3 <title>Alignment Window Menus</title>
7 <p><strong>Alignment Window Edit Menu</strong></p>
9 <li><strong>Undo (Control Z)</strong><em><br>
10 This will undo any edits you make to the alignment. This applies to
11 insertion or deletion of gaps, cutting residues or sequences from the
12 alignment or pasting sequences to the current alignment or sorting the
13 alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,
14 adjustments to group sizes, or changes to the annotation panel. </em></li>
15 <li><strong>Redo (Control Y)<br>
16 </strong><em>Any actions which you undo can be redone using redo. </em></li>
17 <li><strong>Cut (Control X)<br>
18 </strong><em>This will make a copy of the currently selected residues
19 before removing them from your alignment. Click on a sequence name if
20 you wish to select a whole sequence. <br>
21 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
22 <li><strong>Copy (Control C)</strong><br>
23 <em>Copies the currently selected residues to the system clipboard
24 - you can also do this by pressing <CTRL> and C (<APPLE>
25 and C on MacOSX). <br>
26 If you try to paste the clipboard contents to a text editor, you will
27 see the format of the copied residues FASTA.</em></li>
28 <li><strong>Paste </strong>
30 <li><strong>To New Alignment (Control Shift V)<br>
31 </strong><em>A new alignment window will be created from sequences
32 previously copied or cut to the system clipboard. <br>
33 Use <CTRL> and <SHIFT> and V(<APPLE> and
34 <SHIFT;> and and V on MacOSX) to paste.</em></li>
35 <li><strong>Add To This Alignment (Control V)<br>
36 </strong><em>Copied sequences from another alignment window can be added
37 to the current Jalview alignment. </em></li>
40 <li><strong>Delete (Backspace)<br>
41 </strong><em>This will delete the currently selected residues without
42 copying them to the clipboard. Like the other edit operations, this can
43 be undone with <strong>Undo</strong>.</em></li>
44 <li><strong>Remove Left (Control L)<br>
45 </strong><em>If the alignment has marked columns, the alignment will be
46 trimmed to the left of the leftmost marked column. To mark a column,
47 mouse click the scale bar above the alignment. Click again to unmark a
48 column, or select "Deselect All" to deselect all columns.</em></li>
49 <li><strong>Remove Right (Control R)<br>
50 </strong><em>If the alignment has marked columns, the alignment will be
51 trimmed to the left of the leftmost marked column. To mark a column,
52 mouse click the scale bar above the alignment. Click again to unmark a
53 column, or select "Deselect All" to deselect all columns.</em></li>
54 <li><strong>Remove Empty Columns (Control E)<br>
55 </strong><em>All columns which only contain gap characters ("-",
56 ".") will be deleted.<br>
57 You may set the default gap character in <a
58 href="../features/preferences.html">preferences</a>. </em></li>
59 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
60 <em>Gap characters ("-", ".") will be deleted
61 from the selected area of the alignment. If no selection is made, ALL
62 the gaps in the alignment will be removed.<br>
63 You may set the default gap character in <a
64 href="../features/preferences.html">preferences</a>. </em></li>
65 <li><strong>Remove Redundancy (Control D)<br>
66 </strong><em>Selecting this option brings up a window asking you to select
67 a threshold. If the percentage identity between any two sequences
68 (under the current alignment) exceeds this value then one of the
69 sequences (the shorter) is discarded. Press the "Apply"
70 button to remove redundant sequences. The "Undo" button will
71 undo the last redundancy deletion.</em></li>
72 <li><strong>Pad Gaps<br>
73 </strong><em>When selected, the alignment will be kept at minimal width (so
74 there no empty columns before or after the first or last aligned
75 residue) and all sequences will be padded with gap characters to the
76 before and after their terminating residues.<br>
77 This switch is useful when making a tree using unaligned sequences and
78 when working with alignment analysis programs which require 'properly
79 aligned sequences' to be all the same length.<br>
80 You may set the default for <strong>Pad Gaps</strong> in the <a
81 href="../features/preferences.html">preferences</a>. </em></li>