3 <title>Alignment Window Menus</title>
7 <p><strong>Alignment Window File Menu</strong></p>
9 <li><strong>Fetch Sequence</strong><br>
10 <em>Shows a dialog window in which you can select known ids from
11 Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
12 the European Bioinformatics Institute. See <a
13 href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>
14 <li><strong>Add Sequences</strong><em><br>
15 Add sequences to the visible alignment from file, URL, or cut &
16 paste window </em></li>
17 <li><strong>Reload</strong><em><br>
18 Reloads the alignment from the original file, if available.<br>
19 <strong>Warning: This will delete any edits, analyses and
20 colourings applied since the alignment was last saved, and cannot be
21 undone.</strong></em></li>
22 <li><strong>Save (Control S)</strong><em><br>
23 Saves the alignment to the file it was loaded from (if available), in
24 the same format, updating the original in place. </em></li>
25 <li><strong>Save As (Control Shift S)<br>
26 </strong><em>Save the alignment to local file. A file selection window will
27 open, use the "Files of type:" selection box to determine
28 which <a href="../io/index.html">alignment format</a> to save as.</em></li>
29 <li><strong>Output to Textbox<br>
30 </strong><em>The alignment will be displayed in plain text in a new window,
31 which you can "Copy and Paste" using the pull down menu, or
32 your standard operating system copy and paste keys. The output window
33 also has a <strong>"New Window"</strong> button to import the
34 (possibly edited) text as a new alignment.<br>
35 Select the format of the text by selecting one of the following menu
38 <li><strong>FASTA</strong> <em></em></li>
39 <li><strong>MSF</strong></li>
40 <li><strong>CLUSTAL</strong></li>
41 <li><strong>BLC</strong></li>
42 <li><strong>PIR</strong></li>
43 <li><strong>PFAM</strong></li>
46 <li><strong>Print (Control P)<br>
47 </strong><em>Jalview will print the alignment using the current fonts and
48 colours of your alignment. If the alignment has annotations visible,
49 these will be printed below the alignment. If the alignment is wrapped
50 the number of residues per line of your alignment will depend on the
51 paper width or your alignment window width, whichever is the smaller. </em></li>
52 <li><strong>Export Image</strong> <em><br>
53 Creates an alignment graphic with the current view's annotation,
54 alignment background colours and group colours. If the alignment is <a
55 href="../features/wrap.html">wrapped</a>, the output will also be
56 wrapped and will have the same visible residue width as the open
60 </strong><em>Create a <a href="../io/export.html">web page</a> from your
63 </strong><em>Create an <a href="../io/export.html">Encapsulated
64 Postscript</a> file from your alignment.</em></li>
66 </strong><em>Create a <a href="../io/export.html">Portable Network
67 Graphics</a> file from your alignment.</em></li>
70 <li><strong>Export Features</strong><em><br>
71 All features visible on the alignment can be saved to file or displayed
72 in a textbox in either Jalview or GFF format</em></li>
73 <li><strong>Export Annotations</strong><em><br>
74 All annotations visible on the alignment can be saved to file or
75 displayed in a textbox in Jalview annotations format. </em></li>
76 <li><strong>Load Associated Tree<br>
77 </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
78 trees</a> stored in the Newick file format, and associate them with the
79 alignment. Note: the ids of the tree file and your alignment MUST be
81 <li><strong>Load Features / Annotations<br>
82 </strong><em>Load files describing precalculated <a
83 href="../features/featuresFormat.html">sequence features</a> or <a
84 href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>
85 <li><strong>Close (Control W)</strong><br>
86 <em>Close the alignment window. Make sure you have saved your
87 alignment before you close - either as a Jalview project or by using
88 the <strong>Save As</strong> menu.</em></li>