Key Strokes
-Jalview responds a number of key strokes, and has two distinct modes of -keyboard operation. The F2 key switches between 'Normal' and -'Cursor' mode operation. +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 | -
| Up Arrow | Normal | Moves selected sequence(s) up the -alignment|
| Down Arrow | Normal | Moves selected sequence(s) down the -alignment.|
| Cursor | Move cursor around alignment | -|
| Control 'A' | Both | Selects all sequences in the alignment | -
| 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 | Pastes the contents of the clipboard -to a new - alignment window. (same as the Alignment Window menu Edit->Paste - command)|
| Control 'X' | Both | Cuts the (fully) selected -sequences from the alignment. | -
| Control 'F' | Both | Launches the search -window |
| 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 '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 @@ -69,18 +220,22 @@ 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 +numeric parameter (p) or repetition number for a cursor movement or edit command. |
| , | Cursor | Separates one or more numeric parameters ([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. |
| [p1]S | Cursor | Jump to the p1'th sequence in the alignment. |
| [p1]P | Cursor | Jump to p1'th amino acid in current sequence. |
| [p1]C | Cursor | Jump to p1'th column in the alignment. |
| , | 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 |
| [p1] Space | Cursor | Inserts p1 gaps at the current position. p1 is optional. Hold down Control or Shift to insert gaps over a sequence group |
| [p1] Delete | Cursor | Remove p1 gaps at the cursor position. p1 is optional. Hold down Control or Shift to insert gaps over a sequence group |