<body>\r
<p><strong>Alignment Annotation</strong></p>\r
\r
-<p>In addition to the definition of groups, Jalview also allows you to\r
-mark particular columns of an alignment and add symbols and text in\r
-the annotation area shown below the alignment (which may be hidden if\r
-<strong>View→Show Annotation</strong> is not ticked).\r
-</p>\r
+<p>In addition to the definition of groups, Jalview also allows you to mark particular \r
+ columns of an alignment and add symbols and text in the annotation area shown \r
+ below the alignment (which may be hidden if <strong>View→Show Annotation</strong> \r
+ is not ticked). </p>\r
+<p>As of Jalview 2.08 precalculated annotations can be added to alignments from \r
+ the command line, drag and drop, or from the "File-> Load Features / \r
+ Annotations" menu item. See the <a href="annotationsFormat.html">Annotations \r
+ File Format</a> for more details.</p>\r
\r
<p>\r
Annotation rows are added using the <strong>Annotation Label</strong>\r
menu, which is obtained by clicking anywhere on the annotation row labels\r
area (below the sequence ID area).\r
-</p><ul>\r
-<li>Add New Row<br>\r
-<em>Adds a new, named annotation row (a dialog box will pop up for you\r
-to enter the label for the new row). </em>\r
-</li><li>Hide Row<br>\r
-<em>Hides the annotation row whose label was clicked in order to bring\r
-up the menu.</em>\r
-</li><li>Delete Row<br>\r
-<em>Deletes the annotation row whose label was clicked in order to bring\r
-up the menu.</em>\r
-</li><li>Show All Hidden Rows<br>\r
-<em>Shows all hidden annotation rows.</em>\r
-</li><li>Show Values in Text Box<br>\r
-<em>Opens a text box with a list of comma-separated values\r
-corresponding to the annotation (numerical or otherwise) at each\r
-position in the row. This is useful to export alignment quality\r
-measurements for further analysis.</em>\r
-</li>\r
+</p>\r
+<ul>\r
+ <li>Add New Row<br>\r
+ <em>Adds a new, named annotation row (a dialog box will pop up for you to \r
+ enter the label for the new row). </em> </li>\r
+ <li>Hide Row<br>\r
+ <em>Hides the annotation row whose label was clicked in order to bring up \r
+ the menu.</em> </li>\r
+ <li>Delete Row<br>\r
+ <em>Deletes the annotation row whose label was clicked in order to bring up \r
+ the menu.</em> </li>\r
+ <li>Show All Hidden Rows<br>\r
+ <em>Shows all hidden annotation rows.</em> </li>\r
+ <li>Show Values in Text Box<br>\r
+ <em>Opens a text box with a list of comma-separated values corresponding to \r
+ the annotation (numerical or otherwise) at each position in the row. This \r
+ is useful to export alignment quality measurements for further analysis.</em> \r
+ </li>\r
</ul>\r
<p>\r
<strong>Editing Label and secondary structure Annotation</strong></p>\r
git://source.jalview.org / jalview.git / blobdiff