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+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 Annotation</title></head>
<body>
<p><strong>Alignment Annotation</strong></p>
Jalview can display symbols and graphs under the columns of an
alignment, and allow you to mark particular columns of an alignment and add symbols and text
in the annotation area shown below the alignment (which may be hidden if <strong>View→Show
- Annotation</strong> is not ticked). </p>
-<p>Web services can also add annotation to an alignment (see the
- <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic
- annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations
- File</a> dragged into the alignment window or loaded from the
- alignment's file menu.</p>
+ Annotation</strong> is not ticked). Any displayed annotation row can be hidden (using the pop-up
+ menu obtained by right-clicking the label), or re-ordered by dragging the label to a new
+ position with the left mouse button.</p>
+<p>
+Web services can also add annotation to an alignment (see the <a
+href="../webServices/jnet.html">JNet</a> and <a
+href="../webServices/proteinDisorder.html">Disorder</a> protein
+structure prediction services), and as of Jalview 2.08 quantitative
+and symbolic annotations can be added to an alignment via an <a
+href="annotationsFormat.html">Annotations File</a> dragged into the
+alignment window or loaded from the alignment's file menu.
+</p>
<p><strong>Interactive Alignment Annotation</strong></p>
<p>
Annotation rows are added using the <strong>Annotation Label</strong>
to the annotation (numerical or otherwise) at each position in the row.
This is useful to export alignment quality measurements for further analysis.</em>
</li>
+ <li><strong>Scale Label To Column</strong><em>(introduced in 2.5)</em><br>
+ <em>Selecting this toggles whether column labels will be shrunk to fit within each column, or displayed using the view's standard font size.</em></li>
</ul>
<p>
<strong>Editing Label and secondary structure Annotation</strong></p>
below). A dialog box will open for you to enter the text. Consecutive
arrows will be joined together to form a single green arrow.</em>
</li>
+<li><a name="rna">RNA Helix</a> (only shown when working with nucleotide sequences)<br>
+<em>Mark selected positions as participating in a base pair
+either upstream or downstream. When the dialog box opens, enter a
+'(' to indicate these bases pair with columns upstream (to right),
+and ')' to indicate this region pairs with bases to the left of the
+highlighted columns.<br />If any brackets do not match up, then an
+orange square will highlight the first position where a bracket was
+found not to match.
+</em>
+</li>
<li>Label<br><em>Set the text label at the selected positions. A
dialog box will open for you to enter the text. If
more that one consecutive position is marked with the same label, only
href="../features/jalarchive.html">Jalview Archives</a>.
</p>
<p><em>Current Limitations</em></p>
-
-<p>In the current version of Jalview, reordering of the annotation
-rows is not possible. If you save
-your annotation as a Jalview file, however, it will be reloaded with user
-annotations at the top (nearest the alignment), above any of the
-automatically generated Conservation, Quality or consensus
-annotations. Finally, the Jalview GUI will not, as yet, allow you to output
-Jalview annotation files for the current alignment, change the line
-colour, display style, or create groups of quantitative annotation rows.</p>
+<p>As of version 2.5, the Jalview user interface does not support the
+creation and editing quantitative annotation (histograms and line graphs), or
+to create annotation associated with a specific sequence. It is also incapable of
+annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an
+<a href="annotationsFormat.html">Annotation file</a>.<br>
+</p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff