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 |
-
+ + +
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 |
+
+