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2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 # This file is part of Jalview.
7 # Jalview is free software: you can redistribute it and/or
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11 # Jalview is distributed in the hope that it will be useful, but
12 # WITHOUT ANY WARRANTY; without even the implied warranty
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14 # PURPOSE. See the GNU General Public License for more details.
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20 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
21 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
23 * This file is part of Jalview.
25 * Jalview is free software: you can redistribute it and/or
26 * modify it under the terms of the GNU General Public License
27 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
29 * Jalview is distributed in the hope that it will be useful, but
30 * WITHOUT ANY WARRANTY; without even the implied warranty
31 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
32 * PURPOSE. See the GNU General Public License for more details.
34 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
37 <title>Alignment Window Menus</title>
41 <p><strong>Alignment Window Edit Menu</strong></p>
43 <li><strong>Undo (Control Z)</strong><em><br>
44 This will undo any edits you make to the alignment. This applies to
45 insertion or deletion of gaps, cutting residues or sequences from the
46 alignment or pasting sequences to the current alignment or sorting the
47 alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,
48 adjustments to group sizes, or changes to the annotation panel. </em></li>
49 <li><strong>Redo (Control Y)<br>
50 </strong><em>Any actions which you undo can be redone using redo. </em></li>
51 <li><strong>Cut (Control X)<br>
52 </strong><em>This will make a copy of the currently selected residues
53 before removing them from your alignment. Click on a sequence name if
54 you wish to select a whole sequence. <br>
55 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
56 <li><strong>Copy (Control C)</strong><br>
57 <em>Copies the currently selected residues to the system clipboard
58 - you can also do this by pressing <CTRL> and C (<APPLE>
59 and C on MacOSX). <br>
60 If you try to paste the clipboard contents to a text editor, you will
61 see the format of the copied residues FASTA.</em></li>
62 <li><strong>Paste </strong>
64 <li><strong>To New Alignment (Control Shift V)<br>
65 </strong><em>A new alignment window will be created from sequences
66 previously copied or cut to the system clipboard. <br>
67 Use <CTRL> and <SHIFT> and V(<APPLE> and
68 <SHIFT;> and and V on MacOSX) to paste.</em></li>
69 <li><strong>Add To This Alignment (Control V)<br>
70 </strong><em>Copied sequences from another alignment window can be added
71 to the current Jalview alignment. </em></li>
74 <li><strong>Delete (Backspace)<br>
75 </strong><em>This will delete the currently selected residues without
76 copying them to the clipboard. Like the other edit operations, this can
77 be undone with <strong>Undo</strong>.</em></li>
78 <li><strong>Remove Left (Control L)<br>
79 </strong><em>If the alignment has marked columns, the alignment will be
80 trimmed to the left of the leftmost marked column. To mark a column,
81 mouse click the scale bar above the alignment. Click again to unmark a
82 column, or select "Deselect All" to deselect all columns.</em></li>
83 <li><strong>Remove Right (Control R)<br>
84 </strong><em>If the alignment has marked columns, the alignment will be
85 trimmed to the left of the leftmost marked column. To mark a column,
86 mouse click the scale bar above the alignment. Click again to unmark a
87 column, or select "Deselect All" to deselect all columns.</em></li>
88 <li><strong>Remove Empty Columns (Control E)<br>
89 </strong><em>All columns which only contain gap characters ("-",
90 ".") will be deleted.<br>
91 You may set the default gap character in <a
92 href="../features/preferences.html">preferences</a>. </em></li>
93 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
94 <em>Gap characters ("-", ".") will be deleted
95 from the selected area of the alignment. If no selection is made, ALL
96 the gaps in the alignment will be removed.<br>
97 You may set the default gap character in <a
98 href="../features/preferences.html">preferences</a>. </em></li>
99 <li><strong>Remove Redundancy (Control D)<br>
100 </strong><em>Selecting this option brings up a window asking you to select
101 a threshold. If the percentage identity between any two sequences
102 (under the current alignment) exceeds this value then one of the
103 sequences (the shorter) is discarded. Press the "Apply"
104 button to remove redundant sequences. The "Undo" button will
105 undo the last redundancy deletion.</em></li>
106 <li><strong>Pad Gaps<br>
107 </strong><em>When selected, the alignment will be kept at minimal width (so
108 there no empty columns before or after the first or last aligned
109 residue) and all sequences will be padded with gap characters to the
110 before and after their terminating residues.<br>
111 This switch is useful when making a tree using unaligned sequences and
112 when working with alignment analysis programs which require 'properly
113 aligned sequences' to be all the same length.<br>
114 You may set the default for <strong>Pad Gaps</strong> in the <a
115 href="../features/preferences.html">preferences</a>. </em></li>