+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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>Load VCF File<br>
- </strong><em>Load VCF annotations from a plain text or tab-indexed file.
- <br>This option is offered for nucleotide alignments, and requires at least one
- sequence to have known genomic coordinates.
- <br>Genomic coordinates are attached to entries retrieved from Ensembl.
- <br>Support for VCF was added in Jalview 2.11.
- </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