-<html>\r
-<head><title>Alignment Window Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Window File Menu</strong></p>\r
-<ul>\r
- <li><strong>File</strong><br>\r
- </li>\r
- <li><strong>Fetch Sequence</strong><br>\r
- <em>Shows a dialog window in which you can select known ids from Uniprot, \r
- EMBL, EMBLCDS or PDB database using Web Services provided by the European \r
- Bioinformatics Institute. See <a href="features/seqfetch.html">Sequence Fetcher</a>.</em></li>\r
-</ul>\r
-<ul>\r
- <li><strong>Save As<br>\r
- </strong><em>Save the alignment to local file. A file selection window will\r
- open, use the "Files of type:" selection box to determine which\r
- <a href="../io/index.html">alignment format</a> to save as.<br>\r
- </em></li>\r
- <li><strong>Export</strong> <em><br>\r
- Creates an alignment graphic with the current annotation,\r
- alignment background colours and group colours. If the alignment is <a\r
- href="../features/wrap.html">wrapped</a>, the output will also\r
- be wrapped and will have the same visible residue width as the\r
- open alignment. \r
- </em>\r
- <ul>\r
- <li><strong>HTML<br>\r
- </strong><em>Create a <a href="../io/index.html#export">web page</a>\r
- from your alignment.</em></li>\r
- <li><strong>EPS<br>\r
- </strong><em>Create an <a href="../io/index.html#export">Encapsulated\r
- Postscript</a> file from your alignment.</em></li>\r
- <li><strong>PNG<br>\r
- </strong><em>Create a <a href="../io/index.html#export">Portable Network\r
- Graphics</a> file from your alignment.<br>\r
- </em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Output to Textbox<br>\r
- </strong><em>The alignment will be displayed in plain text in a new window\r
- which you can "Copy and Paste" using the pull down menu, or your\r
- standard operating system copy and paste keys. <br>\r
- Select the format of the text by selecting one of the following menu items.</em>\r
- <ul>\r
- <li><strong>FASTA</strong> <em></em></li>\r
- <li><strong>MSF</strong></li>\r
- <li><strong>CLUSTAL</strong></li>\r
- <li><strong>BLC</strong></li>\r
- <li><strong>PIR</strong></li>\r
- <li><strong>PFAM</strong><br></li>\r
- </ul>\r
- </li>\r
- <li><strong>Print<br>\r
- </strong><em>Jalview will print the alignment using the current fonts and\r
- colours of your alignment. If the alignment has annotations visible, these\r
- will be printed below the alignment. If the alignment is wrapped the number\r
- of residues per line of your alignment will depend on the paper width or\r
- your alignment window width, whichever is the smaller. <br>\r
- </em></li>\r
- <li><strong>Load Associated Tree<br>\r
- </strong><em>Jalview can <a\r
- href="../calculations/treeviewer.html">view trees</a> stored in\r
- the Newick file format, and associate them with the\r
- alignment. Note: the ids of the tree file and your alignment\r
- MUST be the same.<br>\r
- </em></li>\r
- <li><strong>Load Features / Annotations<br>\r
- </strong><em>Load files describing precalculated <a href="../features/featuresFormat.html">sequence \r
- features</a> or <a href="../features/annotationsFormat.html">alignment \r
- annotations</a>.</em></li>\r
- <li><strong>Close<br>\r
- </strong><em>Close the alignment window. Make sure you have\r
- saved your alignment before you close - either as a Jalview\r
- project or by using the <strong>Save As</strong> menu.<br>\r
- </em></li>\r
- </ul>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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 File Menu</strong>
+ </p>
+ <ul>
+ <li><strong>Fetch Sequence</strong><br> <em>Shows a
+ dialog window in which you can select known ids from Uniprot,
+ EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services
+ provided by the European Bioinformatics Institute. See <a
+ href="../features/seqfetch.html"
+ >Sequence Fetcher</a>
+ </em>.</li>
+ <li><strong>Add Sequences</strong><em><br> 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>
+ <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>
+ <li><strong>Save As (Control Shift S)<br>
+ </strong><em>Save the alignment to local file. A file selection window
+ will 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, which you can "Copy and Paste" using the pull
+ down menu, or 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>FASTA</strong> <em></em></li>
+ <li><strong>MSF</strong></li>
+ <li><strong>CLUSTAL</strong></li>
+ <li><strong>BLC</strong></li>
+ <li><strong>PIR</strong></li>
+ <li><strong>PFAM</strong></li>
+ <li><strong>PileUp</strong></li>
+ <li><strong>AMSA</strong></li>
+ <li><strong>STH</strong></li>
+ <li><strong>PHYLIP</strong></li>
+ <li><strong>JSON</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, these will be printed below the alignment. If the
+ alignment is wrapped 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
+ 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>
+ <ul>
+ <li><strong>HTML<br>
+ </strong><em>Create a <a href="../io/export.html">web page</a> from
+ your alignment.
+ </em></li>
+ <li><strong>EPS<br>
+ </strong><em>Create an <a href="../io/export.html">Encapsulated
+ Postscript</a> file from your alignment.
+ </em></li>
+ <li><strong>PNG<br>
+ </strong><em>Create a <a href="../io/export.html">Portable
+ Network Graphics</a> file from your alignment.
+ </em></li>
+ <li><strong>SVG<br>
+ </strong><em>Create a <a href="../io/export.html">Scalable
+ Vector Graphics</a> file from your alignment for embedding in
+ web pages.
+ </em></li>
+ <li><strong>BioJS<br>
+ </strong><em>Create a <a href="../io/export.html">BioJS MSA
+ Viewer HTML </a> file from your alignment.
+ </em></li>
+ </ul></li>
+ <li><strong>Export Features</strong><em><br> All
+ features visible on the alignment can be saved to file or
+ displayed in a textbox in either Jalview or GFF format</em></li>
+ <li><strong>Export Annotations</strong><em><br> All
+ annotations visible on the alignment can be saved to file or
+ displayed in a textbox in Jalview annotations format. </em></li>
+ <li><strong>Load Associated Tree<br>
+ </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
+ trees</a> stored in the Newick file format, and associate them
+ with the alignment. Note: the ids of the tree file and your
+ alignment MUST be the same.
+ </em></li>
+ <li><strong>Load Features / Annotations<br>
+ </strong><em>Load files describing precalculated <a
+ href="../features/featuresFormat.html"
+ >sequence features</a> or <a
+ href="../features/annotationsFormat.html"
+ >alignment annotations</a>.
+ </em></li>
+ <li><strong>Close (Control W)</strong><br> <em>Close
+ the alignment window. Make sure you have saved your alignment
+ before you close - either as a Jalview project or by using the <strong>Save
+ As</strong> menu.
+ </em></li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff