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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+Alignment Window Menus
+
+
+
+Alignment Window Edit Menu
+
+ - Undo (Control Z)
+ This will undo any edits you make to the alignment. This applies to
+ insertion or deletion of gaps, cutting residues or sequences from the
+ alignment or pasting sequences to the current alignment or sorting the
+ alignment. NOTE: It DOES NOT undo colour changes,
+ adjustments to group sizes, or changes to the annotation panel.
+ - Redo (Control Y)
+ Any actions which you undo can be redone using redo.
+ - Cut (Control X)
+ This will make a copy of the currently selected residues
+ before removing them from your alignment. Click on a sequence name if
+ you wish to select a whole sequence.
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.
+ - Copy (Control C)
+ Copies the currently selected residues to the system clipboard
+ - you can also do this by pressing <CTRL> and C (<APPLE>
+ and C on MacOSX).
+ If you try to paste the clipboard contents to a text editor, you will
+ see the format of the copied residues FASTA.
+ - Paste
+
+ - To New Alignment (Control Shift V)
+ A new alignment window will be created from sequences
+ previously copied or cut to the system clipboard.
+ Use <CTRL> and <SHIFT> and V(<APPLE> and
+ <SHIFT;> and and V on MacOSX) to paste.
+ - Add To This Alignment (Control V)
+ Copied sequences from another alignment window can be added
+ to the current Jalview alignment.
+
+
+ - Delete (Backspace)
+ This will delete the currently selected residues without
+ copying them to the clipboard. Like the other edit operations, this can
+ be undone with Undo.
+ - Remove Left (Control L)
+ If the alignment has marked columns, the alignment will be
+ trimmed to the left of the leftmost marked column. To mark a column,
+ mouse click the scale bar above the alignment. Click again to unmark a
+ column, or select "Deselect All" to deselect all columns.
+ - Remove Right (Control R)
+ If the alignment has marked columns, the alignment will be
+ trimmed to the left of the leftmost marked column. To mark a column,
+ mouse click the scale bar above the alignment. Click again to unmark a
+ column, or select "Deselect All" to deselect all columns.
+ - Remove Empty Columns (Control E)
+ All columns which only contain gap characters ("-",
+ ".") will be deleted.
+ You may set the default gap character in preferences.
+ - Remove All Gaps (Control Shift E)
+ Gap characters ("-", ".") will be deleted
+ from the selected area of the alignment. If no selection is made, ALL
+ the gaps in the alignment will be removed.
+ You may set the default gap character in preferences.
+ - Remove Redundancy (Control D)
+ Selecting this option brings up a window asking you to select
+ a threshold. If the percentage identity between any two sequences
+ (under the current alignment) exceeds this value then one of the
+ sequences (the shorter) is discarded. Press the "Apply"
+ button to remove redundant sequences. The "Undo" button will
+ undo the last redundancy deletion.
+ - Pad Gaps
+ When selected, the alignment will be kept at minimal width (so
+ there are no empty columns before or after the first or last aligned
+ residue) and all sequences will be padded with gap characters
+ before and after their terminating residues.
+ This switch is useful when making a tree using unaligned sequences and
+ when working with alignment analysis programs which require 'properly
+ aligned sequences' to be all the same length.
+ You may set the default for Pad Gaps in the preferences.
+
+
+