X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwedit.html;h=eb8e839ba17675efe8de338244c6d15903b3ac8b;hb=9e66ffdd391a2467fd6821abf9f8f0ca66e5a18d;hp=432cfcb9051504a18973df3766f0a4417867c250;hpb=cd17a7112faa46e4e9fbfbcfc785a549f3baa107;p=jalview.git
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-
-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 FASTA.
- - 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 Sequence Selection
- Any sequence ids currently not selected will replace the current
- selection.
- - Invert Column Selection
- Any columns currently not selected will replace the current column
- 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
- 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 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 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.
+
+
+
+