2 <head><title>Key Strokes</title></head>
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4 <p><strong>Key Strokes</strong></p>
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6 Jalview has two distinct modes of keyboard operation - in 'Normal'
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7 mode, single keystrokes (including those shown next to menu items)
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8 provide short cuts to common commands. In <a
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9 href="features/cursorMode.html">'Cursor'</a> mode (enabled by
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10 <em>F2</em>), some of these are disabled and more complex 'Compound
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11 Keystrokes' can be entered to perform precise navigation, selection
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12 and editing operations.
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16 <td><strong>Key</strong></td>
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17 <td><strong>Which Mode</strong></td>
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18 <td><strong>Action</strong></td>
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21 <td><strong>Escape</strong></td><td>Both</td>
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22 <td>The Panic button.</td></tr>
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25 <td><strong> Escape</strong></td>
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27 <td>Clears the current selection region, highlighted columns and highlghted
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31 <td><strong>Escape</strong></td>
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33 <td>As in normal mode, but also cancels any partially entered commands</td>
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36 <td><strong><em>F1</em></strong></td>
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38 <td>Show Help Documentation</td>
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41 <td><strong><em>F2</em></strong></td>
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43 <td>Toggle Cursor mode on / off</td>
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46 <td><strong>Control 'Z'</strong></td>
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48 <td>Undoes the last sequence edit</td>
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51 <td><strong>Control 'Y'</strong></td>
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53 <td>Redo the last sequence edit undone.</td>
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56 <td><strong>Up Arrow</strong></td>
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58 <td>Moves selected sequence(s) up the alignment</td>
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61 <td><strong>Down Arrow</strong></td>
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63 <td>Moves selected sequence(s) down the alignment.</td>
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66 <td><strong>Left Arrow</strong></td>
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68 <td>Slides selected sequence(s) left. Press Alt key to slide in cursor mode</td>
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71 <td><strong>Right Arrow</strong></td>
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73 <td>Slides selected sequence(s) right. Press Alt key to slide in cursor mode</td>
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76 <td><strong>Cursor Keys<br>
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77 (Arrow Keys)</strong></td>
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79 <td>Move cursor around alignment</td>
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82 <td><strong>Page Up</strong></td>
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84 <td>Scroll up the alignment view</td>
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87 <td><strong>Page Down</strong></td>
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89 <td>Scroll down the alignment view</td>
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92 <td><strong>Control 'A'</strong></td>
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94 <td>Selects all sequences in the alignment</td>
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97 <td><strong>Control 'I'</strong></td>
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99 <td>Invert sequence selection. </td>
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102 <td><strong>Control Alt 'I'</strong></td>
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104 <td>Invert column selection. </td>
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107 <td><strong>Control 'C'</strong></td>
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109 <td>Copies the selected region into the clipboard as a Fasta format file<br>
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110 <em>nb. not available in applet, as no clipboard is available</em></td>
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113 <td><strong>Control 'V'</strong></td>
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115 <td> Paste the contents of the clipboard to the current alignment window.
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116 (Alignment Window->Edit->Paste->Add to this Alignment)<br> <em>nb. if the
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117 paste is from a Jalview alignment, any sequence and alignment annotations
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118 will also be copied over.</em></td>
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121 <td><strong>Control Shift 'V'</strong></td>
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123 <td>Paste the contents of the clipboard to a new alignment window. (Alignment
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124 Window->Edit->Paste->To New Alignment)</td>
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127 <td><strong>Control 'X'</strong></td>
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129 <td>Cuts the (fully) selected sequences from the alignment.
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130 <!-- not yet in this version
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131 This will not happen if only some
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132 columns are selected, you should use the <a href="features/regionHiding.html">Hide Regions feature</a> instead.-->
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136 <td><strong>Control 'F'</strong></td>
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138 <td>Launches the search window</td>
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141 <td><strong>H</strong></td>
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143 <td>Hides / Reveals selected columns and sequences</td>
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146 <td><strong>Control 'H'</strong></td>
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148 <td>Hides / Reveals selected columns</td>
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151 <td><strong>Shift 'H'</strong></td>
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153 <td>Hides / Reveals selected sequences</td>
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156 <td><strong>Control 'O'</strong></td>
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158 <td>Input new alignment from file</td>
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161 <td><strong>Control 'S'</strong></td>
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163 <td>Save alignment with current filename and format</td>
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166 <td><strong>Control Shift 'S'</strong></td>
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168 <td>Save alignment as a new file or with a different format</td>
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171 <td><strong>Control 'P'</strong></td>
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173 <td>Opens the print dialog box to print the current view</td>
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176 <td><strong>Control 'W'</strong></td>
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178 <td>Closes the current view or the current alignment</td>
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181 <td><strong>Backspace</strong></td>
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183 <td>Delete the currently selected rows or columns from the alignment.</td>
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186 <td><strong>Control 'L'</strong></td>
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188 <td>Remove columns to left of left-most column marker.</td>
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191 <td><strong>Control 'R'</strong></td>
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193 <td>Remove columns to right of right-most column marker.</td>
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196 <td><strong>Control 'E'</strong></td>
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198 <td>Remove gapped columns</td>
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201 <td><strong>Control Shift 'E'</strong></td>
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203 <td>Remove all gaps</td>
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206 <td><strong>Control 'D'</strong></td>
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208 <td>Open the 'Remove redundancy' Dialog box.</td>
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211 <td><strong></strong></td>
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216 <p>The compound commands available in the Cursor mode are summarised
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217 below. Single letter commands can be prefixed by digits to specify a repetition
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218 number, and some more complex commands take one or more numeric
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219 parameters (prefixing the command key and separated by commas).</p>
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220 <table border=1><tr><td><strong>Compound
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221 Command</strong></td><td>Mode</td><td>Action (and parameter description)</td></tr>
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222 <tr><td><strong>0-9</strong></td><td>Cursor</td><td>Begin entering a
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223 numeric parameter (<strong><em>p</em></strong>) or repetition number for a cursor movement or edit
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225 <tr><td><strong>,</strong></td><td>Cursor</td><td>Separates one or
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226 more numeric parameters (<em>e.g. <strong>p1</strong>,<strong>p2</strong></em>) for a command.</td></tr>
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227 <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>
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228 <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>
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229 <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>
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230 <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>
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231 <tr><td><strong>Q</strong></td><td>Cursor</td><td>Marks the top left corner of the selection area</td></tr>
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232 <tr><td><strong>M</strong></td><td>Cursor</td><td>Marks the bottom right corner of the selection area</td></tr>
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233 <tr><td><strong><em>[p]</em><br>Space</strong></td><td>Cursor</td><td>Inserts
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234 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>
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235 <tr><td><strong><em>[p]</em><br>Delete<br></strong></td><td>Cursor</td><td>Removes
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236 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>
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237 <tr><td><strong><em>[p]</em><br>Backspace<br></strong></td><td>Cursor</td><td>Removes
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238 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>
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