to the p1'th sequence in the alignment.</td></tr>\r
-<tr><td><strong>[p1]P</strong></td><td>Cursor</td><td>Jump to p1'th amino acid in current sequence.</td></tr>\r
-<tr><td><strong>[p1]C</strong></td><td>Cursor</td><td>Jump to p1'th column in the alignment.</td></tr>\r
-<tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>\r
-<tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>\r
-<tr><td><strong>[p1]Space</strong></td><td>Cursor</td><td>Inserts p1 gaps at the current position.<br><em>p1 is optional. Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
-<tr><td><strong>[p1]Delete</strong></td><td>Cursor</td><td>Remove p1 gaps at the cursor position.<br><em>p1 is optional. Hold down Control or Shift to insert gaps over a sequence group</em></td></tr>\r
-</table>\r
-<p> </p>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head><title>Key Strokes</title></head>
+<body>
+<p><strong>Key Strokes</strong></p>
+<p>
+Jalview has two distinct modes of keyboard operation - in 'Normal'
+ mode, single keystrokes (including those shown next to menu items)
+ provide short cuts to common commands. In <a
+ href="features/cursorMode.html">'Cursor'</a> mode (enabled by
+ <em>F2</em>), some of these are disabled and more complex 'Compound
+ Keystrokes' can be entered to perform precise navigation, selection
+ and editing operations.
+</p>
+<table border="1">
+ <tr>
+ <td><strong>Key</strong></td>
+ <td><strong>Which Mode</strong></td>
+ <td><strong>Action</strong></td>
+ </tr>
+ <!--<tr>
+<td><strong>Escape</strong></td><td>Both</td>
+<td>The Panic button.</td></tr>
+<tr> -->
+ <tr>
+ <td><strong> Escape</strong></td>
+ <td>Normal</td>
+ <td>Clears the current selection region, highlighted columns and highlghted
+ residues. </td>
+ </tr>
+ <tr>
+ <td><strong>Escape</strong></td>
+ <td>Cursor</td>
+ <td>As in normal mode, but also cancels any partially entered commands</td>
+ </tr>
+ <tr>
+ <td><strong><em>F1</em></strong></td>
+ <td>Both</td>
+ <td>Show Help Documentation</td>
+ </tr>
+ <tr>
+ <td><strong><em>F2</em></strong></td>
+ <td></td>
+ <td>Toggle Cursor mode on / off</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'Z'</strong></td>
+ <td>Both</td>
+ <td>Undoes the last sequence edit</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'Y'</strong></td>
+ <td>Both</td>
+ <td>Redo the last sequence edit undone.</td>
+ </tr>
+ <tr>
+ <td><strong>Up Arrow</strong></td>
+ <td>Normal</td>
+ <td>Moves selected sequence(s) up the alignment</td>
+ </tr>
+ <tr>
+ <td><strong>Down Arrow</strong></td>
+ <td>Normal</td>
+ <td>Moves selected sequence(s) down the alignment.</td>
+ </tr>
+ <tr>
+ <td><strong>Left Arrow</strong></td>
+ <td>Normal </td>
+ <td>Slides selected sequence(s) left. Press Alt key to slide in cursor mode</td>
+ </tr>
+ <tr>
+ <td><strong>Right Arrow</strong></td>
+ <td>Normal</td>
+ <td>Slides selected sequence(s) right. Press Alt key to slide in cursor mode</td>
+ </tr>
+ <tr>
+ <td><strong>Cursor Keys<br>
+ (Arrow Keys)</strong></td>
+ <td>Cursor</td>
+ <td>Move cursor around alignment</td>
+ </tr>
+ <tr>
+ <td><strong>Page Up</strong></td>
+ <td>Both</td>
+ <td>Scroll up the alignment view</td>
+ </tr>
+ <tr>
+ <td><strong>Page Down</strong></td>
+ <td>Both</td>
+ <td>Scroll down the alignment view</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'A'</strong></td>
+ <td>Both</td>
+ <td>Selects all sequences in the alignment</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'I'</strong></td>
+ <td>Both </td>
+ <td>Invert sequence selection. </td>
+ </tr>
+ <tr>
+ <td><strong>Control Alt 'I'</strong></td>
+ <td>Both </td>
+ <td>Invert column selection. </td>
+ </tr>
+ <tr>
+ <td><strong>Control 'C'</strong></td>
+ <td>Both</td>
+ <td>Copies the selected region into the clipboard as a Fasta format file<br>
+ <em>nb. not available in applet, as no clipboard is available</em></td>
+ </tr>
+ <tr>
+ <td><strong>Control 'V'</strong></td>
+ <td>Both</td>
+ <td> Paste the contents of the clipboard to the current alignment window.
+ (Alignment Window->Edit->Paste->Add to this Alignment)<br> <em>nb. if the
+ paste is from a Jalview alignment, any sequence and alignment annotations
+ will also be copied over.</em></td>
+ </tr>
+ <tr>
+ <td><strong>Control Shift 'V'</strong></td>
+ <td>Both</td>
+ <td>Paste the contents of the clipboard to a new alignment window. (Alignment
+ Window->Edit->Paste->To New Alignment)</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'X'</strong></td>
+ <td>Both</td>
+ <td>Cuts the (fully) selected sequences from the alignment.
+ <!-- not yet in this version
+This will not happen if only some
+columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Control 'F'</strong></td>
+ <td>Both</td>
+ <td>Launches the search window</td>
+ </tr>
+ <tr>
+ <td><strong>H</strong></td>
+ <td>Both</td>
+ <td>Hides / Reveals selected columns and sequences</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'H'</strong></td>
+ <td>Both</td>
+ <td>Hides / Reveals selected columns</td>
+ </tr>
+ <tr>
+ <td><strong>Shift 'H'</strong></td>
+ <td>Both</td>
+ <td>Hides / Reveals selected sequences</td>
+ </tr>
+ <tr>
+ <td><strong>Control + Shift 'H'</strong></td>
+ <td>Both</td>
+ <td>Hides everything but the current selection</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'O'</strong></td>
+ <td>Both</td>
+ <td>Input new alignment from file</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'S'</strong></td>
+ <td>Both</td>
+ <td>Save alignment with current filename and format</td>
+ </tr>
+ <tr>
+ <td><strong>Control Shift 'S'</strong></td>
+ <td>Both</td>
+ <td>Save alignment as a new file or with a different format</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'P'</strong></td>
+ <td>Both</td>
+ <td>Opens the print dialog box to print the current view</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'W'</strong></td>
+ <td>Both</td>
+ <td>Closes the current view or the current alignment</td>
+ </tr>
+ <tr>
+ <td><strong>Backspace</strong></td>
+ <td>Normal</td>
+ <td>Delete the currently selected rows or columns from the alignment.</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'L'</strong></td>
+ <td>Left</td>
+ <td>Remove columns to left of left-most column marker.</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'R'</strong></td>
+ <td>Both</td>
+ <td>Remove columns to right of right-most column marker.</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'E'</strong></td>
+ <td>Both</td>
+ <td>Remove gapped columns</td>
+ </tr>
+ <tr>
+ <td><strong>Control Shift 'E'</strong></td>
+ <td>Both</td>
+ <td>Remove all gaps</td>
+ </tr>
+ <tr>
+ <td><strong>Control 'D'</strong></td>
+ <td>Both</td>
+ <td>Open the 'Remove redundancy' Dialog box.</td>
+ </tr>
+ <tr>
+ <td><strong></strong></td>
+ <td>Normal</td>
+ <td></td>
+ </tr>
+</table>
+<p>The compound commands available in the Cursor mode are summarised
+below. Single letter commands can be prefixed by digits to specify a repetition
+number, and some more complex commands take one or more numeric
+parameters (prefixing the command key and separated by commas).</p>
+<table border=1><tr><td><strong>Compound
+Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>
+<tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a
+numeric parameter (<strong><em>p</em></strong>) or repetition number for a cursor movement or edit
+command.</td></tr>
+<tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or
+more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>) for a command.</td></tr>
+<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>
+<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>
+<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>
+<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>
+<tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>
+<tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>
+<tr><td><strong><em>[p]</em><br>Space</strong></td><td>Cursor</td><td>Inserts
+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>
+<tr><td><strong><em>[p]</em><br>Delete<br></strong></td><td>Cursor</td><td>Removes
+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>
+<tr><td><strong><em>[p]</em><br>Backspace<br></strong></td><td>Cursor</td><td>Removes
+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>
+<p> </p>
+<p> </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff