Cursor Mode

Cursor mode is a new feature in Jalview 2.08, and allows more precise selection and editing of alignments through the use of the keyboard for both navigation and the input of editing and selection commands.

F2 Toggles between normal and cursor editing modes. When in cursor mode, a black cursor appears in the residue area of the alignment, and any mouse clicks on that area will move the cursor to that position (this means that the region selection menu is unavailable in cursor mode).

Navigation

- Cursor (Arrow) keys - Move cursor around the alignment.
  Shift+Cursor key - move to next gap or aligned residue

- S - Type a number x then press 'S' to jump to sequence x.

- C - Type a number x then press 'C' to jump to column x.

- P - Type a number x then press 'P' to jump to position x in current sequence.

- 65,82<return> - Quick jump to column 65, sequence 82

Defining Regions

- Q - Define the top left corner of the selection area

- M - Define the bottom right corner of the selection area

Editing The Alignment

- Space - Insert a gap at the cursor position.
  To insert 12 spaces at the current cursor, type 12 before pressing Space.
  To group insert, hold control or shift together with space.

- Delete (or backspace) - Delete a gap at the cursor position.
  To delete 12 spaces at the current cursor, type 12 before pressing Delete (or backspace).
  To group delete, hold down control or shift together with Delete (or backspace).

Some keyboard operations are not available in keyboard mode. See the full list of keystrokes.