+ Editing
-Inserting / removing gaps - hold down the "Shift" key. Click
- a residue with the mouse and drag the residue to the right to insert gaps or
- to the left to remove gaps.
- If the residue selected is within a defined group, hold down either "Alt"
- or "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 +
++ 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 alt, option or 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 (or the "Alt;" on OSX if
+ "Control" does not work) 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 +
++ +