Key Strokes
-Jalview recognises the following keystrokes.
-Escape - Clears the current selection region, highlighted columns and highlghted - residues
-Control 'A' - Selects all sequences in the alignment.
-Control 'C' - Copies the selected region, in Fasta format (Not applet, as no - clipboard is available)
-Control 'V' - Pastes the selected file (Can be external to Jalview) to a new - alignment window.
-Control 'X' - Cuts the selected region from the alignment window.
-Control 'Z' - Undoes the last sequence edit.
-Control 'F' - Launches the search window.
-Up Arrow - Moves selected sequence(s) up the alignment
-Down Arrow - Moves selected sequence(s) down the alignment.
-F1 - Show Help Documentation
-F2 - Toggle Cursor mode on / off
-With Cursor mode on....
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- - + + + +
+ Key Strokes +
++ 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 'Cursor' mode (enabled by + F2), some of these are disabled and more complex 'Compound + Keystrokes' can be entered to perform precise navigation, selection + and editing operations. +
+| Key | +Which Mode | +Action | +
| Escape | +Normal | +Clears the current selection region, highlighted columns + and highlghted residues. | +
| Escape | +Cursor | +As in normal mode, but also cancels any partially entered + commands | +
| F1 | +Both | +Show Help Documentation | +
| F2 | ++ | Toggle Cursor mode on / off | +
| Control 'Z' | +Both | +Undoes the last sequence edit | +
| Control 'Y' | +Both | +Redo the last sequence edit undone. | +
| Up Arrow | +Normal | +Moves selected sequence(s) up the alignment | +
| Down Arrow | +Normal | +Moves selected sequence(s) down the alignment. | +
| Left Arrow | +Normal | +Slides selected sequence(s) left. Press Alt key to slide + in cursor mode | +
| Right Arrow | +Normal | +Slides selected sequence(s) right. Press Alt key to slide + in cursor mode | +
| Cursor Keys (Arrow Keys) + |
+ Cursor | +Move cursor around alignment | +
| Page Up | +Both | +Scroll up the alignment view | +
| Page Down | +Both | +Scroll down the alignment view | +
| Control 'A' | +Both | +Selects all sequences in the alignment | +
| Control 'I' | +Both | +Invert sequence selection. | +
| Control Alt 'I' | +Both | +Invert column selection. | +
| Control 'C' | +Both | +Copies the selected region into the clipboard as a Fasta
+ format file nb. not available in applet, as no + clipboard is available + |
+
| Control 'V' | +Both | +Paste the contents of the clipboard to the current
+ alignment window. (Alignment Window->Edit->Paste->Add to this
+ Alignment) nb. if the paste is from a Jalview + alignment, any sequence and alignment annotations will also be + copied over. + |
+
| Control Shift 'V' | +Both | +Paste the contents of the clipboard to a new alignment + window. (Alignment Window->Edit->Paste->To New Alignment) | +
| Control 'X' | +Both | +Cuts the (fully) selected sequences from the alignment. + | +
| Control 'F' | +Both | +Launches the search window | +
| H | +Both | +Hides / Reveals selected columns and sequences | +
| Control 'H' | +Both | +Hides / Reveals selected columns | +
| Shift 'H' | +Both | +Hides / Reveals selected sequences | +
| Control + Shift 'H' | +Both | +Hides everything but the current selection | +
| Control 'O' | +Both | +Input new alignment from file | +
| Control 'S' | +Both | +Save alignment with current filename and format | +
| Control Shift 'S' | +Both | +Save alignment as a new file or with a different format | +
| Control 'P' | +Both | +Opens the print dialog box to print the current view | +
| Control 'W' | +Both | +Closes the current view or the current alignment | +
| Backspace | +Normal | +Delete the currently selected rows or columns from the + alignment. | +
| Control 'L' | +Left | +Remove columns to left of left-most column marker. | +
| Control 'R' | +Both | +Remove columns to right of right-most column marker. | +
| Control 'E' | +Both | +Remove gapped columns | +
| Control Shift 'E' | +Both | +Remove all gaps | +
| Control 'D' | +Both | +Open the 'Remove redundancy' Dialog box. | +
| + | Normal | ++ |
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).
+| Compound Command | +Mode | +Action (and parameter description) | +
| 0-9 | +Cursor | +Begin entering a numeric parameter (p) + or repetition number for a cursor movement or edit command. + | +
| , | +Cursor | +Separates one or more numeric parameters (e.g. p1,p2) + for a command. + | +
| p1,p2 Return |
+ Cursor | +Move cursor to a particular column (p1)
+ and row (p2) in the alignment. + e.g. '5,6<Return>' moves the cursor to the 5th + column in the 6th sequence. |
+
| pS | +Cursor | +Jump to the p'th sequence in + the alignment. + | +
| pP | +Cursor | +Jump to p'th amino acid in + current sequence. + | +
| pC | +Cursor | +Jump to p'th column in the + alignment. + | +
| Q | +Cursor | +Marks the top left corner of the selection area | +
| M | +Cursor | +Marks the bottom right corner of the selection area | +
| [p] Space |
+ Cursor | +Inserts one (or optionally p)
+ gaps at the current position. Hold down + Control or Shift to insert gaps over a sequence group |
+
| [p] Delete |
+ Cursor | +Removes one (or optionally p)
+ gaps at the cursor position. Hold down Control + or Shift to insert gaps over a sequence group |
+
| [p] Backspace |
+ Cursor | +Removes one (or optionally p)
+ gaps at the cursor position. Hold down Control + or Shift to insert gaps over a sequence group |
+
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