Editing
-There are two major ways to edit alignments - in 'Normal mode', -gaps are inserted and deleted at the mouse pointer in various ways by -clicking the left mouse button and pressing a combination of either -shift and control (or the apple key on Macs) and dragging the mouse. Pressing -F2 toggles the alternative 'Cursor -mode' keyboard editing facility, where the space bar and delete -keys add and remove gaps at the current editing position. The key -strokes for both these modes are summarised in the keystrokes table.
-Tip: For large alignments, deselect "Calculate -> - Autocalculate Consensus" to prevent the alignment performing lengthy calculations - after every edit.
-Inserting / removing gaps - hold down the
- "Shift" key. Click on a residue with the mouse and drag it
- to the left or right to insert gaps and remove gaps.
- If the current selection is a group over all sequences in the
- alignment, or a group over some sequences or all columns in the
- alignment, then hold down either "Control"
- key and drag the residue left or right to edit all sequences in the defined
- group at once.
Copy/paste/cut/delete - any sequences which are in the current selection - box (indicated in red) may be cut and / or copied to a new alignment or deleted. -
-Undo / redo - editing of sequences (insertion/removal of gaps, removal - of sequences, trimming sequences etc) may be undone or redone at any time using - the appropriate menu items from the edit menu. The undo history list only allows - a maximum of 10 actions. -
Trimming alignment - First select a column by clicking the scale indicator - (above the sequences) The alignment may then be trimmed to the left or right - of this column. If multiple columns are selected, the alignment is trimmed to - the right of the rightmost selected column (or to the left of the leftmost selected - column)
-Remove gapped columns - Removes columns within the alignment which - contain only space characters ("-" or "." or " ")
-Removing gaps - Removes all gaps from the alignment. Gaps are "-" - or "." or " ".
-Set gap character - Switches the gap character between "." - and "-". If the "Render Gaps" option from the "View" - menu is unticked all gaps will appear as blank spaces.
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Editing In Selection Areas
-Editing can be restricted to the current selection area. -This allows the user to "Lock" the alignment either side of the selection -area. Any gap insertions or deletions will only affect the current selection area. -
In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, - the same number of gaps will be inserted at position 116, (between M and L). -
-Locked selection area based editing was introduced in Jalview 2.08
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