<body>\r
<p><strong>Alignment Window File Menu</strong></p>\r
<ul>\r
- <li><strong>File</strong><br>\r
- </li>\r
+ <li> <strong>Add Sequences</strong><em><br>\r
+ Add sequences to the visible alignment from file, URL, or cut & paste \r
+ window </em></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
+ <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 \r
+ Fetcher</a></em>.</li>\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.</em></li>\r
+ <li><strong>Export</strong> <em><br>\r
+ Creates an alignment graphic with the current annotation, alignment background \r
+ colours and group colours. If the alignment is <a\r
+ href="../features/wrap.html">wrapped</a>, the output will also be wrapped \r
+ and will have the same visible residue width as the open alignment. </em> \r
+ <ul>\r
+ <li><strong>HTML<br>\r
+ </strong><em>Create a <a href="../io/export.html">web page</a> from your \r
+ alignment.</em></li>\r
+ <li><strong>EPS<br>\r
+ </strong><em>Create an <a href="../io/export.html">Encapsulated Postscript</a> \r
+ file from your alignment.</em></li>\r
+ <li><strong>PNG<br>\r
+ </strong><em>Create a <a href="../io/export.html">Portable Network Graphics</a> \r
+ file from your alignment.</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></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 your \r
+ alignment window width, whichever is the smaller. </em></li>\r
+ <li><strong>Export Features</strong><em><br>\r
+ All features visible on the alignment can be saved to file or displayed in \r
+ a textbox in either Jalview or GFF format</em></li>\r
+ <li><strong>Export Annotations</strong><em><br>\r
+ All annotations visible on the alignment can be saved to file or displayed \r
+ in a textbox in Jalview annotations format. </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 the Newick \r
+ file format, and associate them with the alignment. Note: the ids of the tree \r
+ file and your alignment MUST be the same.</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 annotations</a>.</em></li>\r
+ <li><strong>Close</strong><br>\r
+ <em>Close the alignment window. Make sure you have saved your alignment before \r
+ you close - either as a Jalview project or by using the <strong>Save As</strong> \r
+ menu.</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/export.html">web page</a>\r
- from your alignment.</em></li>\r
- <li><strong>EPS<br>\r
- </strong><em>Create an <a href="../io/export.html">Encapsulated\r
- Postscript</a> file from your alignment.</em></li>\r
- <li><strong>PNG<br>\r
- </strong><em>Create a <a href="../io/export.html">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
git://source.jalview.org / jalview.git / commitdiff