<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+<p><strong>Alignment Window Edit Menu</strong></p>
+<ul>
+ <li><strong>Undo (Control Z)</strong><em><br>
+ 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. <strong>NOTE:</strong> It DOES NOT undo colour changes,
+ adjustments to group sizes, or changes to the annotation panel. </em></li>
+ <li><strong>Redo (Control Y)<br>
+ </strong><em>Any actions which you undo can be redone using redo. </em></li>
+ <li><strong>Cut (Control X)<br>
+ </strong><em>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. <br>
+ Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
+ <li><strong>Copy (Control C)</strong><br>
+ <em>Copies the currently selected residues to the system clipboard
+ - you can also do this by pressing <CTRL> and C (<APPLE>
+ and C on MacOSX). <br>
+ If you try to paste the clipboard contents to a text editor, you will
+ see the format of the copied residues FASTA.</em></li>
+ <li><strong>Paste </strong>
+ <ul>
+ <li><strong>To New Alignment (Control Shift V)<br>
+ </strong><em>A new alignment window will be created from sequences
+ previously copied or cut to the system clipboard. <br>
+ Use <CTRL> and <SHIFT> and V(<APPLE> and
+ <SHIFT;> and and V on MacOSX) to paste.</em></li>
+ <li><strong>Add To This Alignment (Control V)<br>
+ </strong><em>Copied sequences from another alignment window can be added
+ to the current Jalview alignment. </em></li>
+ </ul>
+ </li>
+ <li><strong>Delete (Backspace)<br>
+ </strong><em>This will delete the currently selected residues without
+ copying them to the clipboard. Like the other edit operations, this can
+ be undone with <strong>Undo</strong>.</em></li>
+ <li><strong>Remove Left (Control L)<br>
+ </strong><em>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.</em></li>
+ <li><strong>Remove Right (Control R)<br>
+ </strong><em>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.</em></li>
+ <li><strong>Remove Empty Columns (Control E)<br>
+ </strong><em>All columns which only contain gap characters ("-",
+ ".") will be deleted.<br>
+ You may set the default gap character in <a
+ href="../features/preferences.html">preferences</a>. </em></li>
+ <li><strong>Remove All Gaps (Control Shift E)</strong><br>
+ <em>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.<br>
+ You may set the default gap character in <a
+ href="../features/preferences.html">preferences</a>. </em></li>
+ <li><strong>Remove Redundancy (Control D)<br>
+ </strong><em>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.</em></li>
+ <li><strong>Pad Gaps<br>
+ </strong><em>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.<br>
+ 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.<br>
+ You may set the default for <strong>Pad Gaps</strong> in the <a
+ href="../features/preferences.html">preferences</a>. </em></li>
+</ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff