Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwedit.html;h=eb8e839ba17675efe8de338244c6d15903b3ac8b;hb=16d109024847af92482237e43f99b82fd997451a;hp=fabfbc2d5c4680107245dac1ccf65fccd97ae5e1;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html index fabfbc2..eb8e839 100755 --- a/help/html/menus/alwedit.html +++ b/help/html/menus/alwedit.html @@ -1,101 +1,115 @@ + * 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 no empty columns before or after the first or last aligned - residue) and all sequences will be padded with gap characters to the - 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.

+ 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 right of the rightmost 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. +