-<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>View</strong></li>\r
-</ul>\r
-<blockquote> \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. <br>\r
- </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 \r
- end of an alignment as well as showing the alignment position above each \r
- sequence row. <br>\r
- <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot \r
- be edited or have regions selected on it. <br>\r
- </em><strong> </strong></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<br>\r
- </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." <br>\r
- </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.<br>\r
- </em></li>\r
- <li><strong>Colour Text<br>\r
- </strong><em>If this is selected the residues will be coloured according \r
- to the background colour associated with that residue. The colour is slightly \r
- darker than background so the amino acid symbol remains visible. <br>\r
- </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 \r
- appear as blank spaces. <br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>.<br>\r
- </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><br>\r
- </li>\r
- <li><strong>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 \r
- feature 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><br>\r
- </li>\r
- <li><strong>Seqence Settings </strong><em><br>\r
- <em>If features have been added to the alignment then the priority of rendering \r
- the features can be altered so that overlapping features can be displayed \r
- or hidden. See <a href="features/seqfeatures.html">Sequence Features</a>.</em><br>\r
- </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><strong> </strong></li>\r
- </ul>\r
-</blockquote>\r
-</body>\r
-</html>\r
+<html>
+<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>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff