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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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<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>
+ <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