X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwedit.html;h=4e0c8b03b85e2076f48eed00692a9d1ec2c58a1d;hb=2802a0cc6cf1087c25db84c1005c786aa687c4bc;hp=dcd7d68e5d0c8bd9557a19f2fbb69d665b1d4d54;hpb=f902741a45fba3856958b893e37c74344d397a60;p=jalview.git diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html index dcd7d68..4e0c8b0 100755 --- a/help/html/menus/alwedit.html +++ b/help/html/menus/alwedit.html @@ -3,111 +3,90 @@

Alignment Window Edit Menu

+Edit

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. +

-
-
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. -
-
-