X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwannotations.html;h=7375e636665e29f07dbed6cc02adb59bc6946faa;hb=bb49a7496f16118471764acae958b416e08c152c;hp=9508b24e7fe4495903e4de01981b1c4016409ec3;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index 9508b24..7375e63 100755
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.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.
+ -->
Annotation Panel Menus
@@ -29,9 +32,16 @@
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
- Hides the annotation row whose label was clicked in order to bring
- up the menu.
+ 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.
+ 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 Row
Deletes the annotation row whose label was clicked in order to bring
up the menu.
@@ -46,12 +56,26 @@
This is useful to export alignment quality measurements for further analysis.
- The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:
+ The following additional entries are available when the popup menu is opened on a consensus sequence annotation row:
+
- Ignore Gaps in Consensus
If this checkbox is selected, all consensus calculations performed in
the current Alignment window will be done without counting gaps as a consensus
character.
+ - Show Consensus Histogram
+ Enable or disable the display of the histogram above the consensus sequence.
+
+ -
+ Show Consensus Logo
+ Enable or disable the display of the sequence logo above the consensus sequence.
+
+ - Normalise Consensus Logo
+ When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.
+
+ -
- Copy Consensus Sequence
Copies the consensus sequence to the clipboard in Fasta format, to allow
the consensus sequence to be added to an alignment. Note the copied sequence