3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Alignment Window Menus</title>
28 <strong>Alignment Window File Menu</strong>
31 <li><strong>Fetch Sequence</strong><br> <em>Shows a
32 dialog window in which you can select known ids from Uniprot,
33 EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services
34 provided by the European Bioinformatics Institute. See <a
35 href="../features/seqfetch.html"
38 <li><strong>Add Sequences</strong><em><br> Add
39 sequences to the visible alignment from file, URL, or cut &
40 paste window </em></li>
41 <li><strong>Reload</strong><em><br> Reloads the
42 alignment from the original file, if available.<br> <strong>Warning:
43 This will delete any edits, analyses and colourings applied
44 since the alignment was last saved, and cannot be undone.</strong></em></li>
45 <li><strong>Save (Control S)</strong><em><br> Saves
46 the alignment to the file it was loaded from (if available), in
47 the same format, updating the original in place. </em></li>
48 <li><strong>Save As (Control Shift S)<br>
49 </strong><em>Save the alignment to local file. A file selection window
50 will open, use the "Files of type:" selection box to
51 determine which <a href="../io/index.html">alignment format</a>
54 <li><strong>Output to Textbox<br>
55 </strong><em>The alignment will be displayed in plain text in a new
56 window, which you can "Copy and Paste" using the pull
57 down menu, or your standard operating system copy and paste
58 keys. The output window also has a <strong>"New
59 Window"</strong> button to import the (possibly edited) text as a
60 new alignment.<br> Select the format of the text by
61 selecting one of the following menu items.
64 <li><strong>FASTA</strong> <em></em></li>
65 <li><strong>MSF</strong></li>
66 <li><strong>CLUSTAL</strong></li>
67 <li><strong>BLC</strong></li>
68 <li><strong>PIR</strong></li>
69 <li><strong>PFAM</strong></li>
70 <li><strong>PileUp</strong></li>
71 <li><strong>AMSA</strong></li>
72 <li><strong>STH</strong></li>
73 <li><strong>PHYLIP</strong></li>
74 <li><strong>JSON</strong></li>
76 <li><strong>Page Setup ...</strong><br> <em>Open the
77 printing system's Page Setup dialog box, to control page size,
78 layout and orientation.</em></li>
79 <li><strong>Print (Control P)<br>
80 </strong><em>Jalview will print the alignment using the current fonts
81 and colours of your alignment. If the alignment has annotations
82 visible, these will be printed below the alignment. If the
83 alignment is wrapped the number of residues per line of your
84 alignment will depend on the paper width or your alignment
85 window width, whichever is the smaller. </em></li>
86 <li><strong>Export Image</strong> <em><br> Creates an
87 alignment graphic with the current view's annotation, alignment
88 background colours and group colours. If the alignment is <a
89 href="../features/wrap.html"
90 >wrapped</a>, the output will also be wrapped and will have the same
91 visible residue width as the open alignment. </em>
94 </strong><em>Create a <a href="../io/export.html">web page</a> from
98 </strong><em>Create an <a href="../io/export.html">Encapsulated
99 Postscript</a> file from your alignment.
102 </strong><em>Create a <a href="../io/export.html">Portable
103 Network Graphics</a> file from your alignment.
106 </strong><em>Create a <a href="../io/export.html">Scalable
107 Vector Graphics</a> file from your alignment for embedding in
110 <li><strong>BioJS<br>
111 </strong><em>Create a <a href="../io/export.html">BioJS MSA
112 Viewer HTML </a> file from your alignment.
115 <li><strong>Export Features</strong><em><br> All
116 features visible on the alignment can be saved to file or
117 displayed in a textbox in either Jalview or GFF format</em></li>
118 <li><strong>Export Annotations</strong><em><br> All
119 annotations visible on the alignment can be saved to file or
120 displayed in a textbox in Jalview annotations format. </em></li>
121 <li><strong>Load Associated Tree<br>
122 </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
123 trees</a> stored in the Newick file format, and associate them
124 with the alignment. Note: the ids of the tree file and your
125 alignment MUST be the same.
127 <li><strong>Load Features / Annotations<br>
128 </strong><em>Load files describing precalculated <a
129 href="../features/featuresFormat.html"
130 >sequence features</a> or <a
131 href="../features/annotationsFormat.html"
132 >alignment annotations</a>.
134 <li><strong>Close (Control W)</strong><br> <em>Close
135 the alignment window. Make sure you have saved your alignment
136 before you close - either as a Jalview project or by using the <strong>Save