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.
++
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
++ +