X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwedit.html;h=c187d93970d95e2ae11928637266d1b91cfcbf5b;hb=d423f22792e47dbc800ae220a58677f988971d06;hp=dcd7d68e5d0c8bd9557a19f2fbb69d665b1d4d54;hpb=f902741a45fba3856958b893e37c74344d397a60;p=jalview.git
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@@ -1,113 +1,101 @@
-
-Alignment Window Menus
-
-
-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 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.
+
+
+