-<html>\r
-<head>\r
-<title>Alignment Window Menus</title>\r
-</head>\r
-\r
-<body>\r
-<p><strong>Alignment Window View Menu</strong></p>\r
-<ul>\r
- <li><strong>New View (Control T)</strong><em><br>\r
- Creates a new view from the current alignment view. </em></li>\r
- <li><strong>Expand Views (X)</strong><em><br>\r
- Display each view associated with the alignment in its own alignment window, \r
- allowing several views to be displayed simultaneously. </em></li>\r
- <li><strong>Gather Views (G)</strong><em><br>\r
- Each view associated with the alignment will be displayed within its own tab \r
- on the current alignment window. </em></li>\r
- <li><strong>Show→(all Columns / Sequences)</strong><em><br>\r
- All hidden Columns / Sequences will be revealed. </em></li>\r
- <li><strong>Hide→(all Columns / Sequences)</strong><em><br>\r
- Hides the all the currently selected Columns / Sequences</em></li>\r
- <li><strong>Show Annotations<br>\r
- </strong><em>If this is selected the "Annotation Panel" will be \r
- displayed below the alignment. The default setting is to display the conservation \r
- calculation, quality calculation and consensus values as bar charts. </em></li>\r
- <li><strong>Show Sequence Features</strong><br>\r
- <em>Show or hide sequence features on this alignment.</em></li>\r
- <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>\r
- Opens the Sequence Feature Settings dialog box to control the colour and display \r
- of sequence features on the alignment, and configure and retrieve features \r
- from DAS annotation servers.</em></li>\r
- <li><strong>Alignment Properties<br>\r
- </strong><em>Displays simple properties of current alignment view with additional \r
- global alignment properties</em></li>\r
- <li><strong><a href="../features/overview.html">Overview Window</a><br>\r
- </strong><em>A scaled version of the alignment will be displayed in a small \r
- window. A red box will indicate the currently visible area of the alignment. \r
- Move the visible region using the mouse. </em></li>\r
-</ul>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 / 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>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>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
+ <ul><li>
+ <strong>Apply to all groups<br></strong>
+ When ticked, any modification to the current settings will be applied to all autocalculated annotation.
+ </li>
+ <li>
+ <strong>Show Consensus Histogram<br></strong>
+ Enable or disable the display of the histogram above the consensus sequence.
+ </li>
+ <li>
+ <strong>Show Consensus Logo<br></strong>
+ Enable or disable the display of the sequence logo above the consensus sequence.
+ </li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.</em></li>
+
+ <li>
+ <strong>Group Conservation<br></strong>
+ When ticked, display a conservation row for all groups (only available for protein alignments).
+ </li>
+ <li>
+ <strong>Apply to all groups<br></strong>
+ When ticked, display a consensus row for all groups.
+ </li>
+ </ul>
+ </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">Seqence 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