<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 View Menu</strong></p>
-<ul>
- <li><strong>New View (Control T)</strong><em><br>
- Creates a new view from the current alignment view. </em></li>
- <li><strong>Expand Views (X)</strong><em><br>
- Display each view associated with the alignment in its own alignment
- window, allowing several views to be displayed simultaneously. </em></li>
- <li><strong>Gather Views (G)</strong><em><br>
- Each view associated with the alignment will be displayed within its
- own tab on the current alignment window. </em></li>
- <li><strong>Show→(all Columns / Sequences)</strong><em><br>
- All hidden Columns / Sequences will be revealed. </em></li>
- <li><strong>Hide→(all Columns / Sequences)</strong><em><br>
- Hides the all the currently selected Columns / Sequences</em></li>
- <li><strong>Show Annotations<br>
- </strong><em>If this is selected the "Annotation Panel" will be
- displayed below the alignment. The default setting is to display the
- conservation calculation, quality calculation and consensus values as
- bar charts. </em></li>
- <li><strong>Show Sequence Features</strong><br>
- <em>Show or hide sequence features on this alignment.</em></li>
- <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>
- <em>Opens the Sequence
- Feature Settings dialog box to control the colour and display of
- sequence features on the alignment, and configure and retrieve features
- from DAS annotation servers.</em></li>
- <li><strong><a href="../features/overview.html">Overview
- Window</a><br>
- </strong><em>A scaled version of the alignment will be displayed in a small
- window. A red box will indicate the currently visible area of the
- alignment. Move the visible region using the mouse. </em></li>
- <strong> </strong>
-</ul>
-<p> </p>
+ <p>
+ <strong>Alignment Window View Menu</strong>
+ </p>
+ <ul>
+ <li><strong>New View (Control T)</strong><em><br>
+ Creates a new view from the current alignment view. </em></li>
+ <li><strong>Expand Views (X)</strong><em><br> Display
+ each view associated with the alignment in its own alignment
+ window, allowing several views to be displayed simultaneously. </em></li>
+ <li><strong>Gather Views (G)</strong><em><br> Each
+ view associated with the alignment will be displayed within its
+ own tab on the current alignment window. </em></li>
+ <li><strong>Show→(all Columns / Sequences /
+ Sequences and Columns</strong>)</strong><em><br> All hidden Columns /
+ Sequences / Sequences and Columns will be revealed. </em></li>
+ <li><strong>Hide→(all Columns / Sequences /
+ Selected Region / All but Selected Region)</strong><em><br>
+ Hides the currently selected Columns / Sequences / Region or
+ everything but the selected Region.</em></li>
+ <li><strong>Automatic Scrolling<br>
+ </strong><em>When selected, the view will automatically scroll to
+ display the highlighted sequence position corresponding to the
+ position under the mouse pointer in a linked alignment or
+ structure view.</em></li>
+ <li><strong>Show Sequence Features</strong><br> <em>Show
+ or hide sequence features on this alignment.</em></li>
+ <li><strong><a href="../features/featuresettings.html">Sequence
+ Feature Settings...</a></strong><em><br> Opens the Sequence
+ Feature Settings dialog box to control the colour and display of
+ sequence features on the alignment, and configure and retrieve
+ features from DAS annotation servers.</em></li>
+ <li><strong>Sequence ID Tooltip</strong><em> (application
+ only) <br>This submenu's options allow the inclusion or
+ exclusion of non-positional sequence features or database cross
+ references from the tooltip shown when the mouse hovers over the
+ sequence ID panel.
+ </em></li>
+ <li><strong>Alignment Properties...<br>
+ </strong><em>Displays some simple statistics computed for the current
+ alignment view and any named properties defined on the whole
+ alignment.</em></li>
+ <li><strong><a href="../features/overview.html">Overview
+ Window</a><br> </strong><em>A scaled version of the alignment
+ will be displayed in a small window. A red box will indicate the
+ currently visible area of the alignment. Move the visible region
+ using the mouse. </em></li>
+ </ul>
+ <p> </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff