Alignment Window Menus

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwedit.html;h=334706a782b6199f81faf0531169756d88324a3b;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=4e0c8b03b85e2076f48eed00692a9d1ec2c58a1d;hpb=ac5cc638b08386985f91503c81b27263230046e3;p=jalview.git diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html index 4e0c8b0..334706a 100755 --- a/help/html/menus/alwedit.html +++ b/help/html/menus/alwedit.html @@ -1,92 +1,117 @@ - -Alignment Window Menus - - -

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. -

- - + + + +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. +

+ +