<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
<head>
<title>Alignment Window Menus</title>
</head>
Add sequences to the visible alignment from file, URL, or cut &
paste window </em></li>
<li><strong>Reload</strong><em><br>
- Reloads the alignment from the original file, if available.<br><strong>Warning:
- This will delete any edits, analyses and colourings applied since the
- alignment was last saved, and cannot be undone.</strong></em></li>
+ Reloads the alignment from the original file, if available.<br>
+ <strong>Warning: This will delete any edits, analyses and
+ colourings applied since the alignment was last saved, and cannot be
+ undone.</strong></em></li>
<li><strong>Save (Control S)</strong><em><br>
Saves the alignment to the file it was loaded from (if available), in
the same format, updating the original in place. </em></li>
open, use the "Files of type:" selection box to determine
which <a href="../io/index.html">alignment format</a> to save as.</em></li>
<li><strong>Output to Textbox<br>
- </strong><em>The alignment will be displayed in plain text in a new window
+ </strong><em>The alignment will be displayed in plain text in a new window,
which you can "Copy and Paste" using the pull down menu, or
- your standard operating system copy and paste keys. <br>
+ your standard operating system copy and paste keys. The output window
+ also has a <strong>"New Window"</strong> button to import the
+ (possibly edited) text as a new alignment.<br>
Select the format of the text by selecting one of the following menu
items.</em>
<ul>
<li><strong>PFAM</strong></li>
</ul>
</li>
+ <li><strong>Page Setup ...</strong><br>
+ <em>Open the printing system's Page Setup dialog box, to
+ control page size, layout and orientation.</em></li>
<li><strong>Print (Control P)<br>
</strong><em>Jalview will print the alignment using the current fonts and
colours of your alignment. If the alignment has annotations visible,
the number of residues per line of your alignment will depend on the
paper width or your alignment window width, whichever is the smaller. </em></li>
<li><strong>Export Image</strong> <em><br>
- Creates an alignment graphic with the current view's annotation, alignment
- background colours and group colours. If the alignment is <a
+ Creates an alignment graphic with the current view's annotation,
+ alignment background colours and group colours. If the alignment is <a
href="../features/wrap.html">wrapped</a>, the output will also be
wrapped and will have the same visible residue width as the open
alignment. </em>
git://source.jalview.org / jalview.git / blobdiff