<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
- *
+ * 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/>.
--->
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
<head><title>Alignment Annotation</title></head>
<body>
<p><strong>Alignment Annotation</strong></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 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>
+<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><a name="seqannots"/><strong>Sequence Reference Annotation</strong>
+</p>
+<p>
+ Sequence reference annotation is created from 3D structure
+ data, and from the results of sequence based prediction of
+ <a href="../webServices/jnet.html">secondary structure</a> and <a
+ href="../webServices/proteinDisorder.html">disordered region</a>
+ prediction methods.
+</p>
<p><strong>Interactive Alignment Annotation</strong></p>
<p>
Annotation rows are added using the <strong>Annotation Label</strong>
area (below the sequence ID area).
</p>
<ul>
- <li>Add New Row<br>
+ <li><strong>Add New Row</strong><br>
<em>Adds a new, named annotation row (a dialog box will pop up for you to
enter the label for the new row). </em> </li>
- <li>Hide Row<br>
+ <li><strong>Edit Label/Description</strong><br>
+ <em>This opens a dialog where you can change the name (displayed label), or the description
+ (as shown on the label tooltip) of the clicked annotation. </em> </li>
+ <li><strong>Hide This Row</strong><br>
<em>Hides the annotation row whose label was clicked in order to bring up
the menu.</em> </li>
- <li>Delete Row<br>
+ <li><strong>Hide All <em><label></em></strong><br>
+ <em>Hides all annotation rows whose label matches the one clicked.
+ (This option is only shown for annotations that relate to individual sequences,
+ not for whole alignment annotations. Since Jalview 2.8.2.)</em> </li>
+ <li><strong>Delete This Row</strong><br>
<em>Deletes the annotation row whose label was clicked in order to bring up
the menu.</em> </li>
- <li>Show All Hidden Rows<br>
+ <li><strong>Show All Hidden Rows</strong><br>
<em>Shows all hidden annotation rows.</em> </li>
<li><strong>Export Annotation</strong> <em>(Application only)</em><br>
<em>Annotations can be saved to file or output to a text window in either the
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
git://source.jalview.org / jalview.git / blobdiff