Alignment Window Edit Menu
Edit
- Undo
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
Any actions which you undo can be redone using redo.
- Cut
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
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 is a tab separated list
NAME START_RES END_RES SEQUENCE
- Paste
- To New Alignment
A new alignment window will be created from sequences previously
copied or cut to the system clipboard.
Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.
- Add To This Alignment
Copied sequences from another alignment window can be added
to the current Jalview alignment.
- Delete
This will delete the currently selected residues without copying
them to the clipboard. Like the other edit operations, this can be undone
with Undo.
- Select All
Selects all the sequences and residues in the alignment.
Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
- Deselect All
Removes the current selection box (red dashed box) from the alignment
window. All selected sequences, residues and marked columns will be deselected.
Use <ESCAPE> to deselect all.
- Invert Selection
Any sequence ids currently not selected will replace the current
selection.
- Undefine Groups
The alignment will be reset with no defined groups.
WARNING: This cannot be undone.
- Remove Left
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
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
All columns which only contain gap characters ("-",
".") will be deleted.
You may set the default gap character in preferences.
- Remove All Gaps
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
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
Adds gaps to the end of all the sequences so they are all the
same length. This is useful for making a tree using unaligned sequences.
You may set the default gap character in preferences.