X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=49128c229543bf651cb3307d96693150a9f38d2d;hb=b4b901505310c3bdd1809f122abed6799c2fa664;hp=7e0d23bcdd835e19f8d56b31cfca8b2af8152332;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git
diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 7e0d23b..49128c2 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -1,21 +1,24 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Alignment Annotation
Alignment Annotation
@@ -27,11 +30,15 @@
Annotation 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.
-Web services can also add annotation to an alignment (see the
- JNet web service), and as of Jalview 2.08 quantitative and symbolic
- annotations can be added to an alignment via an Annotations
- File dragged into the alignment window or loaded from the
- alignment's file menu.
+
+Web services can also add annotation to an alignment (see the JNet and Disorder protein
+structure prediction services), and as of Jalview 2.08 quantitative
+and symbolic annotations can be added to an alignment via an Annotations File dragged into the
+alignment window or loaded from the alignment's file menu.
+
Interactive Alignment Annotation
Annotation rows are added using the Annotation Label
@@ -39,16 +46,23 @@ menu, which is obtained by clicking anywhere on the annotation row labels
area (below the sequence ID area).
- - Add New Row
+ - Add New Row
Adds a new, named annotation row (a dialog box will pop up for you to
enter the label for the new row).
- - Hide Row
+ - Edit Label/Description
+ 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.
+ - Hide This Row
Hides the annotation row whose label was clicked in order to bring up
the menu.
- - Delete Row
+ - Hide All <label>
+ 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.)
+ - Delete This Row
Deletes the annotation row whose label was clicked in order to bring up
the menu.
- - Show All Hidden Rows
+ - Show All Hidden Rows
Shows all hidden annotation rows.
- Export Annotation (Application only)
Annotations can be saved to file or output to a text window in either the
@@ -82,6 +96,16 @@ arrow oriented from left to right), and optional text label (see
below). A dialog box will open for you to enter the text. Consecutive
arrows will be joined together to form a single green arrow.
+- RNA Helix (only shown when working with nucleotide sequences)
+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.
If any brackets do not match up, then an
+orange square will highlight the first position where a bracket was
+found not to match.
+
+
- Label
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