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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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<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>
+ <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>