X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwedit.html;h=eb8e839ba17675efe8de338244c6d15903b3ac8b;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=dcd7d68e5d0c8bd9557a19f2fbb69d665b1d4d54;hpb=f902741a45fba3856958b893e37c74344d397a60;p=jalview.git diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html index dcd7d68..eb8e839 100755 --- a/help/html/menus/alwedit.html +++ b/help/html/menus/alwedit.html @@ -1,113 +1,115 @@ - -
Alignment Window Edit Menu
--- - + + + +-
-- 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
-
- All gap characters ("-", ".") will be deleted from - the alignment.
- 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. -
+ Alignment Window Edit Menu +
+