-<html>\r
-<head><title>Alignment Window Menus</title></head>\r
-\r
-<body>\r
-<p><strong>Alignment Window View Menu</strong></p>\r
-<ul>\r
- <li> <strong>Font<br>\r
- </strong><em>Change the font of the display from the "Choose Font" \r
- dialog box, which is shown when this item is selected. </em></li>\r
- <li><strong>Smooth Fonts</strong><em><br>\r
- If selected, the alignment will be drawn with anti-aliasing on which looks \r
- better, but performace is reduced. </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>Wrap<br>\r
- </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>" \r
- to the width of the alignment window. This is useful if your alignment has \r
- only a few sequences to view its full width at once.<br>\r
- Options are available to show the residue numbering at the start and/or end \r
- of an alignment as well as showing the alignment position above each sequence \r
- row. <br>\r
- <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot \r
- be edited or have regions selected on it. </em></li>\r
- <li><strong>Show Full Sequence ID<br>\r
- </strong><em>If this box is selected the sequence name will have the start \r
- and end position of the sequence appended to the name, in the format NAME/START-END</em></li>\r
- <li><strong>Boxes</strong><em><br>\r
- If this is selected the background of a residue will be coloured using the \r
- selected background colour. Useful if used in conjunction with "Colour \r
- Text." </em></li>\r
- <li><strong>Text<br>\r
- </strong><em>If this is selected the residues will be displayed using the \r
- standard 1 character amino acid alphabet.</em></li>\r
- <li><strong>Colour Text<br>\r
- </strong><em>If this is selected the residues will be coloured according to \r
- the background colour associated with that residue. The colour is slightly \r
- darker than background so the amino acid symbol remains visible. </em></li>\r
- <li><strong>Show Gaps<br>\r
- </strong><em>When this is selected, gap characters will be displayed as "." \r
- or "-". If unselected, then gap characters will appear as blank \r
- spaces. <br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</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>Fetch Sequence Features<br>\r
- </strong><em>If the sequence names are Swissprot entries Jalview will use \r
- the names to retrieve <a href="../features/seqfeatures.html">sequence features</a> \r
- from the EBI. Features which are 1 residue in length are coloured red, sequences \r
- longer than 1 residue are coloured blue. Move the mouse over a coloured feature \r
- to display the details of the feature. <br>\r
- Note: The retrieved information will update the sequence start and end labels \r
- if they are incorrect. </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>Seqence Feature Settings...</strong><em><br>\r
- <em>Control the colour and display of sequence features on the alignment. \r
- See <a\r
- href="../features/featuresettings.html">Sequence Feature Settings</a>.</em></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
- <strong> </strong>\r
-</ul>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<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 Profile<br></strong>
+ Enable or disable the display of the sequence logo above the consensus sequence.
+ </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