-<html>\r
-<head><title>Alignment Window Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Window Edit Menu</strong></p>\r
-<strong>Edit</strong> \r
-<ul>\r
- <li><strong>Undo</strong><em><br>\r
- This will undo any edits you make to the alignment. This applies to insertion \r
- or deletion of gaps, cutting residues or sequences from the alignment or pasting \r
- sequences to the current alignment or sorting the alignment. <strong>NOTE:</strong> \r
- It DOES NOT undo colour changes, adjustments to group sizes, or changes to \r
- the annotation panel. </em></li>\r
- <li><strong>Redo<br>\r
- </strong><em>Any actions which you undo can be redone using redo. </em></li>\r
- <li><strong>Cut<br>\r
- </strong><em>This will make a copy of the currently selected residues before \r
- removing them from your alignment. Click on a sequence name if you wish to \r
- select a whole sequence. <br>\r
- Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>\r
- <li><strong>Copy</strong><br>\r
- <em>Copies the currently selected residues to the system clipboard - you can \r
- also do this by pressing <CTRL> and C (<APPLE> and C on MacOSX). \r
- <br>\r
- If you try to paste the clipboard contents to a text editor, you will see \r
- the format of the copied residues is a tab separated list</em><br>\r
- NAME START_RES END_RES SEQUENCE </li>\r
- <li><strong>Paste </strong> \r
- <ul>\r
- <li><strong>To New Alignment<br>\r
- </strong><em>A new alignment window will be created from sequences previously \r
- copied or cut to the system clipboard. <br>\r
- Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>\r
- <li><strong>Add To This Alignment<br>\r
- </strong><em>Copied sequences from another alignment window can be added \r
- to the current Jalview alignment. </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Delete<br>\r
- </strong><em>This will delete the currently selected residues without copying \r
- them to the clipboard. Like the other edit operations, this can be undone \r
- with <strong>Undo</strong>.</em></li>\r
- <li><strong>Select All<br>\r
- </strong><em>Selects all the sequences and residues in the alignment. <br>\r
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>\r
- <li><strong>Deselect All<br>\r
- </strong><em>Removes the current selection box (red dashed box) from the alignment \r
- window. All selected sequences, residues and marked columns will be deselected. \r
- </em><em> <br>\r
- Use <ESCAPE> to deselect all.</em></li>\r
- <li><strong>Invert Selection<br>\r
- </strong><em>Any sequence ids currently not selected will replace the current \r
- selection. </em></li>\r
- <li><strong>Undefine Groups<br>\r
- </strong><em>The alignment will be reset with no defined groups.<br>\r
- <strong>WARNING</strong>: This cannot be undone.</em></li>\r
- <li><strong>Remove Left<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be trimmed \r
- to the left of the leftmost marked column. To mark a column, mouse click the \r
- scale bar above the alignment. Click again to unmark a column, or select "Deselect \r
- All" to deselect all columns.</em></li>\r
- <li><strong>Remove Right<br>\r
- </strong><em>If the alignment has marked columns, the alignment will be trimmed \r
- to the left of the leftmost marked column. To mark a column, mouse click the \r
- scale bar above the alignment. Click again to unmark a column, or select "Deselect \r
- All" to deselect all columns.</em></li>\r
- <li><strong>Remove Empty Columns<br>\r
- </strong><em>All columns which only contain gap characters ("-", \r
- ".") will be deleted.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
- </em></li>\r
- <li><strong>Remove All Gaps</strong><br>\r
- <em>Gap characters ("-", ".") will be deleted from the \r
- selected area of the alignment. If no selection is made, ALL the gaps in the \r
- alignment will be removed.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
- </em> </li>\r
- <li><strong>Remove Redundancy<br>\r
- </strong><em>Selecting this option brings up a window asking you to select \r
- a threshold. If the percentage identity between any two sequences (under the \r
- current alignment) exceeds this value then one of the sequences (the shorter) \r
- is discarded. Press the "Apply" button to remove redundant sequences. \r
- The "Undo" button will undo the last redundancy deletion.</em></li>\r
- <li><strong>Pad Gaps<br>\r
- </strong><em>Adds gaps to the end of all the sequences so they are all the \r
- same length. This is useful for making a tree using unaligned sequences.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
- </em></li>\r
-</ul>\r
- <blockquote> </blockquote>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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 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.<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