<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
-\r
+<p>In addition to the definition of groups and sequence features,\r
+ Jalview can display symbols and graphs under the columns of an\r
+ alignment, and allow you to mark particular columns of an alignment and add symbols and text \r
+ in the annotation area shown below the alignment (which may be hidden if <strong>View→Show \r
+ Annotation</strong> is not ticked). </p>\r
+<p>Web services can also add annotation to an alignment (see the\r
+ <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic\r
+ annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations \r
+ File</a> dragged into the alignment window or loaded from the\r
+ alignment's file menu.</p>\r
+<p><strong>Interactive Alignment Annotation</strong></p>\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
</li>\r
</ul>\r
<p>\r
-Annotation is stored and retrieved using <a\r
-href="../features/jalarchive.html">Jalview Archives</a>. Quantitative\r
-annnotation is also possible, but currently only possible with the\r
-JNet web service, or by creating your own Jalview Archive (which\r
-contains XML conforming to the Jalview-Vamsas XML schema).\r
+User defined annotation is stored and retrieved using <a\r
+href="../features/jalarchive.html">Jalview Archives</a>.\r
</p>\r
<p><em>Current Limitations</em></p>\r
\r
your annotation as a Jalview file, however, it will be reloaded with user \r
annotations at the top (nearest the alignment), above any of the\r
automatically generated Conservation, Quality or consensus\r
-annotations.</p>\r
+annotations. Finally, the Jalview GUI will not, as yet, allow you to output\r
+Jalview annotation files for the current alignment, change the line\r
+colour, display style, or create groups of quantitative annotation rows.</p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff